Plant Energy Biology |
2012
W
plantenergy.uwa .edu.au
TABLE OF CONTENTS
Table of Contents
Page 1
THE CENTRE
Page 3
Overview
Meet the Chief Investigators
The Director’s View
Page 4
Page 6
Page 7
OUR RESEARCH
Page 9
What is Plant Energy Biology?
Discovery Frontiers
P1. Organelle Biogenesis
P2. Organelle Metabolism
P3. Organelle Signalling
P4. Energy Systems
Technology Platforms
Arabidopsis, Rice and Beyond
Page 10
JOINT INITIATIVES
Page 25
Centre for Comparative Analysis
of Biomolecular Networks and CABIN
Centre of Excellence for Computational
Systems Biology
Centre of Excellence for Plant Metabolomics
Joint Research Laboratory in Genomics
and Nutriomics
Page 12
Page 14
Page 16
Page 18
Page 20
Page 22
Page 26
Page 27
Page 28
Page 29
EDUCATION, OUTREACH & TRAINING
Page 31
Overview
Education Programs
Outreach Programs
Training Programs
Page 32
Page 33
Page 34
Page 35
PEOPLE
Page 37
Centre Management
Scientific Advisory Board
Centre Personnel
Page 38
Page 39
Page 40
Selected Centre Publications
Publication Fast Facts
Page 41
Page 44
ARC CPEB 2012 / PAGE 01
A country that can't control
it's energy sources, can't control
it's future.
Barack Obama
ARC CPEB 2012 / PAGE 02
The Centre
ARC CPEB 2012 / PAGE 03
CENTRE OVERVIEW
Plants harvest huge amounts of energy from sunlight.
This energy feeds, clothes and fuels our world. Tapping
into this potential is what drives the ARC Centre of
Excellence for Plant Energy Biology (PEB).
Plant Energy Biology Fast Facts 2012
Critical research problem
We focus on unlocking the secrets of plant energy
metabolism. By unlocking these fundamental processes
we are able to better understand plant biomass
productivity, fruit and grain yield, plant nutrient
composition, and adaptation to abiotic and biotic
stresses.
• 3 Collaborating Universities: University of
Western Australia, Australian National
University and University of Adelaide.
• 7 Chief Investigators.
• 110 internationally competitive staff and
students.
• $22.5 million (2005) + $9.8 million (2009) from
the Australian Research Council and $13.7
million (2005-2013) from the partner
universities fund the Centre through to 2013.
• Centre authors have contributed to over 330
publications including key breakthroughs
published in Nature, Cell, Science,
Proceedings of the National Academy of
Sciences USA and The Plant Cell.
• Over the last 5 years, 21% of the Australian
papers in the top plant science journals
included authors from our Centre.
• 2545 students and members of the public
participated in interactive, hands-on Centre
outreach programs.
• 170,154 people saw our travelling 'Secrets of a
Tiny Powerplant' science photography
exhibition which also won the “Science as Art
Prize” at the Australian Science
Communicators Conference.
National strategic importance
Plants are the lungs and bread-bowl of the earth. In
addition to plants' role in extracting atmospheric CO2
and renewing supplies of oxygen for virtually all life
forms to breathe, they are major contributors through
agriculture to the global and Australian economies.
Independent analyses of climate change predict
declines in agricultural productivity associated with
altered weather patterns, with Australia being negatively
impacted to a greater extent than most other regions.
Plants expend energy to protect themselves against the
adverse impact of environmental changes, such as
reduced water availability and quality, increased light
intensity and temperature, higher wind speed and
frosts. This leads to decreases in biomass and yield.
A major focus of the Centre's research is to discover
how plants perceive such environmental changes, and
understanding the genetically driven chain of events that
are associated with response, tolerance and
adaptation.
• 5,940 members of the public “liked” our
“Science is Amazing” Facebook page.
• A prospective audience of 5,530,441* for our
Science Posters during National Science Week
(*from Conads Advertising report).
• Over 670 positive media commentaries
internationally.
Mission and Vision
Our mission is the discovery and characterisation of the
molecular components that drive energy metabolism in
plant cells. Our vision is to be recognised as a world
leader in plant energy research and a centrepiece in
fundamental plant science in Australia.
Strategic Priorities
• To generate new knowledge through research and
ultimately, rationally design plants for the benefit of
Australian agriculture.
• To engage Australia with plant science and create
dialogue between scientists, growers and the general
public through education, training and outreach
activities.
• To develop innovative biotechnological applications.
• To recruit and train a new generation of highly skilled
biologists through staff and student development.
ARC CPEB 2012 / PAGE 04
Highly innovative research
In subsequent pages we report on current activities
within the Centre, not only the highly innovative
discovery research underway and the pipeline of
publications to date, but also on our progress with
training the next generation of plant scientists.
We report on our successes connecting with the
Australian community at multiple levels, building their
awareness of the importance of plants and this Centre's
research, and on progress with translating our research
into outcomes of national economic, social and cultural
benefit.
CENTRE NODES
The University of
Western Australia
University of Adelaide
The Australian
National University
The Centre is made up of over 100 scientists working across 3 University nodes.
“By collaborating across three leading Australian Universities, all teams gain massive benefits by avoiding long and expensive
delays whilst new approaches are developed in-house and personnel are trained to use them. By sharing expertise and
collaborating on research projects, we gain access to a suite of techniques and datasets that are not all available at any
single university, keeping our research at the cutting-edge.”
The University of Western Australia
Perth | Western Australia
University of Adelaide
Adelaide | South Australia
The Australian National University
Canberra | Australian Capital Territory
ARC CPEB 2012 / PAGE 05
CHIEF INVESTIGATORS
The University of Western Australia node:
Professor Ian Small (Director)
Ian joined UWA as a WA State Premier's Fellow in
February 2006, becoming Centre Director in April 2006.
His research interests involve understanding how plants
coordinate the expression of nuclear and energy
organelle genes.
Email:
[email protected]
Telephone:
+61 8 6488 4499
Professor Harvey Millar (Deputy Director 2013)
Harvey is an ARC Future Fellow and was awarded the
Fenner Medal for biological research in 2012 from the
Australian Academy of Science for his research aiming
to understand the role mitochondria play in the primary
carbon and nitrogen metabolism of plants and their
response to oxidative stress.
The Australian National University node:
Professor Murray Badger (Deputy Director 2005/12)
Murray is closely involved with the National Plant
Phenomics Facility. His wide-ranging research interests
cover various aspects of photosynthesis research
relating to plant biochemistry and plant physiology.
Email:
[email protected]
Telephone:
+61 2 6125 3741
Professor Barry Pogson
Email:
[email protected]
Telephone:
+61 8 6488 7245
Professor Steven Smith
Barry is the Australian representative on the Multinational
Arabidopsis Steering Committee. Current research in
his group is defining novel roles for carotenoids in plant
developmental processes. Complementary research
into organelle signalling is identifying the mechanisms by
which plants perceive and respond to drought and
excess light.
Steve joined UWA in 2005 as an ARC Federation
Fellow. His research focuses on discovering new
enzymes and new metabolic pathways, forcing a
rethinking of energy metabolism in plant cells.
Email:
[email protected]
Telephone:
+61 2 6125 5629
Email:
[email protected]
Telephone:
+61 8 6488 4403
University of Adelaide node:
Professor Stephen Tyerman
Professor Jim Whelan
Jim played a major role in establishing the Centre as
Interim Director throughout the latter half of 2005 and
early 2006. Currently his research is combining
morphological, biochemical, genetic and 'omic'
approaches to understand organelle function and
biogenesis.
Email:
[email protected]
Telephone:
+61 8 6488 1749
ARC CPEB 2012 / PAGE 06
Stephen joined the Centre in 2011 while leading the
plant transport lab at Uni Adelaide. His research
expertise centres around membrane transport, a critical
part of the organelle-cell interactions in all cells. This
expertise flows into projects on nutrient distribution and
transport systems in plants.
Email:
[email protected]
Telephone:
+61 8 8303 6663
DIRECTOR’S VIEW
The Centre had a great year in 2012, with several major
projects reaching their goals and even more new
projects starting up. Almost every record we have set in
previous years tumbled in 2012 as the Centre
continues to expand and improve.
Growth & Development
The Centre attracts the very best young scientists to
develop their projects in collaboration with us, taking
advantage of the exciting intellectual environment and
the wonderful modern facilities at each of our three
nodes. In 2012, two new Future Fellows (Ryan Lister
and Josh Mylne) joined our UWA node as affiliates and
set up their new labs adjacent to the Centre labs in the
Bayliss Building.
Our UA node welcomed Matthew Gilliham, an equally
promising young plant scientist (and SA 'Tall Poppy'!),
whilst our ANU node are celebrating their role in a
successful $7M application to the Bill & Melinda Gates
Foundation.
Murray Badger will be heavily involved in this new
intitiative to study carbon-concentrating mechanisms in
photosynthesis, and as a result is stepping down as
Deputy Director of our Centre, passing on the baton to
Harvey Millar. I take this opportunity to thank Murray for
all his enthusiasm and hard work over the last 7 years
and wish him every success in this new venture.
Coming to Fruition
The Centre published 85 papers in 2012, a 60%
increase over any previous year, proof that our staff and
students are just as keen and motivated as ever. Many
of the projects started early in the life of the Centre are
now reaching their most productive phases, a telling
example of the advantages of sustained funding for big
projects over a 5-7 year period.
A Bountiful Harvest
The Centre rightly prides itself on the excellent science
coming from its labs, but also strives to make sure that
its discoveries are relevant to society. That takes skill in
choosing the right topics to study, but also a lot of hard
work in ensuring that we know what stakeholders are
interested in, and that end-users and the public know
what we are working on.
In 2012, there were some strong signs that we are on
the right track.
Over 670 media stories featured work from our centre,
with the three most popular stories being:
• the characterisation of a gene conferring a significant
degree of salt tolerance to a variety of wheat
(published in Nature Biotechnology);
• the discovery of a code governing recognition of RNA
by RNA-binding proteins (published in PLoS
Genetics);
• continuing interest in our characterisation of a new
signalling pathway in plant cells subject to water
deficit (published in Plant Cell, 2011; Trends in Plant
Science, 2012).
These discoveries are relevant to agriculture and the
biotech industry and in each case we're working to
develop these discoveries as quickly as possible in
collaboration with Rural R&D Corporations and/or
commercial partners.
Prof. Ian Small
Director
This productivity is not coming at the price of quality,
and the Centre's papers remain highly sought after in
the top plant science journals. Using citations as a
metric, the Centre rivals many of the world's bestknown and respected plant science centres, and
Centre investigators have never been more popular as
presenters at international conferences.
ARC CPEB 2012 / PAGE 07
I think (as many others do) that
biology will be the science that sees
the most spectacular advances in
this century. Technological
advances have made it possible to
dream of addressing the biggest
challenges in biology, such as
identifying the major causes of
disease and aging, characterising
the major determinants of plant
performance and productivity
or cataloguing biodiversity
across the globe.
Chief Investigator Steven Tyerman
ARC CPEB 2012 / PAGE 08
OUR RESEARCH
ARC CPEB 2012 / PAGE 09
What is Plant Energy Biology?
The metabolic reactions that make up plant energy
biology are the most important biological processes on
the planet. These reactions produce the oxygen we
breathe, the food we eat and remove our waste carbon
dioxide from the atmosphere.
Every year, plants worldwide produce 80 gigatonnes of
oxygen and fix about 100 gigatonnes of carbon dioxide
into carbohydrates such as sugar, starch and cellulose.
These products of plant energy metabolism contain in
the order of 2x1023 joules of captured, renewable, clean
energy from sunlight.
This represents a colossal amount of energy; annual
worldwide energy flux through photosynthesis and plant
respiration is a thousand times the energy stored in all
of Australia’s natural gas reserves.
A significant fraction of this ‘plant energy’ is already
used by us in the form of food, fuel or fibre, but given
the pressures an ever-growing world population is
placing on our increasingly degraded environment,
improvements in the efficiency with which we make use
of plant energy are vital for our future.
Despite the importance of plant energy biology to all our
lives, we still know surprisingly few details about how
plants capture, store and mobilise their energy.
Certainly, we do not know enough to rationally design
perfect plants for innovative uses such as biofuels or
ideal nutritional balance.
Our long-term goal is to comprehend this system well
enough to not only understand how plants function at a
cellular level, but to be able to design optimal energy
metabolism for particular functions (for example, starch,
sugar or biofuel production), or in response to harsh
environmental conditions.
Our belief is that research into plant energy biology will
lead to exciting breakthroughs in these areas.
Huge energy potential...
150,000,000 kg of CO2 is
made into starches and sugar
by plants every minute!
ARC CPEB 2012 / PAGE 10
What Is Plant Energy Biology
 Peroxisomes are the third energy organelle in plant
cells. They contain a set of enzymes for breaking
down oil and fat and are particularly important during
seed germination when oil reserves power the
growth of the young seedling. Peroxisomes also
have important roles later in the plant growth cycle,
notably in photorespiration and in removing
damaging chemicals such as hydrogen peroxide
generated by energy metabolism.
Much of energy biology takes place in three specialised
subcellular compartments (organelles) present in all cells
of the plant.
 Green chloroplasts are the site of photosynthesis,
the chemical reactions that trap the energy of
sunlight in the form of useful carbohydrates. Whilst
doing this, chloroplasts remove carbon dioxide from
the air and release oxygen from water, thus rendering
our atmosphere breathable for animal life. They also
provide much of the energy and raw materials for
growth of the plant. Chloroplasts in leaves (and nongreen plastids elsewhere in the plant) are the major
site for the production of useful plant products;
including sugars, starch, oils and many vitamins.
Chloroplasts derive from bacteria that took up
residence in plant cells billions of years ago and
contain their own set of genes.
These three energy organelles work together to form a
highly complex network of metabolic and genetic
interactions that make up the framework of plant energy
biology. The Centre has defined four strategic research
areas that encompass all of plant energy biology. These
are outlined on the following pages:
These four areas are:
 Organelle biogenesis
(How are energy organelles made?)
 Organelle metabolism
 Mitochondria are found in all plant and animal cells
(What do energy organelles do?)
PLAST
O
 Organelle signalling
(How do energy organelles talk to each other?)
 Energy systems
(How does the system function as a whole?)
OXISO
ER
E
M
P
where they provide energy by respiring
carbohydrates. Mitochondria power not only our own
muscles, but roots and other parts of a plant that
can't photosynthesise. Like chloroplasts they derive
from free-living bacteria billions of years ago and still
contain their own set of genes.
Mitoch
ndrion
CHLOR
o
0 Genes
500 Proteins
100 Genes
3,500 Proteins
CLEUS
NU
35 Genes
1,500 Proteins
30,000 Genes
The energy producing and coordinating compartments of the cell; the nucleus, peroxisomes, mitochondria and chloroplasts work together to form a
highly complex network of metabolic and genetic interactions that make up plant energy biology. Understanding these interactions is our challenge.
ARC CPEB 2012 / PAGE 11
discovery Frontiers
P1. Organelle Biogenesis
Coordinator: Harvey Millar
How are organelles made and maintained?
In the vital process of photosynthesis, energy from
sunlight is trapped as chemical energy within
chloroplasts. The mitochondria transform this stored
chemical energy into the plant's principal energy
currency (adenosine triphosphate or ATP). Still further
chemical inter-conversions of energy take place in
peroxisomes. Yet in a dry seed, prior to its germination,
none of these three energy organelles are present in a
functional form. These partially-formed organelles lay
waiting for triggers.
With the addition of water, peroxisomes and
mitochondria rapidly form and begin converting stored
starch and fats in the seed into energy to power growth.
In parallel, the chloroplasts develop, ready to take over
the task of providing energy through photosynthesis
once the leaves of the seedling have emerged.
This processes of building functional organelles is called
"organelle biogenesis". The architecture and
composition of the final functional units is particularly
important in this field of study.
We want to understand the processes that control and
coordinate organelle assembly inside plant cells. To do
this, we study plants with alterations in organelle
biogenesis. We then use a combination of molecular
profiling techniques to analyse the impact of these
alterations on organelle activity, on nuclear gene
expression, and on metabolite profiles.
What have we done so far?
To achieve the Centre's goal of understanding organelle
biogenesis, we have been working towards:
 Identifying which proteins accumulate as organelle
components
 Determining how proteins synthesized outside the
organelle are able to enter the organelles
 Discovering regulatory mechanisms controlling
protein synthesis inside organelles
 Understanding how organelle biogenesis varies
within plant tissues and throughout development.
Protein Complexes
We have systematically identified the proteins present in
peroxisomes and mitochondria using proteomics,
protein-tagging and bioinformatics predictions. New
electrophoresis techniques are enabling us to examine
the protein complexes that these proteins are
associated with and postulate how they are formed.
Using such analyses we can identify which proteins are
critical to each organelle for its maintenance and proper
functioning.
Protein Import
We have identified proteins critical for protein transport
into mitochondria and more specifically, the receptor
proteins on the outer of the two mitochondrial
membranes. Analysis of knockout plants for particular
receptors has provided insights into pathways for
protein import, has identified new import receptors in
plants and found new links between import
components and mitochondrial function.
Research Highlight
Unexpected links between the process of
mitochondrial biogenesis and the respiratory
apparatus itself.
Why is organelle biogenesis important?
The relative abundance and activity of these energy
organelles has an enormous impact on plant growth
and productivity. Without sufficient chloroplasts, plants
would lack energy for growth. Without sufficient
mitochondria, plants would be unable to mobilise
energy reserves and would cease to grow. The balance
in activity between these two organelles governs
biomass accumulation.
Without peroxisomes, lipids couldn't be broken down
efficiently to drive seed germination. By getting the
balance right, cells can develop optimally. By specifically
altering the balance we can speed, slow or alter plant
growth and development.
ARC CPEB 2012 / PAGE 12
We always thought that the process of importing
proteins into mitochondria and their activity were
separate issues that were independently regulated.
However we have now found a protein that is common
to both the import apparatus and complex I of the
respiratory chain, and changing its abundance
differentially affects both protein complexes.
This is a first for mitochondria in plants and opens up the
possibility of exploiting the inverse relationship between
import complexes and respiration complexes to control
respiratory function in plant cells.
Wang Y, Carrie C, Giraud E, Elhafez D, Narsai R, Duncan O, Whelan J,
Murcha M. (2012) Dual Location of the Mitochondrial Preprotein
Transporters B14.7 and Tim23-2 in Complex I and the TIM17:23
Complex in Arabidopsis Links Mitochondrial Activity and Biogenesis.
The Plant Cell 24(6):2675-2695
discovery Frontiers
P1. Organelle Biogenesis
Gene expression in energy organelles
The genomes of chloroplasts and mitochondria encode
key components in energy metabolism. Our research
has shown that both mitochondrial and chloroplast
gene expression is largely regulated not by the process
of transcription, but rather through changes to the RNA
transcript or whether the transcript is used for protein
synthesis. We have shown the specific role of many
nucleus-encoded factors in RNA processing events
required for organelle function.
To be able to monitor the results of such experiments, we
are developing techniques for quantifying selected
proteins and measuring the turnover of proteins based on
recent advances in proteomics technology. With the
acquisition of new facilities in 2012 and a large
collaborative project with Agilent Technologies, we are
positioning ourselves at the forefront of international efforts
in plant sciences in this area.
Personal Success: Dr Cory Solheim
After a stellar 4 year post-doctoral research role at the
Centre, Dr Solheim returned to her native Canadian soil as
the Field R&D specialist for Novozymes Biologicals Inc. As
part of the BioAg Division, Dr Solheim plans, oversees and
implements all aspects of the field and greenhouse trials
run across Canada to generate data on new biofertility and
biological control products and new product use patterns.
Organelle biogenesis throughout development
Development and modification of organelle functions are
inextricably linked to plant development, productivity
and environmental tolerance. We have made detailed
studies of organelle development during the germination
process, in different tissue types and in metabolic
mutants. These studies have unravelled some of the
complexity involved in organelle biogenesis and
plasticity, and the links between energy production,
environmental stress and metabolic function.
Where are we going?
As our understanding of organelle biogenesis improves,
we want to use this knowledge to express novel
proteins or alter the expression of proteins already
present in order to achieve desired objectives. In
particular, we want to explore the role of RNA and
protein metabolism in defining and manipulating
organelle functional states.
Dr Solheim commented that “the expertise in plant
biochemistry and metabolism that I gained at ARC PEB has
brought a missing element to the role and the team, which
has traditionally been more focused at the level of
agronomy. Being involved in several projects
simultaneously at PEB has strengthened my ability to multitask and collaborate, which are skills I use every day in my
new corporate position.”
“While I am responsible for Canada, I am part of a greater
global team and the international experience that I gained at
PEB certainly played a role in my selection for this position,”
she said.
Research Highlight
How fast do plant organelle proteins turnover?
Simple question, but hard to answer! We have now
developed an approach of progressive incorporation of
the heavy natural abundance stable isotope of N ( 15N)
into plant proteins as they are made, so we can follow
'new' proteins by mass spectrometry. By following the
kinetics of this process we can calculate the 'age' of
different proteins. This shows that mitochondrial, plastid
and peroxisome proteins have different rates of turnover,
and highlights that specific classes of proteins have
faster turnover rates in organelles.
We plan to use this information to follow the biogenesis
process of organelles and define the most important
times for biogenesis of organelles in vivo in different
tissues and environmental conditions.
Li L, Nelson CJ, Solheim C, Whelan J, Millar AH (2012) Determining
degradation and synthesis rates of Arabidopsis proteins using the
kinetics of progressive 15N labeling of 2D gel-separated protein spots.
Molecular and Cellular Proteomics 11(6):M111.010025
ARC CPEB 2012 / PAGE 13
discovery Frontiers
P2. Organelle Metabolism
Coordinator: Murray Badger
What is organelle metabolism?
Metabolism refers to the chemical reactions typical of
living cells that are necessary for growth and
development. Metabolic processes interconvert organic
compounds such as carbohydrates, fats and amino
acids with the aid of specific enzymes that catalyse
these chemical reactions. Plant energy organelles each
carry out hundreds of distinct reactions linked either to
energy conversion processes such as photosynthesis
and respiration, or to other biosynthetic processes such
as the formation of vitamins.
Why is organelle metabolism important?
The energy and carbohydrate producing processes of
photosynthesis and respiration underpin growth,
development and reproduction of all plants. In turn,
plant growth is the basis in all biomass production at the
base of the food chain, and potentially the foundation of
future bioenergy production to replace fossil fuels.
The aim of this research program is to analyse the
energy-handling metabolic pathways associated with
the three plant organelles. We aim to discover novel
genes, proteins and mechanisms by which metabolite
flux and energy flow is managed at the cellular level. By
understanding these processes we can identify ways to
optimize organelle function for improved plant growth,
product quality and yield.
What have we done so far?
To achieve the Centre's goal of understanding the
components and pathways of energy metabolism in the
plant cell, we have been working towards:
 Identifying the enzymes and metabolites involved in
energy metabolism in each of the organelles
 Investigating the function of key energy enzymes and
metabolite transporters
 Discovering how organelle energy metabolism
contributes to plant growth and yield
Identifying enzymes and metabolites
Our data have led to the identification of hundreds of
organellar proteins of which many are enzymes involved
in energy metabolism. We have focused in particular on
two processes where energy metabolism is crucial to
plant development and leaf function – early seedling
development and photorespiration.
Being able to identify and quantify key metabolic
intermediates is central to studies which investigate
metabolic function. To achieve this, we have developed
a powerful GC/MS metabolomics platform to be able to
identify and measure sugars, organic acids, amino
acids, sterols, fatty acids and triglycerides.
Research Highlight
An ancestral salt pump gene provides salt
tolerance in wheat
Years ago, careful physiological screening of ancient
wheat varieties turned up an ancestral wheat relative
that was able to better exclude sodium from entering
its leaves and therefore limit salt damage. Our Centre
has helped characterise the gene responsible for this
salt tolerance. Remarkable results were demonstrated
when this gene was "bred" back into a commercial
durum wheat variety, increasing yield in saline soil by
25% over the parental variety, with no yield penalty
under non saline conditions.
The research, led by Dr Matthew Gilliham at our
University of Adelaide node, was an example of the
power of a strong collaborative research effort that
also involved researchers at CSIRO and the ACPFG.
“Over 20% of Australia's agricultural land is classified
as saline and 69% of Australia's wheat belt is
susceptible to salinity," explains Dr Matthew Gilliham.
"There are many reasons for this, but as wheat has
been bred for millennia in favourable conditions for
traits like yield, many desirable traits like salt tolerance
have been lost along the way.”
Dr Gilliham led the effort to discover the gene of
interest, which encodes a salt transporter that pumps
salt out of the vascular system of the plant. This
transporter stops salt from accumulating in the leaves
where it interferes with processes such as
photosynthesis, thus decreasing crop yield.
Munns RJ, James RA, Xu B, Athman A, Conn SJ, Jordans C, Byrt
CS, Hare RA, Tyerman SD, Tester M, Plett D and Gilliham M. Grain
yield of modern wheat on saline soils is improved by ancestral HKT
gene. Nature Biotechnology 30: 360-U173
ARC CPEB 2012 / PAGE 14
discovery Frontiers
P2. Organelle Metabolism
Gates Foundation Funds Research Into
Photosynthesis For Improvement Of Crops
The Earth's population is expected to increase 50% by
2050 and the UN predicts that we will need to increase
our crop yields by 70% to feed everyone. CI Murray
Badger, co-recipient of a breakthrough grant from the
Gates Foundation explains, "This increase in food
supply is a massive ask of agriculture. Conventional
breeding techniques simply cannot deliver this increase
in food. In this collaborative effort, we are seeking to
understand the fundamental reaction at the centre of all
life on Earth - photosynthesis - to help feed the world.”
Of particular interest to Professor Badger are algal
bicarbonate transporters that actively transport CO2 to
Rubisco, the key carbon-fixing enzyme in
photosynthesis. His group's aim is to engineer these
transporters into crop plants, resulting in greater growth
rates and higher crop yields.
The importance of this work has been recognised by a
$7 million grant from the Bill & Melinda Gates Foundation
to researchers working in collaboration from the
University of Illinois, the Universities of Essex, Berkley,
Louisiana State, Shanghai, Rothamsted Research and
the ANU node of our Centre.
The role of key organelle proteins in limiting plant
metabolism and growth under various environmental
conditions will be identified and used to design strategies
for improving the growth and performance of plants.
Personal Success
South Australian Tall Poppy Award for Matthew
Gilliham
As both a clever scientist (see p.14) and creative
communicator, Dr. Matthew Gilliham has won a South
Australian Tall Poppy award in 2012. Tall Poppy Awards
recognise scientists who are not only able to deliver
scientific breakthroughs, but can effectively promote
their science in the wider community.
Matt's Nature paper describing a 25% increase in wheat
yields on salty soil and his ability to engage the media
with this research finding was obviously noted by the
judges. In 2012, Matt has also been awarded the
Viticulture & Oenology Science and Innovation Award for
Young People in Agriculture, Fisheries and Forestry and
a fellowship by the GO8 Australia-China Young
Researchers Exchange Program.
Congratulations Matt!
For more information, visit www.waiteresearchinstitute.
wordpress.com/2012/08/23/south-australian-tallpoppies-dr-kerry-wilkinson-and-dr-matt-gilliham/
Genes to energy...
Research Highlight
Where are we going?
We aim to continue to identify and characterise the genes,
proteins and metabolites involved in the metabolic
pathways of the three energy organelles by focusing on
the reactions involving the main compounds involved in
primary carbon/nitrogen metabolism.
ARC CPEB 2012 / PAGE 15
discovery Frontiers
P3. Organelle Signalling
Coordinator: Barry Pogson
What is organelle signalling?
Cell compartmentation is key to the success of plants
and animals. However, the co-existence of specialized
compartments (i.e. organelles) also requires
communication between them. Many factors have been
suggested to be involved in these signalling pathways,
which are still largely undiscovered.
We recognise two major classes of signals:
 signals required to coordinate organelle biogenesis,
which we refer to as biogenic control;
 signals that respond to changes in the environment
or function of the organelles, which we refer to as
operational control.
Why is organelle signalling important?
Plants need to respond to a constantly changing
environment by altering their energy metabolism to suit
the prevailing conditions (light, temperature, availability
of water, etc.).
To coordinate these responses, energy organelles must
signal their status to each other, and to the nucleus,
which has overall control of cellular functions.
A shock to the system
Plants are sensitive to both high and low
temperatures, being unable to take shelter and
having relatively few means of thermoregulation.
Sudden chills or hot spells can have serious
consequences for agricultural production. Energy
organelles are particularly sensitive to sudden
changes in temperature but also have many
undiscovered mechanisms for coping with these
changes.
Over the last year, in collaboration with
researchers from the USA and Europe, the
Centre has made important progress in identifying
RNA-binding factors implicated in protecting
energy organelles against both kinds of
temperature extremes.
Kim M, Lee U, Small I, Colas des Francs-Small C, Vierling E. Mutations
in a mitochondrial transcription termination factor (mTERF)-related
protein enhance thermotolerance in the absence of the major
molecular chaperone HSP101. The Plant Cell 24(8):3349-65
Kupsch C, Ruwe H, Gusewski S, Tillich M, Small I, SchmitzLinneweber C. Arabidopsis Chloroplast RNA Binding Proteins CP31A
and CP29A Associate with Large Transcript Pools and Confer Cold
Stress Tolerance by Influencing Multiple Chloroplast RNA Processing
Steps. The Plant Cell 24(10):4266-80
Cell compartmentation is key...
Any breakdown in these signalling pathways leads to
mismatches in energy metabolism and often damage to
the energy organelles, leading to extremely poor plant
growth. Anticipating and controlling these signals is one
of the most promising avenues for improving plant
performance in the future.
Research Highlight
ARC CPEB 2012 / PAGE 16
discovery Frontiers
P3. Organelle Signalling
What have we done so far?
To understand how organelles talk to each other, to the
rest of the cell, and to other tissues we have been:
 Discovering how organelle function is regulated by
environmental cues and affected by abiotic stresses
 Identifying components in the signal transduction
pathways that detect and respond to these signals
 Identifying how the expression of genes encoding
organelle proteins is regulated by these signal
transduction pathways
 Examining aspects of the communication between
organelles and plant development processes.
Personal Success
Kai Chan wins ANU
Hiroto Naora Award
For his clear and informative talk into his findings on how
a gene called SAL1 participates in chloroplast-nucleus
signalling and is regulated during stress – part of the
research highlighted on the right - Kai took home the
Hiroto Naora Award for Plant Science. This award
recognises the best speaker in their field at the ANU
Research School of Biology PhD Student Conference.
Kai is a member of Barry Pogson's group, who are
particularly interested in secondary sulphur metabolism
in cells during stress and the production of stressresponsive retrograde signals such as PAP (Estavillo et al
(2011) Plant Cell). In fact, the group recently found that
mutating a gene called SAL1 results in a build-up of the
small molecule PAP in the nucleus, closing the leaf
stomata and creating drought resistance in the cell.
From his training with the ARC Centre for Excellence in
Plant Energy Biology at the ANU, Kai describes the most
important skills he has learnt so far as critical thinking and
effective communication with a general audience.
Congratulations Kai!
In addition, over the last 6 years, we have dissected
critical signalling events in response to changes in light
intensity, temperature shock, water supply and nutrient
availability at the genetic, biochemical and physiological
level.
Outcomes from a better understanding of these
processes have included the development of tools and
strategies to modulate the function of select signalling
pathways. For example, we have received commercial,
ARC Linkage and GRDC funding to manipulate a
chloroplast signalling pathway to induce drought
tolerance in rice and canola.
Where are we going?
Despite recent progress by our Centre and other
groups around the world, key questions still remain that
include:
1) What are the signals?
2) What regulates the production, transmission and
reception of these signals?
3) How do interactions between different organelles
influence organelle and plant function?
Research Highlight
Balancing metabolites during drought
A key plant response to drought is the accumulation of
specific sets of metabolites that act as
osmoprotectants, osmolytes, antioxidants, and/or
stress signals. An emerging question is: how do plants
regulate metabolism to balance the 'competing
interests' between metabolites during stress?
Recent research connects primary sulphur metabolism
(e.g. sulphate transport in the vasculature, its
assimilation in leaves, and the recycling of sulphurcontaining compounds) with the drought stress
response. We have highlighted key steps in sulphur
metabolism that play significant roles in drought stress
signalling and responses. We propose that a complex
balancing act is required to coordinate primary and
secondary sulphur metabolism during the drought
stress response in plants.
Chan KX, Wirtz M, Phua SY, Estavillo GM, Pogson BJ. Balancing
metabolites in drought: the sulfur assimilation conundrum Trends Plant
Sci. 2013 18(1):18-29
Not until 2011 had anyone unequivocally identified a
signal in plants that physically moves from an energy
organelle to the nucleus. To identify such a signal has
been viewed by many as a 'holy grail' in molecular plant
sciences – hence the great interest in the Centre's
2011 discovery of a signalling pathway involving a
nucleotide by-product of sulphur metabolism called
PAP.
Further research into this area has resulted in an award
for PhD student Kai Xun Chan in 2012 (see highlight).
Our future research will focus on:
 identifying the major switches that coordinate
responses to temperature shocks, high light and
drought;
 an understanding of the switches that coordinate
mitochondrial and chloroplast signalling;
 manipulation of transcription factors to control
expression of genes involved in organelle biogenesis
and organelle stress responses.
ARC CPEB 2012 / PAGE 17
discovery Frontiers
P4. Energy Systems
Coordinator: Ian Small
What are energy systems?
By 'energy systems' we refer to the large-scale
interactions between the myriad of components that
participate in energy metabolism in plants. Plant energy
systems consist of thousands of genes coding for
thousands of proteins and are extremely complex.
Several hundred of these proteins are enzymes, each
catalysing energy reactions involving the interconversion of two or more energy metabolites such as
starch, sugars, fats and amino acids.
To study these large networks of components,
computational methods are essential, and this, our
fourth research programme consists almost exclusively
of computational data analysis. Our analyses integrate
data from our three 'wet lab' research areas together
with data from international repositories and our
collaborative partnerships.
Our data are mined for novel correlations to be followed
up for breakthrough discoveries, and are analysed with
the aim of producing accurate, predictive models of
plant energy metabolism and the patterns of gene
expression that control it. The state-funded Centre of
Excellence in Computational Systems Biology is
working in conjunction with the ARC Centre of
Excellence in Plant Energy Biology to apply the latest
systems biology approaches to our data.
Why are energy systems important?
Plant energy systems provide the oxygen we breathe,
the food we eat and the fibre we clothe ourselves with.
However, plant energy systems are so complex that
scientists are incapable of following the full effects of
experiments on the whole system without
computational support. There are thousands of genes,
proteins and metabolites involved.
Only by assembling and integrating existing and future
data will a complete picture emerge. We are playing a
major role in the world scientific community by bringing
together and analysing the relevant data for plant energy
biology.
What have we done so far?
To achieve the Centre's goal of understanding these
plant energy systems, we have been working towards:
 Defining the major components of the energy
systems in plants
 Defining the key links between these components
and creating interaction networks
 Modelling the system in sufficient detail to make
useful predictions.
Energy system components
We have developed three major databases/software
tools, which are providing clear insights into the massive
data sets describing plant energy systems. Much of our
data on the components of the plant energy systems is
collated within the SUBA database
(http://suba.plantenergy.uwa.edu.au/).
SUBA contains bioinformatics predictions and
experimental data (both ours and other data collated
from hundreds of relevant publications) that describe
the protein components of plant energy systems,
including their location and their interactions. SUBA is
now considered by the international community to be
the reference on the subcellular location of proteins
within plant cells.
Energy system links
In order to help define the key links between plant
energy components, such as metabolic connections,
protein-protein interactions and changes in gene
expression, the AnnoJ program was developed. AnnoJ
is a powerful software tool, able to deal with huge
datasets. This program allows the visualization and
analysis of deep sequencing data. This program was
developed by the Centre and has been used in
landmark publications in Cell and Nature.
Research Highlight
Growing green leaves
Plants are very good at growing leaves - a big tree can
have over 200,000 of them. It's actually a very
complicated process, with each leaf starting life as a
bump a tenth of a millimetre across, containing just a few
cells.
A large consortium of top European plant science labs
joined with our Centre to carry out one of the most
comprehensive and systematic analyses of leaf growth
ever undertaken. Arabidopsis plants were grown under
tightly controlled conditions in France, and then a single
leaf from each plant was collected for analysis in
Belgium, Germany, Switzerland and Australia for their
content in cells, DNA, RNA, proteins, enzymes and
metabolites using some of the most sophisticated
technology for biological analysis available anywhere.
Our role in the project was to analyse the development of
the energy organelles as the leaf grows, particularly the
changes in the chloroplasts at the onset of
photosynthesis. Developing leaves undergo a key
transition from being 'fed' by the rest of the plant in their
early stages to providing energy for growth of future
leaves as they mature. The results from this project
provide a reference against which many future
experiments on this transition can be compared.
Each of these three stages is now well advanced.
Baerenfaller et al. (2012) Molecular profiling and integrated analysis of
Arabidopsis leaf growth reveals adaptation to water deficit. Molecular
Systems Biology 18:06
ARC CPEB 2012 / PAGE 18
discovery Frontiers
P4. Energy Systems
Modelling energy systems
The final stage in the development of these software
programs is their ability to build predictive models of
plant energy systems. We are collaborating with
colleagues at the University of Queensland and in
Europe to construct genome-wide network models of
Arabidopsis metabolism capable of simulating a wide
range of metabolic states specific to different cells
within the plant. This work depends heavily on the
protein localisation data within SUBA.
Research Highlight
Exploring the cell
Bit by bit, researchers are exploring every nook and cranny
of the plant cell, compiling increasingly accurate lists of the
proteins to be found in each compartment. We
systematically store and analyse all of this data in SUBA,
which underwent a huge upgrade in 2012 (to SUBA3), with
almost 6 times more data now included.
This is a vital computational resource for all attempts to
describe and model plant metabolism, not just for us, but for
all plant scientists around the world. SUBA3 contains not
just more data, but many new features, including data on
protein-protein interactions and a new tool for interpreting
multiple lines of evidence using Bayesian statistics. Despite
all the extra information, SUBA3 is more intuitive and easier
to use than ever.
Tanz et al. SUBA3: a database for integrating experimentation and
prediction to define the SUBcellular location of proteins in Arabidopsis.
Nucleic Acids Research, in press.
With our demonstrated expertise in the analysis of deep
sequencing data, we are well-placed to benefit from the
recent massive advances made in sequencing
technology. Huge new datasets are coming (over 3000
genome projects are underway around the world) and
the analysis of genome and transcriptome sequencing
data will be a special focus for us. With the acquisition
of a deep sequencing facility in 2011, we are
positioning ourselves at the forefront of the international
efforts in plant sciences in this area.
Research Highlight
Cracking the code
One of the dreams of modern biology is to be able to
deliberately design proteins to carry out specific tasks; socalled 'synthetic' biology. Work connected to the Centre has
brought this dream a little closer by cracking the code that
governs recognition of RNA sequences by
pentatricopeptide repeat (PPR) proteins.
The ~500 PPR proteins in plants are key factors controlling
gene expression in energy organelles, each acting by
binding tightly to a specific target site. We now know how
they manage this, opening the way to designing synthetic
proteins capable of binding any desired target sequence,
with potential applications in agriculture and medicine. This
collaborative work between researchers at UWA and the
University of Oregon is being followed up via joint grants and
patent applications.
Barkan et al. (2012) A Combinatorial Amino Acid Code for RNA Recognition
by Pentatricopeptide Repeat Proteins. PLoS Genetics 8(8) Code for RNA
repair is cracked. New Scientist, September 2012
Food security...
Where are we going?
A model is only as good as its ability to predict the
behaviour of the real system it seeks to replicate. We
are validating our models by modelling the effects of
known perturbations to the system (e.g. reproducing
the metabolism of specific knockout mutants), and
subsequently using the model(s) to make testable
predictions of the effects of as yet uninvestigated
perturbations to the system.
We intend to use the models to predict necessary
changes to the system to achieve desired outcomes in
biotechnology or agriculture.
ARC CPEB 2012 / PAGE 19
Technology Platforms
Our ability to answer scientific questions is always
constrained by the technology available. With the
advent of new technologies, answers that were once
out of reach become attainable. Therefore an important
function of our Centre is to continually develop and
apply the newest technologies, and where possible,
make them available for other researchers across
Australia (for example via the Australian Plant Phenomics
Facility and Bioplatforms Australia).
Arabidopsis phenotyping platform
Measuring plant growth and function (phenotyping) is
key to identifying the roles of the genes, proteins and
regulators that we study. Our range of controlled growth
cabinets (> 100 m2) and glasshouse space (>60 m2)
allow measurement of plant growth under varying light,
temperature and CO2 conditions across all 3 nodes.
Our phenomic analysis platforms include:
• Gas exchange systems for analysis of CO2 and O2
exchange, including isotope analysis to monitor
photosynthesis and respiration. In 2012 we installed
several new plant growth rooms and purchased a
multiplexed gas exchange system from Qubit
Systems, funded by ARC LIEF.
• Chlorophyll fluorescence imaging systems for
monitoring spatial and temporal changes in leaf
chloroplast properties both in high-resolution and
high-throughput.
• Imaging-based growth analysis systems for monitoring
the growth of plant shoots under various conditions. In
2012, ARC LIEF funded a joint project between UWA
and ANU Centre researchers to build new climatemimicking growth environments with sophisticated
LED lighting and cameras to build climate scenarios
and measure plant responses. Our in-house facilities
are complemented by the NCRIS-funded Australian
Plant Phenomics Facility, with CI's Pogson and
Badger on the Executive Management Committee of
the High-Resolution Plant Phenotyping Centre in
Canberra.
• An extracellular flux analyser from Seahorse
Biosciences, being used for the first time in plants to
measure respiratory and glycolytic rates using
fluorescence ion selective probes. In addition, our
new Oroboros Oxygraph-2K for simultaneous
measurements of oxygen consumption rate and
reactive oxygen species production has applications
for a variety of centre projects working on the role of
ROS as a signalling molecule in plants.
ARC CPEB 2012 / PAGE 20
Molecular profiling platforms
The first steps in molecular profiling involve isolating the
cells to be profiled and extracting the molecules that we
wish to identify and quantify. Increasingly we need to be
able to deal with very small samples and high numbers
of samples in parallel. Two new platforms relevant to
these needs were acquired in 2012.
Firstly, we obtained a laser capture micro-dissection
platform (Zeiss PALM MicroBeam). Precision lasers
allow the capture of cells and cell components from
fresh, paraffinized or frozen plant tissue sections to
create accurate and repeatable molecular analysis of
DNA, RNA and proteins.
In a single day of use, the
Hi-Seq Illumina Deep Sequencer
allows researchers to obtain the sequence
equivalent of the entire human
genome project, which took
4 billion dollars and 10 years to
complete over a decade ago.
Secondly, our new platform at ANU will include a robot
for high-throughput sample preparation from frozen
plant tissue, funded from ARC LIEF. This will accelerate
our extractions of DNA and metabolites from large
numbers of samples, making large-scale projects
feasible that weren't previously.
Once we have taken these samples from the plants of
interest, the following technology allows us to analyse
the DNA, RNA, proteins or metabolites.
Next-generation sequencing
Both UWA and ANU have next-generation deep
sequencing platforms installed. Our Illumina Hi-Seq
Deep Sequencer is one of the most powerful platforms
for next generation sequencing. This platform can
analyse both DNA and RNA samples, i.e. genome and
transcriptome sequencing.
Transcriptomics
Our transcriptomics platform consists of a complete
Affymetrix microarray platform, Roche 480 Lightcyclers
for high-throughput real-time PCR, and associated
support instruments such as Bioanalysers and robotics
for liquid handling. Future transcriptomics projects will
benefit from the deep-sequencing platform.
Technology Platforms
Proteomics
The principal tools we use in the Centre for proteome
analysis are electrophoresis and our four mass
spectrometers (ESI-Q-TOF, ESI-TRAP, ESI-QQQ and
MALDI-TOF-TOF). These enable us to identify novel
proteins, as well as determine small changes in protein
quantities, generated either by changes in levels of
gene transcription, translation of mRNA, protein
degradation, or post-translational modification.
Metabolomics
Our principal tools in metabolomics are separation
technologies (organelle separation by centrifugation;
metabolite separation by liquid and gas
chromatography) and mass spectrometry. We obtain
quantitative data for potentially hundreds of energy
metabolites in a single mass spectrometric analysis.
We have also taken an active role in developing a
metabolomics database and analysis software which is
available to researchers in the Centre and at
International institutions with our Metabolome Express
website (www.metabolome-express.org).
This can be done in a cell where there is either a low
background of native transport (Xenopus laevis oocytes)
or in cells where particular transport proteins are
silenced (usually yeast). The UA node houses the
Membrane Transporter Expression Facility, originally setup by a LIEF grant and funding from the SA
government.
Informatics Platform
Our informatics expertise and resources benefit greatly
from the Centre of Excellence in Computational
Systems Biology funded through the WA Centres of
Excellence in Science and Innovation scheme.
The Centre is linked to the iVEC network of highperformance computing facilities across Perth. We have
constructed several databases to house and analyse
molecular profiling data integrated into genomic data
sets based on Arabidopsis genome sequencing and
annotation from international sources. Web-based
interfaces to our databases and software are available
through our website at www.plantenergy.uwa.edu.au.
Understanding our world...
We were key proponents of the $9.5M NCRIS
investment in Metabolomics Australia and play an
important management role in the facilities installed in
WA.
Membrane Transporter Expression Facility
Communication and energy exchange between
organelles and between cells requires highly specialised
protein channels and transporters. To fully understand
their function, they must be expressed in cells where
they can be characterized in isolation from other related
transport proteins.
ARC CPEB 2012 / PAGE 21
Arabidopsis, Rice & Beyond
The Centre's initial research focus on the
model plant Arabidopsis thaliana has had
excellent outcomes in fundamental plant
research and forming collaborative links.
Building on this fundamental knowledge,
Centre staff are expanding their activities to
solve problems of direct relevance to the
wider community.
RL
BA EY
In particular, plant energy biology is highly
relevant to many of the most pressing
problems faced in agriculture.
Improving nitrogen use efficiency in
barley & maize
The amount of energy available to a plant
constrains its ability to extract water and
nutrients from the ground, affects its ability
to defend itself against insects and disease
and limits its ability to produce pollen,
seeds and fruit and thus crop yields.
Over-use of nitrogen fertilizers causes many
problems due to run-off into waterways, not to
mention the waste of money and resources. We
are working with partners to understand the
metabolic processes that can be altered to allow
nitrogen fertilisers to be taken up and used more
efficiently, focussing on barley and maize in the
first instance. With the addition of Steve
Tyerman's group to the team we are able to
functionally characterise the nitrogen and
phosphate transporters and also investigate the
link with water flow.
NEYBE
O
ES
H
Our Centre scientists are finding that their
discoveries are applicable in a wide and
growing range of agricultural, horticultural
and even medical contexts.
Safeguarding pollination and honeybees
Devastating declines in global honeybee populations
are threatening the pollination of more than 80
agricultural crops and many native flowering plants.
These losses are primarily caused by parasites and
pathogens. A collaborative project between the Centre
and the CIBER honeybee research group is
harnessing the Centre's expertise in genomics and
proteomics to study honeybees. The central research
aim is to understand host-parasite interactions and
sexual reproduction on a molecular scale, and to
transfer research breakthroughs to honeybee industry
partners. We provide information for breeding stronger
and more productive bees.
ARC CPEB 2012 / PAGE 22
RICE
EA
WH T
Building stress tolerant wheat
Fortifying rice by improving nutrient uptake
BIDOPS
A
I
R
S
A
Research on Arabidopsis is complemented by a strong
focus on rice - an important model plant which shares a
close evolutionary past with many crop species. Up to 40
million people across the globe eat Australian rice every
day. In collaboration with experts in China, we aim to
drastically reduce the use of phosphate fertilisers by
breeding crop plants far more efficient at drawing out the
many billions of dollars worth of currently unusable
phosphate fertiliser locked into the world's soils.
The wheat industry worldwide is susceptible to
drought, salinity and the effects of climate change.
Previous droughts in Australia have halved our $6
billion-a-year production. Finding ways to create
more resistant wheat varieties is of great importance
to us. A collaborative project with the GRDC is
addressing drought survival using the SAL1 gene. In
salt tolerance improvement, our projects include a
wide screening of different wheat varieties for salinity
tolerance using translational approaches with the
Department of Agriculture WA. Further research to
improve wheat performance using an ancestral salttolerance gene has seen a 25% increase in yield
under saline conditions. All of these projects build
upon discoveries and techniques pioneered in
Arabidopsis, including a provisional patent on SAL1.
MANS
U
H
Mapping epigenomes in humans
Technologies developed in Arabidopsis can be applied to
virtually any organism. A collaboration with the SALK
Institute for Biological Studies using our expertise in
genetics has provided a complete map of the human
epigenome. This map has major implications in the
treatment of human diseases and for the development of
stem-cell based medicine.
APES
R
G
Protecting grape harvests
We are working with growers in Carnarvon to
uncover the molecular mechanisms behind
inconsistent fruiting in grapes in sub-tropical
Western Australia. The project requires our
molecular profiling skills, honed in Arabidopsis, and
aims to discover the metabolism driving bunch
abortion and ultimately increase consistency in
yield.
With the addition of Steve Tyerman to the team,
our research will extend to optimising water
relations in grapes by seeking understanding of
key water transporters (aquaporins), the function of
water channels in roots, the distribution of nutrients
in leaves and to determine new and efficient ways
of measuring plant water status in the field.
ARC CPEB 2012 / PAGE 23
Plants have to be supremely
adaptable to changes in the
environment; they can't just move if
the conditions get nasty. They have
more genes, more enzymes and more
metabolites than we do. As a result,
at the molecular level they are
fascinatingly complicated, and
able to do things in so many
different ways.
Director Ian Small
ARC CPEB 2012 / PAGE 24
Joint Initiatives
ARC CPEB 2012 / PAGE 25
Joint Initiatives
UWA Centre for Comparative Analysis of Biomolecular
Networks (CABiN)
The Centre
The UWA Centre for Comparative Analysis of
Biomolecular Networks (CABiN) facilitates transfer of
knowledge and technology from ARC CoE projects to
related projects in other areas at UWA and
internationally (www.cabin.uwa.edu.au). Professor
Harvey Millar is the director of CABiN. This centre brings
together ARC CoE researchers and other researchers
working on real-world problem solving.
Research Goals
CABiN offers a pathway for scientists to perform
collaborative research across discipline divides using
cutting edge analytical tools to provide molecular insight
into diverse biological questions. It focuses on protein
and metabolite analysis by mass spectrometry. CABiN
uses data visualisation to show the landscape of
networks and aid discovery of novel biological insights.
Centre for Integrative Bee
Research (CIBER)
The Centre
CIBER is dedicated to facilitate interdisciplinary research
on honeybees (www.ciber.science.uwa.edu.au). CIBER
offers a working platform for scientists to perform
collaborative research on honeybees alongside industry
partners. The ultimate goal is to better understand
honeybees and counter the dramatic losses currently
occurring. To achieve this CIBER combines expertise
from beekeepers with decades of experience,
sociobiologists and their insights into the functioning of
bee societies, evolutionary ecologists and their
understanding of evolutionary processes and molecular
biologists that provide expertise to harness the
honeybee genome and proteome.
Research Goals
The agricultural importance of honeybees as pollinators
for crops is very significant and they are major sources
for commercial honey, pollen, and wax production.
Honeybees have been a model species for a broad
range of scientific studies for many years and the full
sequencing of the genome has now opened the way to
new opportunities for functional genomics research.
PEB collaborates with CIBER researchers on key
aspects of bee reproduction, bee immunity and their
role as pollinators of crops.
Applied outcomes...
The rapid accumulation of network-related data from
many species provides unprecedented opportunities to
study the function and evolution of biological systems.
Evolution acts on these networks as functional units,
rather than on single molecules. The basic goal of
network comparison is to uncover identical or similar
sub-networks by mapping changes in one network to
another. Such analysis can reveal important biological
links, and explain how networks evolved, how natural
variation alters networks, and how engineering of
networks can provide novel biological outcomes.
Current projects include insect reproductive biology and
epigenetics, plant productivity in stressful environments,
nutrient use efficiency in crops, cell senescence and
MS imaging in plant tissues. The work is connected
through innovation in data management and storage in
collaboration with Agilent Technologies, and has
collaborations with CEB (Centre for Evolutionary Biology,
www.ceb.uwa.edu.au), Department of Agriculture and
Food WA, and Umea Plant Science Centre, Sweden.
ARC CPEB 2012 / PAGE 26
Joint Initiatives
Staff and Resources
The CoE for Computational Systems Biology expanded
considerably in 2012. Professor Ryan Lister was
appointed as Winthrop Professor of Computational
Systems Biology at UWA in December 2011 and is
working in close association with the Centre. His
research covers genome-wide analysis of epigenetic
markers in Arabidopsis and humans.
Establishment of the Centre
The State Government of Western Australia, through its
Centre's of Excellence in Science and Innovation
Program is currently funding the Centre of Excellence
for Computational Systems Biology as an adjunct to the
ARC Centre of Excellence in Plant Energy Biology. The
state funding will amount to $2.72M in total (20062013). The Centre of Excellence is housed within the
laboratories and administrative structure of the ARC
Centre and shares common goals, resources and
outputs.
Goals of the Centre
The central role of the CoE for Computational Systems
Biology is to provide the essential infrastructure and
expertise needed to visualize and analyse the large
quantities of complex data being generated by the ARC
Centre of Excellence in Plant Energy Biology.
Our Centre is expanding as systems approaches are
becoming increasingly important across all areas of
biology (including biomedical research). We are
therefore providing expertise that benefits other
research programs in related areas.
Systems biology requires a new breed of biologists, well
versed in computational techniques, statistics and
mathematics as well as biology. Our research is
attracting good students and young researchers keen
to learn modern functional and computational genomics
approaches.
The Centre of Excellence for Computational Systems
Biology currently employs five postdoctoral staff. We
aim to build an ambitious computational biology group
by expanding our recruitment of students and
postgraduates.
The CoE for Computational Systems Biology has
established a high-performance rack of data servers
and associated storage and backup facilities sited
within the iVEC@UWA facilities at UWA. These facilities
are linked to the iVEC high-performance computing
network in WA and notably to the bioinformatics servers
at the Centre for Comparative Genomics at Murdoch
University. The iVEC supercomputing facilities are used
for ultra-high-performance applications required for
analysis of certain large data sets.
The CoE for Computational Systems Biology handles
the ARC Centre of Excellence in Plant Energy Biology's
databases and runs specialist applications for treatment
of Centre data. In 2011-12, significant upgrades of the
computing facilities were made to handle data from the
new Terabase sequencing facility installed within the
ARC Centre of Excellence in Plant Energy Biology.
The research happening within the Centre of Excellence
for Computational Systems Biology is described under
'Energy Systems' on pages 18-19.
High throughput science...
Centre of Excellence for Computational Systems
Biology
ARC CPEB 2012 / PAGE 27
Joint Initiatives
Establishment of the Centre
The Centre was created with an award of $1.5M from
the Government of Western Australia, Department of
Industry and Resources, to Chief Investigator Steve
Smith in support of his ARC Federation Fellowship. The
Centre was initially funded for a period of 5 years from
September 2006 and has since secured further funding
from ARC Discovery and Linkage projects.
The Centre of Excellence for Plant Metabolomics is
housed within the laboratories and administrative
structure of the ARC Centre of Excellence, sharing
many common goals, resources and outputs.
Research
The research goals of the Centre of Excellence focus
on the discovery of genes that direct resource
partitioning in plants. Such discoveries are expected to
lead to better understanding of:
– Mechanisms by which carbon is partitioned – or
transported - from photosynthetic tissues to other
parts of the plant, in between organelles in cells and
between different major cellular products in plants.
– Molecular mechanisms by which carbon partitioning
is regulated by environmental factors such as water
stress, salinity and nitrogen supply.
– Regulation of carbon partitioning between different
metabolic sinks.
A recent research success has been the redirection of
an existing and crucial biochemical pathway in plants terpene metabolism - into novel plant sterols that can
provide new physiological adaptations, nutritional
benefits, and deterrence against insects in these plants.
Resources
The Centre is undergoing a transition from Government
of Western Australia funding to separate projects
supported by industry, ARC, and other Federal funding.
A fusion with the West Australian node of Metabolomics
Australia is providing a wider range of equipment,
resources services and expertise for the wider
community.
ARC CPEB 2012 / PAGE 28
Highlights in 2012
Strigolactones are highly interesting because of their
role in stimulating germination of invasive parasitic
plants. Knowledge of the chemical mode of action of
strigolactones is vital for synthetic chemists to produce
novel strigolactones and antagonists to block parasitic
plant growth or encourage the growth of productive
crop plants. Until now, this has remained a challenge to
chemical biologists.
Our studies of karrikin molecules from bushfire smoke
and strigolactone hormones has led to the identification
of two closely related hydrolase-type proteins that are
required for activity of these growth regulators. The two
proteins can distinguish karrikins and strigolactones,
even though they are chemically very similar. Each
signal elicits a distinct response to control different
aspects of plant growth. This discovery was published
in 'Development' and attracted much interest, with 30
citations in its first year.
In related research, it was discovered that the
DWARF27 gene discovered in rice is also present in
Arabidopsis where it was shown to function in the
control of shoot branching (Waters et al., Plant
Physiology, 2012). The DWARF27 gene is required for
strigolactone biosynthesis and was shown to act
upstream of another gene controlling strigolactone
synthesis and shoot branching, namely MAX1. The
control of shoot branching and architecture is a major
determinant of plant productivity through its effect on
efficiency of interception of solar energy. These genes
can also influence root architecture, and hence the
ability of plants to acquire mineral nutrients from the soil.
Pathways to Possibilities...
Centre of Excellence for Plant Metabolomics
Joint Initiatives
Additionally Sophia has developed new collaborations
with Prof Ming Fang Zhang (Laboratory of Genetic
Resources and Functional Improvement for Horticultural
Plants, Department of Horticulture, Zhejiang University),
involving mitochondrial retrograde responses with two
masters students Wenhui Lv and Lu Li.
The Joint Research Laboratory in Genomics and
Nutriomics was opened on 28th March, 2006. The joint
laboratory is a centrepiece of strengthening scientific
collaboration between The University of Western
Australia (UWA) and Zhejiang University (ZJU),
Hangzhou, China. Professor Jim Whelan heads this
initiative at UWA.
The aim of the joint laboratory is to investigate energy
metabolism and nutrition in plants. The expertise in
energy biology and Arabidopsis research at the ARC
Centre of Excellence in Plant Energy Biology at UWA is
complemented by the expertise in plant nutrition and
rice genetics at the College of Life Sciences at ZJU.
The joint laboratory is funded by both universities and
currently has several PhD students and researchers
working on joint research projects. Several joint
publications attest to the success of the collaboration.
We have had an extremely busy and productive year in
2012. New personnel have joined the laboratory, our
collaboration has been extended, and our public
outreach programs are of growing in popularity in China.
New personnel
Dr Sophia Ng has joined the laboratory as a full time
researcher and has stepped straight into a number of
joint projects working on phosphate and iron nutrition in
rice with Prof Wu Ping and Prof Huixia Shou, at the
College of Life Science.
A Productive Research Year
This year the Joint lab produced 5 research papers,
and several others have been prepared for submission
in 2013. This is the most productive year to date,
representing the efforts of many people over a number
of years.
Teaching and Outreach
Again we have made this area a high priority and we
have been busy! Our annual graduate transcriptomics
course in China was again over-subscribed. Sophia
also ran an advanced journal club for a group of Qiu Shi
students, and Jim gave a number of undergraduate
lectures at Zhejiang University
November and December saw Jim take part in WA
Governor General, Mr Malcolm McCusker’s, visit to
China. The Governor General was keenly interested in
the research being carried on phosphate nutrition in rice
and after a detailed tour of the research facilities, he
relaxed with students and researchers over a cup of tea
to discuss their work in more detail.
The Governor General also hosted a public forum “From
Lab to Dining Table” where Jim Whelan and Rob
Delane, Director General of WA Department of Food
and Agriculture, highlighted the innovation in research
and quality of food production in WA. For Chinese
students or researchers interested in contacting
Professor Whelan about joint research initiatives, try
http://weibo.com/u/2985310590.
Optimising fertiliser use...
Joint Research Laboratory in Genomics and
Nutriomics
ARC CPEB 2012 / PAGE 29
We want to change the way people
feel about plants. We want them to
realiSe the huge and important role
that plants play in keeping us alive.
If we empower people with THE
UNDERSTANDING OF how a plant
works and functions, how cellular
processes work and what genetic
modification actually involves then
attitudes can change. Everyone
benefits from knowing “how stuff
works”.
Chief Investigator Harvey Millar
ARC CPEB 2012 / PAGE 30
EOT
ARC CPEB 2012 / PAGE 31
Education, Outreach & Training
Science Communications Officer (UWA): Alice Trend
We believe that creating positive public dialogue about
science is important. To engage the wider community,
the Centre has created a number of targeted education,
training and outreach programs, which have visited
schools, farmers, teachers, universities, science
museums, field days, careers festivals and even pubs.
We recently received feedback on our education and
outreach programs by Dr Joanne Castelli, Director of
the Science Experience and the Chantelle Carter
Memorial Fund at UWA and organiser of the National
Youth Science Forum at UWA:
“I will certainly be calling on the assistance of the
outreach and education team for the programs I run in
the future, confident in the knowledge that they will
enthusiastically deliver informative, well-targeted, cutting
edge, hands-on and fun activities.”
New Communications Initiatives in 2012
In 2012, the Centre continued to exceed targets for
education and outreach. A focus on engaging new
members of the community with a federal National
Science Week grant allowed us to collaborate with the
International Centre for Radio Astronomy Research
(ICRAR) to produce a science poster campaign for the
month of August, centring around National Science
Week.
Incredibly, 70 people took out their mobiles while in the
cubicle and followed the links to find out more. The
Facebook page has continued to grow since National
Science Week and now has over 7200 members and 7
contributing authors from PEB and ICRAR.
Media in 2012
By building a stronger understanding of best practice
interaction with the media, the Centre is strengthening
its ability to reach Australians. The Centre's media
coverage in 2012 featured over 670 print, radio and
web articles, thanks to some fascinating discoveries by
our scientists. Most notable in the media this year were
Matthew Gilliham (below) and team with their salt
tolerant wheat discovery, Ian Small and collaborators'
cracking of the molecular code for RNA-editing protein
binding sequences and Gonzalo Estavillo and
associates' detection of a molecular drought alarm
in plants.
Game-changing discoveries...
This project successfully reached a potential audience
of 5 million Australians in shopping centres,
pubs and online with four quirky, funny and intriguing
scientific posters. With the tag line, “From plants to
planets, science is amazing,” we aimed to spark an
interest in science where Australians least expected it:
on the back of toilet doors.
As interaction with our posters was difficult to gauge
with this particular audience, we added a QR code
which took visitors to a website and Facebook page
using their mobile phone
(www.facebook.com/scienceweek).
ARC CPEB 2012 / PAGE 32
Education Programs
SCHOOL-TARGETED PROGRAMS
The Centre's targeted school programs reached 1297
secondary students and teachers in 2012.
Powerful Plants
The highly recognised Powerful Plants program has
been a two times runner up in the WA Premier's
Science Awards. This multi-faceted program has
included school incursions, workshops, independent
student projects and teacher professional development.
The program uses passionate scientists to guide
students through fun science projects from a young
age.
250 school students were delighted with visits in 2012.
Students learned about the power of plants, how they
grow, what DNA actually is and took part in messy and
exciting hands-on experiments.
Highlight
Plants in Space!
Research Assistant Professors John Bussell and
Rowena Long created an exciting set of experiments for
Year 5 students of Kyilla Primary School. Students were
asked to consider the question: How would plants grow
in outer space? To find out, students grew “mutant”
plants that were unable to sense which way is 'up' and
which way is 'down'. These “mutants” are unable to
produce the heavy starch molecules that usually fall to
the bottom of special roots-tip cells, thus signalling to the
plant which way is down.
The students were amazed when their plants, which
could not sense gravity, grew with their roots up, down
and sideways! Meanwhile, the normal "control" plants
grew normally. The students then stained the plants to
prove that starch not present in the mutant, compared to
the normal, starch-containing plants and used the
results to assess their original hypotheses about how
plants might grow in space.
“The children really enjoyed participating in the sessions.
Not only were they informative and taught them many
processes, but they fostered a love for science in the
class. During the workshops and after John and
Rowena had left, I used science lessons as an incentive
for the students. I was often heard to say, "If we don't get
this finished we will not have time for our science lesson."
It really motivated them. The students got all their work
done and were then rewarded with science!
Thank you both.” Teacher Judith McCormack
Get into Genes Secondary Program
"Get into Genes" (GIG) is the Centre's curriculumaligned workshop for secondary students and teachers.
Presented by our education team, students and
researchers, GIG also creates an ideal environment for
our scientists to up-skill in science communications.
Students and teachers are able to interact with top
scientists in a working genetics lab, see research in
progress and ask questions about science careers.
2012 saw us perform 8 workshops at UWA, with 172
students and 12 teachers taking part in the program.
Get into Genes Feedback from students in 2012
included:
• Engaging in the extreme. It contained quite intricate
issues but it was presented in an enjoyable and
simplistic manner.
• Amazing pracs and hands on experience, as well as
teaching us something new. Really cool! Hands-on
activities were amazing!
• Loved speaking to the scientists about uni and their
different projects.
The Get into Genes program is an education
collaboration with the education officers and managers
of the Australian Centre for Plant Functional Genomics
and Dairy Futures CRC, which allows us to share
resources, expertise and promote our research
examples more widely across Australia.
TERTIARY EDUCATION
As well as programs for school students, Centre
researchers share their insights and knowledge with
undergraduate students in lectures and laboratories.
Highlight
International Book Prize
The Grapevine - from the
science to the practice of
growing vines for wine by
Patrick Iland, Peter Dry, Tony
Proffitt & Steve Tyerman.
When four of Australia's leading viticulturists come
together to write a book about grapevines, you'd expect
it to be good. And it is! Chief Investigator Steve Tyerman,
Patrick Iland, Peter Dry and Tony Proffitt's book “The
Grapevine…” for tertiary students and grape growers
has been recognised as the best book in Viticulture in
2012 by the International Organisation of Vine and Wine.
These awards recognise a significant contribution to the
field's knowledge: and this book has done just that,
providing a comprehensive review of the scientific
literature and discussing its application to current and
future practices in viticulture.
ARC CPEB 2012 / PAGE 33
Outreach Programs
Our Public Outreach programs communicate our
research to a range of community groups and end
users. Our programs are innovative, creative and
comprehensive outreach products that create
opportunities to communicate current research and
demonstrate the role of plant energy biology in everyday
life.
One of the main drivers behind the Giant Plant Cell is to
create an educational tool that helps the community
understand how new technology such as genetic
modification works in order facilitate informed choices
on GM. We want to create an inclusive, respectful
arena where people can ask questions about science.
Highlight
Science meets Policymakers: promoting evidencebased policy development
On the 24th of February 2012 over 300 of Australia's top
scientific researchers and policymakers met in
Canberra. PEB representative Dr Christopher Cazzonelli
explained that the meeting aimed to allow Australia to
better address complex and demanding policy changes
by improving the communication ties between scientists
and policymakers.
“Issues such as natural resource availability and
environmental sustainability could become
compromised unless the links between science and
policy are streamlined,” he said. “The summit revealed
that improving the quality and format of information
exchange, esteeming scientific skills within political
teams and providing formal recognition for time spent
driving evidence-based policy development by
scientists should lead to excellent outcomes in this
area.”
Plant Powerstation
Plant Powerstation is a key program in the Centre's
public engagement activities. Our public booths can be
seen where large numbers of Australians congregate,
where passionate scientists and educators talk science
with the public.
Hands-on activities such as DNA extractions from
plants allow our scientists to communicate more about
DNA, genes and gene technology and to better
understand public perceptions. Plant Powerstation has
featured at festivals and open days in WA, NSW, ACT
and SA and has reached over 26,500 members of the
public since 2006.
Enthusing young people in science careers and
creating advocates for scientific discovery is also a
major aim of the Giant Cell. With major changes
happening in the science curriculum, we want to create
resources to support TEE students and teachers with
the transition to high level topics, like gene technology.
When many science teachers attended university, this
technology wasn't even around. We want to help. More
details to come in 2013!
Highlight
Secrets of a Tiny Powerplant Photography
Exhibition – Winner of the 2012 Australian Science
Communicators (ASC) Conference Science as Art
Prize.
Bio-Bounce – the Giant Plant Cell – in development
for 2013.
2012 also saw leaps and bounds in the development of
an interesting new idea, coming to fruition in 2013.
PEB has been working with a 3D animator and
inflatables company to create: Bio-Bounce, the Giant
Inflatable Plant Cell. Bio-Bounce aims to become a
portable, novel, immersive and exciting way of engaging
the public with plant cell biology. The cell is large
enough that people can walk inside, look at the
organelles in context and have memorable, interactive
experience. The giant plant cell will explain the roles of
the nucleus, DNA and genes, energy organelles and
give insights into what biologists and geneticists study.
ARC CPEB 2012 / PAGE 34
In collaboration with WA's science museum (Scitech),
our scientists created a stunning photography display
for the public. Fourteen images were captured using
microscopes, macro cameras and even lasers to
provide a rare view deep inside plants. The images
reveal some of the incredible adaptations and clever
defence tactics that plants use to survive hostile
environments. As winners of the Science as Art award,
several of our images were shown in the fantastic
Science Illustrated Magazine.
In 2012, the collection reached over 170,000 visitors at
Cambridge Library (WA), Sydney Masonic Centre
(NSW) UWA Science Library (WA), Vincent Library (WA)
and Questacon (ACT).
Professional Training
Highlight
Our professional training program provides Centre staff
and students with the opportunity to enhance their
knowledge and skills in current techniques and theory.
As well as up-skilling our own staff, our training courses
and workshops extend our areas of technical expertise
to other end-users nationally and internationally.
Non-model de novo transcriptomics workshop
We recently took time out to talk about the benefits of
training in the Centre with Dr Estelle Giraud.
Researcher Profile
Estelle Giraud, PhD
Field Applications Scientist
Illumina Australia and New Zealand
I had the amazing opportunity to spend 8 years from the
Centre's beginning in 2005 through to 2012, first as an
Honours student, then PhD student and finally as a
Research Associate and Assistant Professor. I studied
the complex and surprising world of plant transcritomics
and regulation of gene expression.
At the Centre I had fantastic access and training on the
latest technology platforms and systems, which has
perfectly enabled my transition into Field Applications
Scientist with Illumina Global. I specialize in their NextGeneration Sequencing applications, which are at the
forefront of genomics research and technology.
Co-funded by UWA and UQ, researchers from across
Australia learnt how next generation sequencing can be
used for de novo transcriptome assembly for non-model
organisms.
Twenty-nine attendees from Illumina Inc., Curtin, ANU,
Murdoch, Monash and the Universities of WA,
Newcastle and Queensland were able to acquire new
research skills in transcriptomics.
Showcasing the quality of the workshop, the Centre has
been asked to run the training course again in 2013.
Building better scientists...
There are many standout features of my time at PEB
that have enabled me to flourish in my current role.
There is little doubt that the opportunities, resources,
infrastructure and technology that PEB provided me
have given me a vast knowledge base and appreciation
for science.
In July 2012, Future Fellow and recent Centre affiliate
Josh Mylne jointly hosted a training program on Next
Generation Sequencing Analysis at UQ with CI Jim
Whelan and international expert Prof Andreas Weber,
lead coordinator of the new Cluster of Excellence in Plant
Sciences in Germany.
ARC CPEB 2012 / PAGE 35
From my perspective PEB is currently
by far the most successful centRE in
the field of plant energy biology on
earth. The Centre is composed of
research teams which optimally
complement each other on
scientific as well as technological
levels. The Centre is a real network
and this in my opinion is something
very rare.
Research at the Centre is truly
innovative and based on new ideas
and concepts
Professor Hans-Peter Braun
Head of Plant Proteomics Department
Hannover University in Germany and
President of the German Society for Proteome Research
ARC CPEB 2012 / PAGE 36
People
ARC CPEB 2012 / PAGE 37
Centre Management
Governing
Board
Scientific Advisory
Board
Chief
Investigators
Centre
Director
Research Staff,
Post Graduates & Students
Organelle
Metabolism
Purchasing
Officer
Organelle
Signalling
Administration
Officer
Senior IT
Officer
Energy
Systems
Combined expertise...
Organelle
Biogenesis
Operations
Manager
Science Communications
Officer
ARC CPEB 2012 / PAGE 38
Scientific Advisory Board
Professor Robert Last
Emeritus Professor Ian Dawes
Emeritus Professor Dawes has a BSc from the University of
New South Wales, a DPhil from the University of Oxford in the
UK and is a Fellow of the Australian Academy of Science. He
is an editor of FEMS Yeast Research and a member of the
editorial boards of Yeast and the Journal of Microbiology. Em.
Professor Dawes has been a Board Member of the Victor
Chang Cardiac Research Institute and of the Australian
Proteomic Analytical Facility, Chairman of the International Yeast
Genetics and Molecular Biology Community and President of
the Australian Society for Biochemistry and Molecular Biology.
Professor Last is Barnett Rosenberg Professor in the
Departments of Biochemistry, Molecular Biology and Plant
Biology at Michigan State University, US. He is currently on the
editorial board of the Arabidopsis Book.
Previously, Professor Last has been a Program Director in the
Plant Genome Research Program at the US National Science
Foundation, the Director of Functional Genomics Research at
Cereon Genomics and Monsanto Co. and a Professor at the
Boyce Thompson Institute for Plant Research at Cornell
University.
Professor Christopher Leaver
CBE, ARCS, DIC, FRS, FRSE
Professor Richard P Oliver
Richard Oliver is Professor of Agriculture at Curtin University.
He is the director of the Australian Centre for Necrotrophic
Fungal Pathogen (ACNFP). He was deputy chairman of the
Western panel of the Australian Grains Research and
Development Corporation and has also served on the ARC
College of Experts. Richard was recently named as a John
Curtin Distinguished professor, one of only 13 ever awarded.
Trained as a plant biochemist, his career at UEA Norwich, the
Carlsberg Laboratory, Zeneca and now the ACNFP has
resulted in molecular tools that have revealed details of the
molecular interactions between plants and their fungal
pathogens. He also leads projects studying fungicide
resistance in Australia. Prof Oliver has published more than
150 papers and delivered tools to Australian plant breeders.
Winthrop Professor Fiona Wood
FRCS, FRACS, AM
Professor Wood is currently a plastic surgeon and Director of
the Burns Service of Western Australia and the Burn Injury
Research Unit UWA. She is the Chairman of the Fiona Wood
Foundation and co-founder Director of Clinical Cell Culture,
now Avitamedical, a skin tissue regenerative medicine
company.
Professor Wood's ongoing commitment to providing
breakthroughs for burns victims has lead to her being named
Australian of the Year and her election as a Member of the
Order of Australia (AM).
Professor Leaver is Emeritus Professor of Plant Science
University of Oxford and Fellow of St John's College. He was
Sibthorpian Professor of Plant Science and Head of
Department 1990-2007. He is a Fellow of the Royal Society,
the Royal Society of Edinburgh, member of the European
Molecular Biology Organisation and Academia Europaea.
His research interests include the molecular, biochemical and
cellular basis of plant development, the regulation of
mitochondrial biogenesis and function in plants, GM crops,
food security and sustainability. He is committed to creating a
dialogue with the public on the understanding of the
importance of plant science.
Dr Elizabeth S. Dennis
Dr Dennis is a leading plant molecular biologist. She is a
CSIRO Fellow and a Distinguished Professor at UTS whose
plant research has lead to outcomes in Australian agriculture.
Her research focuses on gene regulation both genetic and
epigenetic.
Dr Dennis's scientific excellence is acknowledged through
election as a Fellow of both the Australian Academy of
Technological Sciences and Engineering and the Australian
Academy of Science; awards of the Lemberg Medal for
distinguished contributions to biochemistry; the Pharmacia
LKB/Biotechnology medal for Biochemical Research and the
inaugural Prime Minister's Prize for Science together with Dr
Jim Peacock.
Professor David Day
Dr Wayne Gerlach
Dr Gerlach has performed in both Executive Director and
Research Director roles at Johnson & Johnson Research Pty
Ltd and as a Program Leader and Senior Principal Research
Scientist at CSIRO Division of Plant Industry in Canberra.
Dr Gerlach has PhD in Genetics from The University of
Adelaide and a Diploma in Management Development from
Harvard Business School. He has been awarded the CSIRO
Rivett Medal for research and the Lemberg Medal of the
Australian Society for Biochemistry and Molecular Biology.
In a career spanning 30 years, David has established an
international reputation in plant biochemistry and molecular
biology. The focus of his current research is the role of
mitochondria in oxidative stress and the isolation of genes
encoding transport proteins involving symbiotic nitrogen
fixation. His work been published in over 200 articles in leading
international journals and books.
David has had leading roles at the CRC for Plant Science, the
University of WA (Chair of Biochemistry), the University of
Sydney (Executive Dean Sciences) and is currently Deputy
Vice Chancellor (Research) at Flinders University.
ARC CPEB 2012 / PAGE 39
Personnel
Surname
First Name
Role/Grant/Affiliation
Surname
First Name
Role/Grant/Affiliation
UWA NODE
Alexova
Armarego-Marriott
Baer
Baer
Boussardon
Boykin
Bussell
Castleden
Clarke
Colas des Francs-Small
Den Boer
Duncan
Farthing
Fenske
Ford
Gillett
Giraud
Grassl
Hahne
Hartke
Holzmann Illanes
Hooper
Howell
Huang
Ivanova
Jacoby
Kindgren
Kubiszewski-Jakubiak
Law
Lee
Li
Li
Linn
Lister
Liu
Loh
Long
Melonek
Millar
Moyle
Murcha
Mylne
Narsai
Nelson
Ng
Ostersetzer
Paynter
Peng
Pruzinska
Secco
Sew
Shingaki-Wells
Small
Smith
Stroeher
Tanz
Taylor
Timmins
Tomaz
Tonti
Trend
Ralitza
Tegan
Barbara
Boris
Clement
Laura
John
Ian
Michael
Catherine
Susanne
Owen
Rosemarie
Ricarda
Ethan
Jenny
Estelle
Julia
Dorothee
Tamara
Cristian
Cornelia
Kate
Shaobai
Aneta
Richard
Peter
Szymon
Simon
Jae Hoon
Jing
Lei
Josh
Ryan
Sheng
Lyn
Rowena
Joanna
Harvey
Judith
Monika
Joshua
Reena
Clark
Sophia
Oren
Ellen
Yan
Adriana
David
Michelle
Rachel
Ian
Steven
Elke
Sandra
Nicolas
Matthew
Tiago
Julian
Alice
ARC Super Science Fellow
Masters student
Casual Lab Assistant
ARC Future Fellow
PhD student
Research Associate
Research Assistant Professor
Data Base/Systems Engineer
Research Assistant Professor
Research Assistant Professor
Honorary Visiting Research Fellow
Research Associate
Technician
Research Officer
Research Associate
Administrative Officer
Research Assistant Professor
Research Associate
Research Associate
Visiting Fellow
Occ Trainee
Research Assistant Professor
ARC DECRA Fellow
Research Associate
Research Assistant Professor
PhD student
Research Associate - Visiting Fellow
PhD student
PhD student
Honours Student
Research Assistant Professor
PhD student
PhD Student
Winthrop Professor
PhD student
Laboratory technician
Research Assistant Professor
Research Associate
Chief Investigator
Operations Manager
Research Assistant Professor
ARC Future Fellow
Research Assistant Professor
Research Associate
PhD student
Visiting Research Fellow
PhD student
PhD student
ARC DECRA Fellow
ARC Super Science Fellow
PhD student
PhD student
DIRECTOR
Chief Investigator
Australian Postdoctoral Fellowship
ARC DECRA Fellow
Research Assistant Professor
Research Associate
PhD student
PhD student/ Res Assist Prof
Science Communications Officer
Vacher
Van Aken
Van Der Merwe
Walker
Wang
Waters
Wiszniewski
Whelan
Xu
Yap
Yeoman
Yin
Zareie
Zhou
Michael
Olivier
Marna
Hayden
Yan
Mark
Andrew
Jim
Lin
Aaron
Deb
Quinn
Reza
Wenxu
PhD student
Australian Postdoctoral Fellowship
ARC Super Science Fellowship
Senior Computer Support Officer
Research Associate
Research Associate
Casual Research Assistant
Chief Investigator
PhD student
PhD student
Purchasing Officer
Visiting Research Fellow
Research Associate
Research Assistant Professor
ANU NODE
Albrecht
Badger
Bowerman
Carmody
Carroll
Cazzonelli
Chan
Collinge
Crisp
Estavillo
Forster
Ganguly
Gordon
Harper
Hou
Kaines
Kell
Marri
Nisar
Phua
Pogson
Rungrat
Takahashi
Watkins
Whitehead
Yadav
Zhang
Veronica
Murray
Andrew
Melanie
Adam
Chris
Kai
Derek
Peter
Gonzalo
Britta
Diep
Matthew
Rebecca
Xin
Sarah
Prue
Shashikanth
Nazia
Su Yin
Barry
Tepsuda
Shunichi
Jacinta
Lynne
Arun Kumar
Peng
Research Associate
Deputy Director
PhD student
PhD student
Research Associate
Research Associate
PhD student
Research Associate
PhD student
Research Associate
Research Associate (pttime)
Honours student
PhD student
Education Officer
PhD student
Research Associate (pttime)
Research Officer
Research Associate
PhD student - Postdoctoral Fellow
PhD student
Chief Investigator
PhD Student
Research Associate
Honours student
Research Associate (pttime)
Research Associate
Research assistant
ADELAIDE UNI NODE
Athman
Caravia Bayer
Dayod
Gilliham
Henderson
Hocking
Scharwies
Sullivan
Tyerman
Xu
Zhao
Asmini
Luciano
Maclin
Matthew
Sam
Bradley
Johannes
Wendy
Stephen
Bo
Manchun
Technical Officer
PhD student
PhD student
Senior Research Scientist
PhD student
PhD student
Masters Student
Research Assistant
Chief Investigator
PhD student
PhD student
ARC CPEB 2012 / PAGE 40
Selected CENTRE Publications
Alexeyenko A, Millar AH, Whelan J, Sonnhammer ELL.
Chromosomal clustering of nuclear genes encoding mitochondrial
and chloroplast proteins in Arabidopsis. TRENDS IN GENETICS.
2006;22:589-593.
Baker A, Graham IA, Holdsworth M, Smith SM, Theodoulou FL.
Chewing the fat: beta-oxidation in signalling and development.
TRENDS IN PLANT SCIENCE. 2006;11:124-132.
Lister R, Whelan J. Mitochondrial protein import: Convergent
solutions for receptor structure. CURRENT BIOLOGY.
2006;16:R197-R199.
Millar AH, Whelan J, Small I. Recent surprises in protein targeting to
mitochondria and plastids. CURRENT OPINION IN PLANT
BIOLOGY. 2006;9:610-615.
Small I. RNAi for revealing and engineering plant gene functions.
CURRENT OPINION IN BIOTECHNOLOGY. 2007;18:148-153.
Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler
M. A predicted interactome for Arabidopsis. PLANT PHYSIOLOGY.
2007;145:317-329.
Ho LHM, Giraud E, Lister R et al. Characterization of the regulatory
and expression context of an alternative oxidase gene provides
insights into cyanide-insensitive respiration during growth and
development. PLANT PHYSIOLOGY. 2007;143:1519-1533.
Zeeman SC, Smith SM, Smith AM. The diurnal metabolism of leaf
starch. BIOCHEMICAL JOURNAL. 2007;401:13-28.
Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH.
SUBA: The Arabidopsis subcellular database. NUCLEIC ACIDS
RESEARCH. 2007;35:D213-D218.
Cousins AB, Badger MR, Von C, S. Carbonic anhydrase and its
influence on carbon isotope discrimination during C-4
photosynthesis. Insights from antisense RNA in Flaveria bidentis.
PLANT PHYSIOLOGY. 2006;141:232-242.
Schmitz-Linneweber C, Small I. Pentatricopeptide repeat proteins:
a socket set for organelle gene expression. TRENDS IN PLANT
SCIENCE. 2008;13:663-670.
Cousins AB, Badger MR, von C, Susanne. A transgenic approach
to understanding the influence of carbonic anhydrase on (COO)-O18 discrimination during C-4 photosynthesis. PLANT
PHYSIOLOGY. 2006;142:662-672.
Eubel H, Meyer EH, Taylor NL et al. Novel Proteins, Putative
Membrane Transporters, and an Integrated Metabolic Network Are
Revealed by Quantitative Proteomic Analysis of Arabidopsis Cell
Culture Peroxisomes. PLANT PHYSIOLOGY. 2008;148:18091829.
DellaPenna D, Pogson BJ. Vitamin synthesis in plants: Tocopherols
and carotenoids. ANNUAL REVIEW OF PLANT BIOLOGY.
2006;57:711-738.
Legen J, Wanner G, Herrmann RG, Small I, Schmitz-Linneweber
C. Plastid tRNA Genes trnC-GCA and trnN-GUU are essential for
plant cell development. PLANT JOURNAL. 2007;51:751-762.
Lister R, Carrie C, Duncan O et al. Functional definition of outer
membrane proteins involved in preprotein import into mitochondria.
PLANT CELL. 2007;19:3739-3759.
Chateigner-Boutin A-L, Small I. A rapid high-throughput method for
the detection and quantification of RNA editing based on highresolution melting of amplicons. NUCLEIC ACIDS RESEARCH.
2007;35
Murcha MW, Elhafez D, Lister R et al. Characterization of the
preprotein and amino acid transporter gene family in Arabidopsis.
PLANT PHYSIOLOGY. 2007;143:199-212.
Narsai R, Howell KA, Millar AH, O'Toole N, Small I, Whelan J.
Genome-wide analysis of mRNA decay rates and their
determinants in Arabidopsis thaliana. PLANT CELL. 2007;19:34183436.
Cousins AB, Baroli I, Badger MR et al. The role of
phosphoenolpyruvate carboxylase during C-4 photosynthetic
isotope exchange and stomatal conductance. PLANT
PHYSIOLOGY. 2007;145:1006-1017.
Pracharoenwattana I, Cornah JE, Smith SM. Arabidopsis
peroxisomal malate dehydrogenase functions in beta-oxidation but
not in the glyoxylate cycle. PLANT JOURNAL. 2007;50:381-390.
Falcon de Longevialle A, Hendrickson L, Taylor N et al. The
pentatricopeptide repeat gene OTP51 with two LAGLIDADG motifs
is required for the cis-splicing of plastid ycf3 intron 2 in Arabidopsis
thaliana. PLANT JOURNAL. 2008;56:157-168.
Lee CP, Eubel H, O'Toole N, Millar AH. Heterogeneity of the
mitochondrial proteome for photosynthetic and non-photosynthetic
Arabidopsis metabolism. MOLECULAR & CELLULAR
PROTEOMICS. 2008;7:1297-1316.
Takahashi S, Murata N. How do environmental stresses accelerate
photoinhibition? TRENDS IN PLANT SCIENCE. 2008;13:178-182.
Fulton DC, Stettler M, Mettler T et al. beta-AMYLASE4, a
noncatalytic protein required for starch breakdown, acts upstream
of three active beta-amylases in Arabidopsis chloroplasts. PLANT
CELL. 2008;20:1040-1058.
Garmier M, Carroll AJ, Delannoy E et al. Complex I Dysfunction
Redirects Cellular and Mitochondrial Metabolism in Arabidopsis.
PLANT PHYSIOLOGY. 2008;148:1324-1341.
Giraud E, Ho LHM, Clifton R et al. The absence of alternative
oxidase1a in Arabidopsis results in acute sensitivity to combined
light and drought stress. PLANT PHYSIOLOGY. 2008;147:595610.
Takahashi S, Whitney S, Itoh S, Maruyama T, Badger M. Heat
stress causes inhibition of the de novo synthesis of antenna
proteins and photobleaching in cultured Symbiodinium.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF
THE UNITED STATES OF AMERICA. 2008;105:4203-4208.
Rossel JB, Wilson PB, Hussain D et al. Systemic and intracellular
responses to photooxidative stress in Arabidopsis. PLANT CELL.
2007;19:4091-4110.
Gregory BD, O'Malley RC, Lister R et al. A link between RNA
metabolism and silencing affecting Arabidopsis development.
DEVELOPMENTAL CELL. 2008;14:854-866.
Edner C, Li J, Albrecht T et al. Glucan, water dikinase activity
stimulates breakdown of starch granules by plastidial betaamylases. PLANT PHYSIOLOGY. 2007;145:17-28.
Heazlewood JL, Durek P, Hummel J et al. PhosPhAt: a database of
phosphorylation sites in Arabidopsis thaliana and a plant-specific
phosphorylation site predictor. NUCLEIC ACIDS RESEARCH.
2008;36:D1015-D1021.
Eubel H, Lee CP, Kuo J, Meyer EH, Taylor NL, Millar AH. Free-flow
electrophoresis for purification of plant mitochondria by surface
charge. PLANT JOURNAL. 2007;52:583-594.
Falcon de Longevialle A, Meyer EH, Andres C et al. The
pentatricopeptide repeat gene OTP43 is required for trans-splicing
of the mitochondrial nad1 intron 1 in Arabidopsis thaliana. PLANT
CELL. 2007;19:3256-3265.
Takahashi S, Bauwe H, Badger M. Impairment of the
photorespiratory pathway accelerates photoinhibition of
photosystem II by suppression of repair but not acceleration of
damage processes in Arabidopsis. PLANT PHYSIOLOGY.
2007;144:487-494.
Ho LHM, Giraud E, Uggalla V et al. Identification of regulatory
pathways controlling gene expression of stress-responsive
mitochondrial proteins in Arabidopsis. PLANT PHYSIOLOGY.
2008;147:1858-1873.
Huang S, Colmer TD, Millar AH. Does anoxia tolerance involve
altering the energy currency towards PPi? TRENDS IN PLANT
SCIENCE. 2008;13:221-227.
Carroll AJ, Heazlewood JL, Ito J, Millar AH. Analysis of the
Arabidopsis cytosolic ribosome proteome provides detailed insights
into its components and their post-translational modification.
MOLECULAR & CELLULAR PROTEOMICS. 2008;7:347-369.
ARC CPEB 2012 / PAGE 41
Selected CENTRE Publications
Lister R, O'Malley RC, Tonti-Filippini J et al. Highly integrated singlebase resolution maps of the epigenome in Arabidopsis. CELL.
2008;133:523-536.
Chateigner-Boutin A-L, Ramos-Vega M, Guevara-Garcia A et al.
CLB19, a pentatricopeptide repeat protein required for editing of
rpoA and clpP chloroplast transcripts. PLANT JOURNAL.
2008;56:590-602.
Kuehn K, Richter U, Meyer EH et al. Phage-Type RNA Polymerase
RPOTmp Performs Gene-Specific Transcription in Mitochondria of
Arabidopsis thaliana. PLANT CELL. 2009;21:2762-2779.
O'Toole N, Hattori M, Andres C et al. On the expansion of the
pentatricopeptide repeat gene family in plants. MOLECULAR
BIOLOGY AND EVOLUTION. 2008;25:1120-1128.
Takahashi S, Whitney SM, Badger MR. Different thermal sensitivity
of the repair of photodamaged photosynthetic machinery in
cultured Symbiodinium species. PROCEEDINGS OF THE
NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
AMERICA. 2009;106:3237-3242.
Pogson BJ, Woo NS, Foerster B, Small ID. Plastid signalling to the
nucleus and beyond. TRENDS IN PLANT SCIENCE. 2008;13:602609.
Takahashi S, Milward SE, Fan D-Y, Chow W, Badger MR. How
Does Cyclic Electron Flow Alleviate Photoinhibition in Arabidopsis?
PLANT PHYSIOLOGY. 2009;149:1560-1567.
Cousins AB, Pracharoenwattana I, Zhou W, Smith SM, Badger MR.
Peroxisomal malate dehydrogenase is not essential for
photorespiration in Arabidopsis but its absence causes an increase
in the stoichiometry of photorespiratory CO2 release. PLANT
PHYSIOLOGY. 2008;148:786-795.
Lister R, Pelizzola M, Dowen RH et al. Human DNA methylomes at
base resolution show widespread epigenomic differences.
NATURE. 2009;462:315-322.
Pracharoenwattana I, Smith SM. When is a peroxisome not a
peroxisome? TRENDS IN PLANT SCIENCE. 2008;13:522-525.
Gutierrez L, Bussell JD, Pacurar DI, Schwambach J, Pacurar M,
Bellini C. Phenotypic Plasticity of Adventitious Rooting in
Arabidopsis Is Controlled by Complex Regulation of AUXIN
RESPONSE FACTOR Transcripts and MicroRNA Abundance.
PLANT CELL. 2009;21:3119-3132.
Marti MC, Olmos E, Calvete JJ et al. Mitochondrial and Nuclear
Localization of a Novel Pea Thioredoxin: Identification of Its
Mitochondrial Target Proteins. PLANT PHYSIOLOGY.
2009;150:646-657.
Meyer EH, Tomaz T, Carroll AJ et al. Remodeled Respiration in
ndufs4 with Low Phosphorylation Efficiency Suppresses
Arabidopsis Germination and Growth and Alters Control of
Metabolism at Night. PLANT PHYSIOLOGY. 2009;151:603-619.
Cazzonelli CI, Cuttriss AJ, Cossetto SB et al. Regulation of
Carotenoid Composition and Shoot Branching in Arabidopsis by a
Chromatin Modifying Histone Methyltransferase, SDG8. PLANT
CELL. 2009;21:39-53.
Tillich M, Hardel SL, Kupsch C et al. Chloroplast ribonucleoprotein
CP31A is required for editing and stability of specific chloroplast
mRNAs. PROCEEDINGS OF THE NATIONAL ACADEMY OF
SCIENCES OF THE UNITED STATES OF AMERICA.
2009;106:6002-6007.
Delannoy E, Le R, Monique, Faivre-Nitschke E et al. Arabidopsis
tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide
of Chloroplast tRNA(Arg)(ACG) and Is Essential for Efficient
Chloroplast Translation. PLANT CELL. 2009;21:2058-2071.
Millar AH, Carrie C, Pogson B, Whelan J. Exploring the FunctionLocation Nexus: Using Multiple Lines of Evidence in Defining the
Subcellular Location of Plant Proteins. PLANT CELL.
2009;21:1625-1631.
Hammani K, Okuda K, Tanz SK, Chateigner-Boutin A-L, Shikanai T,
Small I. A Study of New Arabidopsis Chloroplast RNA Editing
Mutants Reveals General Features of Editing Factors and Their
Target Sites. PLANT CELL. 2009;21:3686-3699.
Narsai R, Howell KA, Carroll A, Ivanova A, Millar AH, Whelan J.
Defining Core Metabolic and Transcriptomic Responses to Oxygen
Availability in Rice Embryos and Young Seedlings. PLANT
PHYSIOLOGY. 2009;151:306-322.
Giraud E, Van A, Olivier, Ho LHM, Whelan J. The Transcription
Factor ABI4 Is a Regulator of Mitochondrial Retrograde Expression
of ALTERNATIVE OXIDASE1a. PLANT PHYSIOLOGY.
2009;150:1286-1296.
Okuda K, Chateigner-Boutin A-L, Nakamura T et al.
Pentatricopeptide Repeat Proteins with the DYW Motif Have
Distinct Molecular Functions in RNA Editing and RNA Cleavage in
Arabidopsis Chloroplasts. PLANT CELL. 2009;21:146-156.
Howell KA, Narsai R, Carroll A et al. Mapping Metabolic and
Transcript Temporal Switches during Germination in Rice Highlights
Specific Transcription Factors and the Role of RNA Instability in the
Germination Process. PLANT PHYSIOLOGY. 2009;149:961-980.
Rackham O, Davies SMK, Shearwood A-MJ, Hamilton KL, Whelan
J, Filipovska A. Pentatricopeptide repeat domain protein 1 lowers
the levels of mitochondrial leucine tRNAs in cells. NUCLEIC ACIDS
RESEARCH. 2009;37:5859-5867.
Huang S, Taylor NL, Narsai R, Eubel H, Whelan J, Millar AH.
Experimental Analysis of the Rice Mitochondrial Proteome, Its
Biogenesis, and Heterogeneity. PLANT PHYSIOLOGY.
2009;149:719-734.
Sappl PG, Carroll AJ, Clifton R et al. The Arabidopsis glutathione
transferase gene family displays complex stress regulation and cosilencing multiple genes results in altered metabolic sensitivity to
oxidative stress. PLANT JOURNAL. 2009;58:53-68.
Huang S, Taylor NL, Whelan J, Millar AH. Refining the Definition of
Plant Mitochondrial Presequences through Analysis of Sorting
Signals, N-Terminal Modifications, and Cleavage Motifs. PLANT
PHYSIOLOGY. 2009;150:1272-1285.
Wilson PB, Estavillo GM, Field KJ et al. The
nucleotidase/phosphatase SAL1 is a negative regulator of drought
tolerance in Arabidopsis. PLANT JOURNAL. 2009;58:299-317.
Kreuzwieser J, Hauberg J, Howell KA et al. Differential Response of
Gray Poplar Leaves and Roots Underpins Stress Adaptation during
Hypoxia. PLANT PHYSIOLOGY. 2009;149:461-473.
Baer B, Eubel H, Taylor NL, O'Toole N, Millar AH. Insights into
female sperm storage from the spermathecal fluid proteome of the
honeybee Apis mellifera. GENOME BIOLOGY. 2009;10
Bond DM, Wilson IW, Dennis ES, Pogson BJ, Finnegan EJ.
VERNALIZATION INSENSITIVE 3 (VIN3) is required for the response
of Arabidopsis thaliana seedlings exposed to low oxygen
conditions. PLANT JOURNAL. 2009;59:576-587.
Carrie C, Kuehn K, Murcha MW et al. Approaches to defining dualtargeted proteins in Arabidopsis. PLANT JOURNAL.
2009;57:1128-1139.
ARC CPEB 2012 / PAGE 42
Zheng L, Huang F, Narsai R et al. Physiological and Transcriptome
Analysis of Iron and Phosphorus Interaction in Rice Seedlings.
PLANT PHYSIOLOGY. 2009;151:262-274.
Zhou W, Cheng Y, Yap A et al. The Arabidopsis gene YS1
encoding a DYW protein is required for editing of rpoB transcripts
and the rapid development of chloroplasts during early growth.
PLANT JOURNAL. 2009;58:82-96.
Keech O, Pesquet E, Gutierrez L et al. Leaf Senescence Is
Accompanied by an Early Disruption of the Microtubule Network in
Arabidopsis. PLANT PHYSIOLOGY. 2010;154:1710-1720.
Giraud E, Ng S, Carrie C et al. TCP Transcription Factors Link the
Regulation of Genes Encoding Mitochondrial Proteins with the
Circadian Clock in Arabidopsis thaliana. PLANT CELL.
2010;22:3921-3934.
Selected CENTRE Publications
Albrecht V, Simkova K, Carrie C et al. The Cytoskeleton and the
Peroxisomal-Targeted SNOWY COTYLEDON3 Protein Are
Required for Chloroplast Development in Arabidopsis. PLANT
CELL. 2010;22:3423-3438.
Lee CP, Eubel H, Millar AH. Diurnal Changes in Mitochondrial
Function Reveal Daily Optimization of Light and Dark Respiratory
Metabolism in Arabidopsis. MOLECULAR & CELLULAR
PROTEOMICS. 2010;9:2125-2139.
Takahashi S, Milward SE, Yamori W, Evans JR, Hillier W, Badger
MR. The Solar Action Spectrum of Photosystem II Damage. PLANT
PHYSIOLOGY. 2010;153:988-993.
Tan Y-F, O'Toole N, Taylor NL, Millar AH. Divalent Metal Ions in Plant
Mitochondria and Their Role in Interactions with Proteins and
Oxidative Stress-Induced Damage to Respiratory Function. PLANT
PHYSIOLOGY. 2010;152:747-761.
Taylor NL, Howell KA, Heazlewood JL et al. Analysis of the Rice
Mitochondrial Carrier Family Reveals Anaerobic Accumulation of a
Basic Amino Acid Carrier Involved in Arginine Metabolism during
Seed Germination. PLANT PHYSIOLOGY. 2010;154:691-704.
Cazzonelli CI, Pogson BJ. Source to sink: regulation of carotenoid
biosynthesis in plants. TRENDS IN PLANT SCIENCE.
2010;15:266-274.
Chai T-T, Simmonds D, Day DA, Colmer TD, Finnegan PM.
Photosynthetic Performance and Fertility Are Repressed in
GmAOX2b Antisense Soybean. PLANT PHYSIOLOGY.
2010;152:1638-1649.
Tognetti VB, Van A, Olivier, Morreel K et al. Perturbation of Indole-3Butyric Acid Homeostasis by the UDP-Glucosyltransferase
UGT74E2 Modulates Arabidopsis Architecture and Water Stress
Tolerance. PLANT CELL. 2010;22:2660-2679.
Che P, Bussell JD, Zhou W, Estavillo GM, Pogson BJ, Smith SM.
Signaling from the Endoplasmic Reticulum Activates
Brassinosteroid Signaling and Promotes Acclimation to Stress in
Arabidopsis. SCIENCE SIGNALING. 2010;3
Tomaz T, Bagard M, Pracharoenwattana I et al. Mitochondrial
Malate Dehydrogenase Lowers Leaf Respiration and Alters
Photorespiration and Plant Growth in Arabidopsis. PLANT
PHYSIOLOGY. 2010;154:1143-1157.
Chen W, Chi Y, Taylor NL, Lambers H, Finnegan PM. Disruption of
ptLPD1 or ptLPD2, Genes That Encode Isoforms of the Plastidial
Lipoamide Dehydrogenase, Confers Arsenate Hypersensitivity in
Arabidopsis. PLANT PHYSIOLOGY. 2010;153:1385-1397.
Chateigner-Boutin A-L, Colas des Francs-Small C, Delannoy E et
al. OTP70 is a pentatricopeptide repeat protein of the E subgroup
involved in splicing of the plastid transcript rpoC1. PLANT
JOURNAL. 2011;65:532-542.
Narsai R, Law SR, Carrie C, Xu L, Whelan J. In-Depth Temporal
Transcriptome Profiling Reveals a Crucial Developmental Switch
with Roles for RNA Processing and Organelle Metabolism That Are
Essential for Germination in Arabidopsis. PLANT PHYSIOLOGY.
2011;157:1342-1362.
Narsai R, Rocha M, Geigenberger P, Whelan J, van D, Joost T.
Comparative analysis between plant species of transcriptional and
metabolic responses to hypoxia. NEW PHYTOLOGIST.
2011;190:472-487.
Nelson DC, Scaffidi A, Dun EA et al. F-box protein MAX2 has dual
roles in karrikin and strigolactone signaling in Arabidopsis thaliana.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF
THE UNITED STATES OF AMERICA. 2011;108:8897-8902.
Pogson BJ, Albrecht V. Genetic Dissection of Chloroplast
Biogenesis and Development: An Overview. PLANT PHYSIOLOGY.
2011;155:1545-1551.
Delannoy E, Fujii S, Colas des Francs-Small C, Brundrett M, Small
I. Rampant Gene Loss in the Underground Orchid Rhizanthella
gardneri Highlights Evolutionary Constraints on Plastid Genomes.
MOLECULAR BIOLOGY AND EVOLUTION. 2011;28:2077-2086.
Duncan O, Taylor NL, Carrie C et al. Multiple Lines of Evidence
Localize Signaling, Morphology, and Lipid Biosynthesis Machinery
to the Mitochondrial Outer Membrane of Arabidopsis. PLANT
PHYSIOLOGY. 2011;157:1093-1113.
Estavillo GM, Crisp PA, Pornsiriwong W et al. Evidence for a SAL1PAP Chloroplast Retrograde Pathway That Functions in Drought
and High Light Signaling in Arabidopsis. PLANT CELL.
2011;23:3992-4012.
Shingaki-Wells RN, Huang S, Taylor NL, Carroll AJ, Zhou W, Millar
AH. Differential Molecular Responses of Rice and Wheat
Coleoptiles to Anoxia Reveal Novel Metabolic Adaptations in Amino
Acid Metabolism for Tissue Tolerance. PLANT PHYSIOLOGY.
2011;156:1706-1724.
Fernie AR, Aharoni A, Willmitzer L et al. Recommendations for
Reporting Metabolite Data. PLANT CELL. 2011;23:2477-2482.
Foerster B, Pogson BJ, Osmond CB. Lutein from Deepoxidation of
Lutein Epoxide Replaces Zeaxanthin to Sustain an Enhanced
Capacity for Nonphotochemical Chlorophyll Fluorescence
Quenching in Avocado Shade Leaves in the Dark. PLANT
PHYSIOLOGY. 2011;156:393-403.
Okuda K, Hammani K, Tanz SK et al. The pentatricopeptide repeat
protein OTP82 is required for RNA editing of plastid ndhB and
ndhG transcripts. PLANT JOURNAL. 2010;61:339-349.
Fujii S, Bond CS, Small ID. Selection patterns on restorer-like
genes reveal a conflict between nuclear and mitochondrial
genomes throughout angiosperm evolution. PROCEEDINGS OF
THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED
STATES OF AMERICA. 2011;108:1723-1728.
Van A, Olivier, Whelan J, Van B, Frank. Prohibitins: mitochondrial
partners in development and stress response. TRENDS IN PLANT
SCIENCE. 2010;15:275-282.
Takahashi S, Badger MR. Photoprotection in plants: a new light on
photosystem II damage. TRENDS IN PLANT SCIENCE.
2011;16:53-60.
den Boer SPA, Baer B, Boomsma JJ. Seminal Fluid Mediates
Ejaculate Competition in Social Insects. SCIENCE.
2010;327:1506-1509.
Gleason C, Huang S, Thatcher LF et al. Mitochondrial complex II
has a key role in mitochondrial-derived reactive oxygen species
influence on plant stress gene regulation and defense.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF
THE UNITED STATES OF AMERICA. 2011;108:10768-10773.
Pracharoenwattana I, Zhou W, Keech O et al. Arabidopsis has a
cytosolic fumarase required for the massive allocation of
photosynthate into fumaric acid and for rapid plant growth on high
nitrogen. PLANT JOURNAL. 2010;62:785-795.
Richter U, Kuehn K, Okada S, Brennicke A, Weihe A, Boerner T. A
mitochondrial rRNA dimethyladenosine methyltransferase in
Arabidopsis. PLANT JOURNAL. 2010;61:558-569.
Kuehn K, Carrie C, Giraud E et al. The RCC1 family protein RUG3
is required for splicing of nad2 and complex I biogenesis in
mitochondria of Arabidopsis thaliana. PLANT JOURNAL.
2011;67:1067-1080.
Millar AH, Whelan J, Soole KL, Day DA. Organization and
Regulation of Mitochondrial Respiration in Plants. In: Merchant SS,
Briggs WR, Ort D, editors. 62. 2011. p. 79-104.
Hammani K, Gobert A, Hleibieh K, Choulier L, Small I, Giege P. An
Arabidopsis Dual-Localized Pentatricopeptide Repeat Protein
Interacts with Nuclear Proteins Involved in Gene Expression
Regulation. PLANT CELL. 2011;23:730-740.
Jacoby RP, Taylor NL, Millar AH. The role of mitochondrial
respiration in salinity tolerance. TRENDS IN PLANT SCIENCE.
2011;16:614-623.
Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K et al. MASCP Gator:
An Aggregation Portal for the Visualization of Arabidopsis
Proteomics Data. PLANT PHYSIOLOGY. 2011;155:259-270.
Smith SM, Waters MT. Strigolactones: Destruction-Dependent
Perception? CURRENT BIOLOGY. 2012;22:R924-R927.
ARC CPEB 2012 / PAGE 43
Selected CENTRE Publications
Solheim C, Li L, Hatzopoulos P, Millar AH. Loss of Lon1 in
Arabidopsis Changes the Mitochondrial Proteome Leading to
Altered Metabolite Profiles and Growth Retardation without an
Accumulation of Oxidative Damage. PLANT PHYSIOLOGY.
2012;160:1187-1203.
Kindgren P, Kremnev D, Blanco NE et al. The plastid redox
insensitive 2 mutant of Arabidopsis is impaired in PEP activity and
high light-dependent plastid redox signalling to the nucleus. PLANT
JOURNAL. 2012;70:279-291.
Kupsch C, Ruwe H, Gusewski S, Tillich M, Small I, SchmitzLinneweber C. Arabidopsis Chloroplast RNA Binding Proteins
CP31A and CP29A Associate with Large Transcript Pools and
Confer Cold Stress Tolerance by Influencing Multiple Chloroplast
RNA Processing Steps. PLANT CELL. 2012;24:4266-4280.
Takahashi S, Yoshioka-Nishimura M, Nanba D, Badger MR.
Thermal Acclimation of the Symbiotic Alga Symbiodinium spp.
Alleviates Photobleaching under Heat Stress. PLANT
PHYSIOLOGY. 2013;161:477-485.
Law SR, Narsai R, Taylor NL et al. Nucleotide and RNA Metabolism
Prime Translational Initiation in the Earliest Events of Mitochondrial
Biogenesis during Arabidopsis Germination. PLANT PHYSIOLOGY.
2012;158:1610-1627.
Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA.
SUBA3: a database for integrating experimentation and prediction
to define the SUBcellular location of proteins in Arabidopsis.
NUCLEIC ACIDS RESEARCH. 2013;41:D1185-D1191.
Lee S, Lee DW, Yoo Y-J et al. Mitochondrial Targeting of the
Arabidopsis F1-ATPase gamma-Subunit via Multiple Compensatory
and Synergistic Presequence Motifs. PLANT CELL. 2012;24:50375057.
Chan KX, Wirtz M, Phua SY, Estavillo G, Pogson BJ. Balancing
metabolites in drought: the sulfur assimilation conundrum. TRENDS
IN PLANT SCIENCE. 2013;18:18-29.
Barkan A, Rojas M, Fujii S et al. A Combinatorial Amino Acid Code
for RNA Recognition by Pentatricopeptide Repeat Proteins. PLOS
GENETICS. 2012;8
Li L, Nelson CJ, Solheim C, Whelan J, Millar AH. Determining
Degradation and Synthesis Rates of Arabidopsis Proteins Using the
Kinetics of Progressive N-15 Labeling of Two-dimensional Gelseparated Protein Spots. MOLECULAR & CELLULAR
PROTEOMICS. 2012;11
Tanz SK, Kilian J, Johnsson C et al. The SCO2 protein disulphide
isomerase is required for thylakoid biogenesis and interacts with
LCHB1 chlorophyll a/b binding proteins which affects chlorophyll
biosynthesis in Arabidopsis seedlings. PLANT JOURNAL.
2012;69:743-754.
Boussardon C, Salone V, Avon A et al. Two Interacting Proteins Are
Necessary for the Editing of the NdhD-1 Site in Arabidopsis
Plastids. PLANT CELL. 2012;24:3684-3694.
Munns R, James RA, Xu B et al. Wheat grain yield on saline soils is
improved by an ancestral Na+ transporter gene. NATURE
BIOTECHNOLOGY. 2012;30:360-U173.
Nelson DC, Flematti GR, Ghisalberti EL, Dixon K, Smith SM.
Regulation of Seed Germination and Seedling Growth by Chemical
Signals from Burning Vegetation. In: Merchant SS, editor. 63.
2012. p. 107-130.
Colas des Francs-Small C, Kroeger T, Zmudjak M et al. A PORR
domain protein required for rpl2 and ccmFC intron splicing and for
the biogenesis of c-type cytochromes in Arabidopsis mitochondria.
PLANT JOURNAL. 2012;69:996-1005.
Wang Y, Carrie C, Giraud E et al. Dual Location of the
Mitochondrial Preprotein Transporters B14.7 and Tim23-2 in
Complex I and the TIM17:23 Complex in Arabidopsis Links
Mitochondrial Activity and Biogenesis. PLANT CELL.
2012;24:2675-2695.
Waters MT, Nelson DC, Scaffidi A et al. Specialisation within the
DWARF14 protein family confers distinct responses to karrikins and
strigolactones in Arabidopsis. DEVELOPMENT. 2012;139:12851295.
Williams C, van dB, Marlene, Panjikar S, Stanley WA, Distel B,
Wilmanns M. Insights into ubiquitin-conjugating enzyme/coactivator interactions from the structure of the Pex4p:Pex22p
complex. EMBO JOURNAL. 2012;31:391-402.
Keren I, Tal L, des F-S, Catherine C. et al. nMAT1, a nuclearencoded maturase involved in the trans-splicing of nad1 intron 1, is
essential for mitochondrial complex I assembly and function.
PLANT JOURNAL. 2012;71:413-426.
Kim M, Lee U, Small I, des F-S, CatherineColas, Vierling E.
Mutations in an Arabidopsis Mitochondrial Transcription Termination
Factor-Related Protein Enhance Thermotolerance in the Absence
of the Major Molecular Chaperone HSP101. PLANT CELL.
2012;24:3349-3365.
ARC CPEB 2012 / PAGE 44
Xu L, Carrie C, Law SR, Murcha MW, Whelan J. Acquisition,
Conservation, and Loss of Dual-Targeted Proteins in Land Plants.
PLANT PHYSIOLOGY. 2013;161:644-662.
Huang S, Taylor NL, Stroeher E, Fenske R, Millar AH. Succinate
dehydrogenase assembly factor 2 is needed for assembly and
activity of mitochondrial complex II and for normal root elongation in
Arabidopsis. PLANT JOURNAL. 2013;73:429-441.
Jia H, Foerster B, Chow WS, Pogson B, Osmond CB. Decreased
Photochemical Efficiency of Photosystem II following Sunlight
Exposure of Shade-Grown Leaves of Avocado: Because of, or in
Spite of, Two Kinetically Distinct Xanthophyll Cycles? PLANT
PHYSIOLOGY. 2013;161:836-852.
Fast facts about our publications
• Total number of publications: 335
• Publications recognised by Thomson Reuters
Web of Knowledge: 309
• Publications in top journals (impact factor 10
and over): 54
• Publications cited at least 100 times: 13
• 12% of our papers are in the top 1%
worldwide (as judged by Thomson Reuters
Web of Knowledge Essential Indicators)
• Over the last 7 years, over 25% of the
Australian papers in the top plant science
journal, PLANT CELL, included authors from
our Centre
• Number of different countries with whom we
have collaborated: 27
Fast facts about our citations
• Total number of citations: 8120
• Citations per paper: 26 (that's more than
double the average for Australian papers in
plant sciences)
• The twelve organisations that cite us the
most: Chinese Academy of Sciences, Centre
National de la Recherche Scientifique,
Harvard University, Max-Planck Institute for
Molecular Plant Physiology, Tokyo University,
Michigan State University, Cornell University,
Cambridge University, Institut National de la
Recherche Agronomique, University of
California - Berkeley, University of California Davis, University of California - San Diego.
To find out more about our Centre visit:
W
plantenergy.uwa .edu.au
You will find information on:
• The latest news on Centre activities.
• Updates on progress towards our research goals.
• Opportunities to join the Centre's research team
(as a student or a research associate).
• Opportunities to benefit from or invest in the
Centre's research outcomes.
• Information about the outstanding staff and students in the Centre.
• Details of our more than 330 research publications.
ARC Centre of Excellence in Plant Energy Biology
The University of Western Australia M316
35 Stirling Hwy, Crawley, WA, 6009, Australia
Ph: +61 8 6488 4416
Fax: +61 8 6488 4401
ARC CPEB 2012 / PAGE 45
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plantenergy.uwa .edu.au
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