NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
ProgrammeSchedule&Abstracts
IfyouwishtodownloadthePDFsoftcopytoyour
mobilephone,kindlyscanthisQRCodeor
downloadatthisURL:goo.gl/Hggf9W
Day1
26September2016(Monday)
Session1:ChemicalEcology
SessionChair:StephanSchuster
9:00-9:15
OpeningAddress:BertilAndersson
9:15-10:00
AbstractPage
Number
Plenarytalk:IanBaldwin-“Askingtheecosystem”to
understandtheecologicalfunctionofspecialized
metabolism
10:00-10:25 EmmanuelGacquerel-Navigatingstructuraland
regulatorydiversityinplantdefensivemetabolism
10:25-10:50 NaweedNaqvi–Chemicalcommunicationacrossthe
plant-microbeinterfaceduringRiceBlast
10:50-11:15 CoffeeBreak
Session2:SyntheticBiology
SessionChair:MiaoYansong
11:15-11:40 NivAntonovsky–AfunctionalCalvincycleinE.coli
3
11:40-12:05
7
OliverMueller-Cajar–Thediversemolecularmotors
involvedinmaintainingphotosyntheticCO2uptake
12:05-12:30 Jing-KeWeng-Mechanisticbasisformetabolicevolution
inplants
12:30-1:30
Lunch
Session3:PlantGenomics
SessionChair:PeterPreiser
1:30-2:15
Plenarytalk:VictorAlbert–Uncoveringtheadaptive
landscapesofplantgenomes
2:15-2:40
StephanSchuster–Thephytobiome
2:40-3:05
CharlotteLindqvist–Unlockingherbariumcollectionsfor
plantgenomicresearch
3:05-3:20
CoffeeBreak
Session4:PlantBiology
SessionChair:JamesTam
3:20-3:45
MiaoYansong-Host-pathogencommunicationsregulate
plantactincytoskeletonandimmunity
4
5
6
8
9
10
11
12
3:45-4:10
JedrzejJakubSzymanski-Integratingmultileveldatato
reconstructandmodelplantmetabolicnetworks
13
4:10-4:35
AleksandraSkirycz-Venturingintoterraincognitaof
proteinsmallmoleculeinteractionsusingcombinationof
novelandclassicalapproaches
14
4:35-6:00
HappyHour-meetthespeakers
Page 1 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Day2
27September2016(Tuesday)
Session5:EmergingTechnology
SessionChair:HongYan
9:00-9:45
Plenarytalk:LotharWillmitzer–Metabolomics–
technologyandapplicationsinlifesciences
AbstractPage
Number
15
9:45-10:10
TakayukiTohge-Metabolomics-assistedfunctional
genomicsonplantphenolicsecondarymetabolism
16
10:10-10:35
ShashiBhushan-Cryo-EM structure of the chloro-ribosome
17
10:35-11:00
SarojamRajani-Unravellingsecondarymetabolismof
aromaticplants(SpearmintandSweetBasil)byNext
generationsequencing
11:00-11:15 CoffeeBreak
Session6:NaturalProducts
SessionChair:OliverMueller-Cajar
11:20-12:05 Plenarytalk:JamesTam–Moleculardiversityandfuzzy
processingofpeptidylplantproducts
12:05-12:30 InCheolJang-Identificationofbiosynthetic
pathways/genesforfloralvolatileorganiccompounds
12:30-12:55 CamilaCaldana-Decipheringplantmetabolicregulation
puzzle:examplesofmetabolitesaffectingbiomass
production
12:55-2:00
Lunch
Page 2 of 21
18
19
20
21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
“Askingtheecosystem”tounderstandtheecologicalfunctionofspecialized
metabolism
D.Li,S.Poreddy,E.Gaquerel,S.Pandit,I.T.Baldwin
DepartmentofMolecularEcology,MaxPlanckInstituteforChemicalEcology,
Jena,Germany
This talk will highlight the approach that the members of the Department of
Molecular Ecology at the MPICOE have taken with a native tobacco, Nicotiana
attenuata,tounderstandtheecologyfunctionofitsspecializedmetabolism.The
talkwillhighlightbothatargetedapproachtowardunderstandingthefunction
of acyl sugars, diterpene glycosides and pyridine alkaloids, as well as an
untargeted approach analyzing volatile and non-volatile metabolites that uses
natural variation. Native populations are highly genetically diverse for traits
important for the interactions of this plant with insects. To resolve the
chemodiversityexistinginthesepopulations,wedevelopedametabolomicsand
computational pipeline to annotate leaf metabolic responses to Manduca sexta
herbivory. Metabolic profiles were generated from elicited leaves of each plant
using a high throughput UHPLC-qTOFMS method, processed to systematically
infer co-variation patterns among biochemically-related metabolites as well as
unknown ones. Navigating the resulting map of natural variation revealed
metabolicbranch-specificvariationsthatonlypartlyoverlappedwithjasmonate
accumulation polymorphisms and deviated from canonical jasmonate signaling
(Li et al. 2015). The function of the unknowns identified by this approach is
assessedwithfieldworkemployingunbiasednaturalhistorybasedapproaches
andthisapproachwillbehighlightedwithanexamplefromtheon-goingwork
ontheecologicalfunctionofditerpeneglycosides(Poreddyetal.2015).
References:
Li,D.,Baldwin,I.T.,Gaquerel,E.(2015).PNAS,112(30),E4147-E4155.
Poreddy,S.,Mitra,S.,Schöttner,M.,Chandran,J.N.,Schneider,B.,Baldwin,I.T.,
Kumar,P.,Pandit,S.S.(2015).NatureCommunications,6:8525.
Page 3 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Navigatingstructuralandregulatorydiversityinplantdefensive
metabolism
EmmanuelGacquerel
UniversityofHeidelberg,Germany
Navigatingstructuralandregulatorydiversityinplantdefensivemetabolism
Classesofplantspecializedmetaboliteshaveextensivelydiversifiedacrossplant
taxa, thereby suggesting that particular metabolic systems have been recruited
throughnaturalselectionwhenthesetofcompoundsthattheyproduceaddress
specific ecological needs. Interaction with insects is one of the many selection
pressures thought to have sculpted plant metabolism and many specialized
metabolites directly protect plants against herbivore attacks. The overarching
objectiveofourresearchistounderstandthedefensivefunctionagainstinsects
of some of these specialized metabolites as well as the evolutionary history of
theunderlyingbiosyntheticpathways.Alongthisline,weaimatacceleratingthe
process of gene function discovery in specialized metabolism using an
integration of transcriptomics and mass spectrometry (MS)-based
metabolomics.
Inthistalk,IwillarticulaterecentMSmetabolomicsdevelopmentsofmygroup
toimprovethenavigationofintra-andinter-speciesmetabolicvariations.Using
allopolyploid (resulting from hybridization followed by whole genome
duplication)wildtobaccospecies,Iwillillustratehowtheseapproachescanbe
incorporatedinthestudyofallopolyploidizationasakeyevolutionarymotorfor
thediversificationofdefensivespecializedmetabolites.
Page 4 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Chemicalcommunicationacrosstheplant-microbeinterfaceduringRice
Blast
NaweedNaqvi
TemasekLifeSciencesLaboratory,Singapore
Rice Blast represents a model pathosystem, wherein the causal fungus,
Magnaportheoryzae,utilizesappressoriatobreachthehostcuticle.Typically,a
biotrophic phase precedes necrotrophy in Magnaporthe-rice interaction and
establishment of blast disease. Abc3 transporter-based efflux of a digoxin-like
steroidal glycoside (ATS) is essential for the host penetration step of
Magnaporthepathogenesis1,2.ATSregulatesion-homeostasisinappressoriaand
subsequently acts as an elicitor of the host defense response during biotrophic
growth.
A pathogenicity island around the ABC3locus harbors a novel Monooxygenase
gene, ABM, essential for Magnaporthe pathogenesis. Loss of ABM leads to
precocious activation of the host defense response in rice. The Abm
monooxygenasefunctionisessentialforsuppressinginnateimmunityininvaded
ricecellsandplaysanimportantroleinthebiotrophytonecrotrophytransition.
Furthermore, Abm and its major product, 12-hydroxyjasmonate, are directly
involvedinsuppressingthejasmonate-signalingpathwayrequiredforactivating
host defense against Magnaporthe3. Thus, the blast fungus directly interferes
withhormonalsignalinginvolvedinpathogenrecognitionanddefensesystemin
rice. Interestingly, such regulation does not occur during Magnaporthe-barley
interactions. Our data suggests a highly specific and intricate chemical
communication between Magnaporthe and rice during the initiation of blast
disease. Magnaporthe likely acquired ABM through lateral gene transfer from
rhizosphere microbiota and we believe that further understanding of such
chemical communication within the root microbiome and at the fungus-plant
interface would help identify novel activators of plant growth and defense and
aidbroad-spectrumdiseasecontrolstrategiestowardsglobalfoodsecurity.
References:
(1)Sunetal,PlantCell2006.
(2)Patkaretal,PLOSPathogens2012.
(3)Patkaretal,NatureChemicalBiology2015.
Page 5 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
AfunctionalCalvincycleinE.coli
NivAntonovsky
WeizmannInstituteofScience,Rehovot,Israel
The Calvin-Benson-Bassham (CBB) cycle is the gateway to the organic world,
beingthemainpathwayforturninginorganiccarbon(CO2)intobiomassandfor
storingenergyinthebiosphere.Heterotrophicorganismsaredependentonsuch
supply of organic carbon fixed by autotrophs. How difficult is it to evolve from
one trophic mode of growth to another? Specifically, can an obligatory
heterotrophicorganismbeevolvedtosynthesizebiomassdirectlyfromCO2?A
positive answer will affect our understanding of metabolic plasticity and
stimulate exciting avenues towards agricultural productivity as well as
sustainable production of chemicals. We experimentally explore such shift
ofgrowthmodesbyacombinationofrationalmetabolicrewiringandlaboratory
evolution under selective conditions that leads to the emergence of a fully
functional CBB cycle in E. coli. We rewired the metabolic network of an E. coli
hostbyintroducingtwoenzymes(RuBisCOandprk)andseveringtheglycolysis
pathway to decouple carbon-fixation from energy production. After several
monthsunderselectiveconditionsinachemostat,themodifiedbacteriaevolved
to hemiautotrophic growth, in which carbon fixation via the non-native CBB
cyclesolelyprovidesallcarbonsforthesynthesisofsugarsandderivedcellular
buildingblocks.Reducingpower,energyandtherestofthebiomassprecursors
areobtainedbymetabolizingasuppliedorganiccompound(e.g.,pyruvate).The
success in evolving a non-native carbon fixation pathway in an obligatory
heterotrophic host provides a striking demonstration of the capacity for rapid
trophic-modeevolutioninmetabolismwithfuturerelevancetobiotechnology.
Page 6 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
ThediversemolecularmotorsinvolvedinmaintainingphotosyntheticCO2
uptake
OliverMueller-Cajar
SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore
The key photosynthetic CO2-fixing enzyme rubisco has long been known to
become inhibited by its substrate ribulose 1,5-bisphosphate and other sugar
phosphates. In plants this process is counteracted by the molecular chaperone
Rubisco activase (Rca), which belongs to the AAA+ protein superfamily. It now
appearssubstrateinhibitionofrubiscoisawide-spreadphenomenonacrossthe
naturalworld,althoughtheidentityoftheactivaseisdiverseandderivedfrom
convergent evolution. We have recently discovered and mechanistically
characterized a new class of rubisco activases that is widely distributed in
chemoautotrophic bacteria. Multiple isoforms of this CbbQO activation system
exist in the same organism and have evolved to recognize structurally diverse
rubiscoforms.Iwillalsodiscusstheidentityandbiochemicalpropertiesofthe
rubiscoactivaseofred-lineageeukaryoticphytoplankton.Aswellasprovidinga
fascinating example of convergent molecular evolution, Rca proteins can be
consideredpromisingcrop-improvementtargets,duetothethermolabilityofthe
protein found in crop plants. Photosynthesis also appears to be limited by Rca
when light conditions are fluctuating. Synthetic biology strategies aiming to
enhance the autotrophic CO2 fixation machinery will need to take into
considerationtherequirementforrubiscoactivasesaswellastheirproperties.
Page 7 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Mechanisticbasisformetabolicevolutioninplants
Jing-KeWeng
WhiteheadInstituteforBiomedicalResearch,DepartmentofBiology,
MassachusettsInstituteofTechnology,UnitedStatesofAmerica
Metabolic pathways are often considered “perfected” or at least predictable as
substrates efficiently rearrange into products through the intervention of an
optimizedenzyme.Moreover,singlecatalyticstepslinkup,formingamyriadof
metabolic circuits that are often modeled with a high degree of certainty.
However, on closer examination, most enzymes are not precise with respect to
theiractivity,usingnotjustonesubstratebutoftenavarietyandproducingnot
just one product but a diversity. Hence, the metabolic systems assembled from
enzymespossessingvaryingdegreesofwhatcanbetermedcatalyticpromiscuity
arenotclear-cutandrestrictive;rather,theymayattimesoperatestochastically
in the intracellular milieu. This “messiness” complicates our understanding of
normalandaberrantcellularbehavior,whileparadoxicallysowingtheseedsfor
futureadvantageousmetabolicadaptationsforhostorganisms.Inthistalk,Iwill
discusstheevolutionaryimplicationofcatalyticpromiscuitywidelyobservedin
plant specilized metabolic systems and how the systems-level promiscuity in
plant metabolism could be harnessed through synthetic biology approaches to
generatenewnaturalproductchemicallibraries.Iwillalsodisussnewfrontiers
inelucidatingmechanismsofactionunderlyingtraditionalherbalmedicine.
Page 8 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Uncoveringtheadaptivelandscaopesofplantgenomes
VictorAlbert
UniversityatBuffalo(SUNY),NewYork,USA
Thearchitecturalevolutionoffloweringplantgenomesincludesalonghistoryof
geneduplicationanddiversification.Tandemgeneduplicationisanongoingbut
non-global process that generates coding sequence diversity in eukaryotic
genomes through sub- or neofunctionalization of gene copies on an individual
basis. On the other hand, polyploidy events provide scores of genomically
balancedduplicategenes,allatonce,uponwhichdivergentselectionpressures
can act to generate phenotypic diversity. Evidence from several model plant
genomesequencessupportsthetheorythatmodular,dosage-sensitivefunctions
such as transcriptional regulation are enriched among duplicates surviving
polyploidy events, whereas single-gene survivors of local duplication events
havetheopportunitytobeenrichedfordosageresponsivefunctions.Whileithas
been repeatedly noted that polyploidy events correlate with some major plant
radiations, the question as to whether tandem duplicates play equivalent or
different roles in plant adaptation remains more poorly explored. We have
studieddistinctionsinfunctionalenrichmentsinthesetwoduplicatepopulations
acrossmanydifferentspeciesofplants,andhavefoundthatindeed,(1)syntenic
duplicates retained in polyploid blocks are always enriched for transcription
factor functions, after various independent polyploid events at various time
depths in plant evolutionary history (and even after ~200 million years),
whereas (2) gene copies deriving from ongoing tandem duplication events are
enriched in secondary metabolic and environmental response functions.
Althoughtheselatterfunctionssharemanygeneralsimilaritiesamongdifferent
plant species, significantly enriched functions among tandem duplicates in
different species also clearly display species-specific information. We highlight
these findings using the recently sequenced genome of the carnivorous
bladderwort plant, Utricularia gibba, in which anonymous functional
enrichments encoded by the tandemly duplicated gene population includes
several families known to code for enzymes useful in prey digestion.
Page 9 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
ThePhytobiome
StephanSchuster
SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore
Page 10 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Unlockingherbariumcollectionsforplantgenomicresearch
CharlotteLindqvist
UniversityatBuffalo(SUNY),NewYork,USA
With the development of next-generation sequencing technologies it is now
possible to generate large amounts of sequence data for non-model taxa, for
which no reference genomes are available. The ability to sequence herbarium
specimens, which offer excellent catalogs of extirpated or rare plant diversity
and vouchers that can assist in the process of identifying unknown plant
specimens to known species, provides great promise toward understanding
important issues from biogeographic history to domestication, taxonomy, and
conservation.Genomicsequencingtechnologiesarealsopowerfulalternativesto
“DNA barcoding” in accurate authentication of commercial botanical products
and their adulterants. We have used a next-generation sequencing approach to
obtain a high-quality complete plastid genome from an extinct Hawaiian mint
species.Byresequencingcloserelatives,wehavegeneratedadditionalcomplete
genomesandupto86%genomiccoverageforfourotherspecies,includingfrom
100-yearoldherbariummaterial.Sequencingandassemblingcompletegenomes
can still be challenging, particularly from specimens in which DNA is highly
degraded,andincaseswheregeneticdifferentiationateventhegenome-scaleis
limited, e.g., in closely related species, sequencing of targeted hypervariable
regions may be a more cost-effective approach. We targeted ~100 SNPs from
throughout the chloroplast genome using a next-generation amplicon
sequencing approach. This approach generated ~20Kb sequence data per
individualandincreasedthetotalnumberofvariablesitesamong96sequenced
species to ~1,000. Amplification of even more distant relatives was successful
and analysis of such hypervariable regions using high-throughput sequencing
demonstrate the potential of such an approach in rapidly evolved lineages.
Page 11 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Host-pathogencommunicationsregulateplantactincytoskeletonand
immunity
MiaoYansong
SchoolofBiologicalSciences&SchoolofChemicalandBiomedical
Engineering,NanyangTechnologicalUniversity,Singapore
Inter-kingdom communications between hosts and pathogens have profound
effects on industry, human health, agriculture, and the environment.
Communicationbetweenmicroorganismsandtheirhostsreliesonawidearray
of molecular interactions and signals. Host receives small molecule signals that
are delivered from pathogens and triggers a series of immune responses and
defensemechanisms.Bothbacteriadeliveredsignalsandhostactivatedimmune
responseshighlyregulateactincytoskeletonassemblyandmembranetrafficking
in host. We recently identified important small molecule signals that derived
from pathogenic bacteria highly regulate Arabidopsis actin cytoskeleton and
membranetrafficking,aswellasinnateimmunity.Ourcurrentresearchistrying
toidentifythedetailedmoleculemechanismsbywhichpathwaybacteriasignals
regulatehostresponse,andalsocollaboratewithvariousvirulencefactors,using
multidisciplinary approaches including plant pathology assays, next-generation
sequencing,reconstitutionofactinassembly,super-resolutioncellimaging,and
“Omics” approaches. Our research would have broad implications in
development of novel strategies in control of harmful and invading pathogen
speciesinagriculture.
Page 12 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Integratingmultileveldatatoreconstructandmodelplantmetabolic
networks
JedrzejJakubSzymanski
WeizmannInstituteofScienceRehovot,Israel
Nowadays, the ever growing availability of high throughput data significantly
accelerates both the reconstruction of plant metabolic networks as well as the
characterizationoftheirsystem-scaleproperties.HereIpresentourrecentwork
on Arabidopsis and tomato in which we used multi-omics data integration
approachestoidentifynewelementsofthemetabolicnetworksandtogenerate
predictivemetabolicmodels.
Integration of genomics, transcriptomics, and metabolomics data enabled us to
identifynewelementsoftheArabidopsisthalianalipidmetabolism.Alipidomic
analysis of 337 Arabidopsis wild type accessions were coupled with parallel
environmental stress experiment. Collected metabolomic and transcriptomic
data were integrated in frame of a statistical model to perform an unbiased
identificationofgenesconnectedwithspecificlipidomictraitsbothonagenetic
andpathwaylevel.Intheanalysistheknowngenesofthelipidmetabolismwere
effectivelyidentifiedtogetherwithasetofnewcandidatesexhibitingfeaturesof
enzymaticandregulatorygenes.
Inthesecondstudyweusedmultileveldatatoanalyzesystem-scaleproperties
of tomato fruit metabolism. Transcriptomic, proteomic, and metabolomic data
collected for different tissues of developing fruit were used to reconstruct a
genome-scale metabolic model of tomato fruit. The model, under biologically
sound constraints and given objective, predicted metabolic fluxes and systemscale properties of the tomato fruit metabolism during development and
ripening.
Page 13 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Venturingintoterraincognitaofproteinsmallmoleculeinteractionsusing
combinationofnovelandclassicalapproaches
DanielVeyel,MonikaKosmacz,MarcinLuzarowski,IzabelaKasprzyk,Lothar
Willmitzer,AleksandraSkirycz
Max-PlanckInstituteofMolecularPlantPhysiology,Postdam-Golm,
Germany
Interactionsbetweenbiologicalmoleculesenablelife.Thesignificanceofacellwideunderstandingofmolecularcomplexesisthusobvious.Protein–metabolite
interactions (PMIs) have received little interest in the past; technological
progresshasbeencausingthistograduallychange.
For us, the most interesting interactions are between ligand and receptor, the
triggers of signalling events. While the number of small molecules with proven
orproposedsignallingrolesisrapidlygrowing,thelion'sshareoftheirprotein
receptorsremainsunknown.Conversely,therearenumeroussignallingproteins
with predicted ligand-binding domains, the identity of the small-molecule
counterpartsofwhichremainselusive.TheidentificationofsuchsignallingPMIs
stands at the core of this project. In our research we use Arabidopsis cell
cultures; the envisaged technological platform, however, is applicable to other
systems.
Recently, we established a simple yet effective in vivo procedure for global
detection of small molecules bound to proteins. Through combination of size
filtration with size exclusion chromatography (SEC) our protocol facilitates the
unbiased prediction of protein-metabolite interactions in a cell-wide manner
withouttheneedofproteinormetabolitebaits.Amapoftheprotein‒metabolite
complexes obtained from SEC experiments assisted in the selection of novel
PMIs,nowbeingexaminedbytargetedapproaches,includingaffinitypurification
starting either from a protein or a small molecule of interest, and microscale
thermophoresis.
The identification of heretofore unknown PMIs carries the potential to
revolutionise the existing knowledge of small-molecule signalling. In a manner
analogous to biomedical research, this knowledge could be used to modulate
signalling pathways, and hence plant physiology, using chemicals designed to
targetproteinreceptors.
Page 14 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Metabolomics–technologyandapplicationsinlifesciences
LotharWillmitzer
Max-Planck-InstituteforMolecularPlantPhysiology,Potsdam,Germany
Mass spectrometry-based analysis of metabolites has become more and more
advancedinrecentyears.Thedevelopmentofthisfieldhasbeendrivenbythe
continuous improvements of mass spectrometers coupled to various
chromatographic separation techniques, improvements in open source and
commercial software developments allowing data extraction and initial
processing,andtheincreasingqualityandaccessibilityofpublicdatabases.
Still, irrespective of these impressive developments several problems remain
unsolved specifically when dealing with untargeted metabolomic studies. The
mainproblemsstillarepeakannotation,discriminationofbiologicalfromnonbiologicalcompoundsand(relative)quantification.
Anewlydevelopedmulti-isotopelabelling-basedstrategyusingfullylabelled
13C, 15N and 34S plant tissues in addition to unlabeled samples will be
described which allows the direct, unambiguous read-out of the chemical sum
formulaforeachdetectablepeakobviatingthematchagainstexistingdatabases,
enabling a truly unbiased high fidelity analysis of the metabolome/lipidome,
independent of any prior acquired knowledge. This technology allows the
establishment of comprehensive inventories of metabolites present in a given
organism.
Metabolomics has in recent years become a universal tool not only in studying
metabolism of different biological systems but over and above been used as a
diagnostic tool in various areas. Examples will be presented where
metabolomicsisappliedasadiagnostictoolinmedicine,infoodindustryandin
predictive plant breeding. Finally approaches towards identifying genes
responsible for formation of specific metabolites via various modelling
approacheswillbediscussed.
Page 15 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Metabolomics-assistedfunctionalgenomicsonplantphenolicsecondary
metabolism
TakayukiTohge
Max-Planck-InstituteforMolecularPlantPhysiology,Potsdam,Germany
Plantsecondarymetabolitesarewidelydiversifiedintheirchemicalstructures,
since during the long evolutionary period wherein plants have adapted to the
environmental niches, several strategies such as gene duplication and
convergent evolution of some key enzymatic genes have contributed to the
evolutionofthesecondarymetabolism.Forthereasonthatphenolicsecondary
metabolites play important roles in both biotic and abiotic defences in seed
plants as well as being potentially important bioactive compounds with both
nutritionalandmedicinalbenefitsforanimalsandhumans,investigationofthis
metabolism has been highlighted for long years, especially focusing on crop
speciessuchasmaize,beanandtomato.Recenttechnicaldevelopmentsallowing
affordable whole genome sequencing as well as omics studies and available of
several resources such as knockout mutant library, QTL lines and wild
accessions,haveresultedindramaticincreaseinthenumberofapproachesfor
functional genomics, namely metabolic phenotype screening, network analysis,
mQTL and GWAS studies. We integrated these approaches with metabolomic
analysis to refine biosynthetic structure of phenolic secondary metabolism
including natural variance, tissue and species specificity. I will present our
metabolomics-assisted functional genomics approach which resulted in
discovery of key genes involved in chemical diversity in Arabidopsis and crop
species.
Page 16 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Cryo-EMstructureofthechloro-ribosome
ShashiBhushan
SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore
Protein synthesis in the chloroplast is mediated by the chloroplast ribosome
(chloro-ribosome). Although, recent developments in cryo-electron microscopy
(cryo-EM)haveprovideddetailedhigh-resolutionstructuresofribosomesfrom
manydifferentsources,ahigh-resolutionstructureofthechloro-ribosomeisstill
lacking. I will present our recent cryo-EM structure of the large subunit of the
chloro-ribosomefromspinachatanaverageresolutionof3.4Å.High-resolution
map enabled us to localize and model chloro-ribosome proteins, chloroplastspecificproteinextensions,twoPSRPs(PSRP5and6)andthreerRNAmolecules
presentinthechloro-ribosome.AlthoughcomparabletoE.coli,thepolypeptide
tunnel and the tunnel exit site show chloroplast-specific features.
Page 17 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Unravellingsecondarymetabolismofaromaticplants(Spearmintand
SweetBasil)byNextgenerationsequencing
RajaniSarojam
TemasekLifeSciencesLaboratory,Singapore
Most of the aromatic plants produce their valuable essential oils in specialised
glandulartrichomesknownaspeltateglandulartrichomes(PGT).Theseorgans
arecapableofproducingandstoringlargeamountsofvolatilesecretions.Plants
produce these essential oils as part of their secondary metabolism and are
mostly composed of terpenes and phenylproponoids. Due to their commercial
worth, the processes by which they are synthesised and stored in plants are
main target for genetic manipulation for increased yield. But our knowledge
about the development of secretory glandular trichomes and essential oil
productionanditsregulationisverylimitedmakingitdifficulttoengineerthese
metabolic pathways. Generation of sufficient genomic information with deep
coverageisrequiredtogaininsightsintotheregulatorymechanismofsecondary
metabolism and glandular trichome development. We performed RNA-seq of
differenttissuesofspearmintandsweetbasil-namelyPGT,leafstrippedofPGTs
and leaf to gain insights into the gene expression profile of PGT. Our
transcriptome sequencing of glandular trichomes of spearmint has helped to
identify potential transcription factors involved in terpene biosynthesis.
Understanding the role of transcription factors in secondary metabolism
pathway will aid in metabolic engineering for increased yield of secondary
metabolites and also development of new production techniques for valuable
metabolites. An update on our progress on characterizing these transcription
factorswillbepresented.
Page 18 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Moleculardiversityandfuzzyprocessingofpeptidylplantproducts
JamesTam
SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore
To ward off pathogens and pests, plants have evolved complex and diverse
chemical weapons. These chemicals or natural products range from smallmolecule metabolites to large biomolecules, natural products which have
becomeessentialfordrugdiscoveryandusefulformodulatinghumandiseases
(Tam et al., 2015). Among the pathogenesis-related biomolecules, cysteine-rich
peptidesof2−6kDaareunder-exploredandunder-representedintherapeutics.
A common theme of cysteine-rich peptides in the chemical space of 2−6 kDa is
their stable structures which invariably contain three to five intramolecular
disulfidesascross-bracestorenderthemexceptionallyresistanttothermaland
proteolyticdegradation.Thisfavorablefeatureplustheirlargefootprintswhich
minimizeoff-targetsidereactionsastherapeuticshavepromptedourlaboratory
to develop an herbalomic program to discover cysteine-rich peptides in
medicinalherbsasdrugcandidates.
In this presentation, I will report our recent progress on three areas: 1)
occurrenceanddiversityofcysteine-richpeptides;2)mechanismscontributing
to their molecular diversity, and in particular, fuzzy processing and posttranslational modifications and; 3) their functions and therapeutic values and,
importantly,theirrelevancytoherbalmedicine(Nguyenetal.,2015;Serraetal.,
2016).
In drug design, the molecular diversity of cysteine-rich peptides provides a
repertoireofstablescaffoldsusefulforgraftinglinearbioactivepeptidestogain
metabolic stability and oral bioavailability. We will illustrate this in our
engineering of a bradykinin antagonist onto a cyclotide scaffold to achieve an
orallyactiveanalgesic(Wongetal.,2012).
References
Nguyen,P.Q.,Luu,T.T.,Bai,Y.,Nguyen,G.K.,Pervushin,K.,andTam,J.P.(2015).Allotides:ProlineRichCystineKnotalpha-AmylaseInhibitorsfromAllamandacathartica.JNatProd78(4),
695-704.
Serra,A.,Hemu,X.,Nguyen,G.K.,Nguyen,N.T.,Sze,S.K.,andTam,J.P.(2016).Ahigh-throughput
peptidomicstrategytodecipherthemoleculardiversityofcycliccysteine-richpeptides.
SciRep6,23005.
Tam, J.P., Wang, S., Wong, K.H., and Tan, W.L. (2015). Antimicrobial peptides from plants.
Pharmaceuticals8(4),711-757.
Wong,C.T.,Rowlands,D.K.,Wong,C.H.,Lo,T.W.,Nguyen,G.K.,Li,H.Y.,etal.(2012).Orallyactive
peptidic bradykinin B1 receptor antagonists engineered from a cyclotide scaffold for
inflammatorypaintreatment.AngewChemIntEdEngl51(23),5620-5624.
Page 19 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Identificationofbiosyntheticpathways/genesforfloralvolatileorganic
compounds
SavithaDhandapani1,2,JingjingJin1,MiJungKim1,VishweshwaranSridhar1,
Nam-HaiChua3,andIn-CheolJang1,2
1TemasekLifeSciencesLaboratory,1ResearchLink,NationalUniversityof
Singapore,Singapore117604,Singapore
2DepartmentofBiologicalSciences,NationalUniversityofSingapore,
Singapore117543,Singapore
3LaboratoryofPlantMolecularBiology,TheRockefellerUniversity,1230York
Avenue,NewYork,NY10065,USA
Flowers emit a large group of volatile organic compounds (VOCs) that play
crucial roles in interactions with other organisms. In general, floral VOCs are
considered not only to serve to attract pollinators to ensure successful
reproduction,butalsotoactasdefenseagentsagainstmicrobesandherbivores.
Most of floral VOCs that are synthesized on the petals of the flowers fall into
three major classes of VOCs named terpenoids, phenylpropanoids/benzenoids
and volatile fatty acid and amino acid derivatives. The quality and quantity of
floralVOCsemitteddeterminefloralscentsandarealsovitalindeterminingthe
economic value of flowering plants as well as its usage in the flavors and
fragrancesindustry.ThediversityofflowerVOCshasstimulatedbroadsystems
biology approaches to identify the pathways/genes involved in their
biosynthesis. Here, we integrate metabolome and transcriptome analysis of
fragrant flowers to unravel biosynthetic pathways for VOCs. Our metaboliteguidedtranscriptomicsandmolecularandbiochemicalcharacterizationofgenes
have been identified specific gene members encoding enzymes involved in the
biosynthesis of diverse terpenoids and phenylpropanoids. Moreover, our
understandingofthebiosyntheticpathwaysofVOCshasfacilitatedtheenhanced
productionofhigh-valueterpenesinplant.
Page 20 of 21
NTUPlantSciencesSymposium2016
26–27September2016(Monday–Tuesday)
Decipheringplantmetabolicregulationpuzzle:examplesofmetabolites
affectingbiomassproduction
CamilaCaldana
CTBE/BrazilianCenterforResearchinEnergyandMaterial,Brazil
Plants are exceptional chemical systems, which efficiently convert
photochemical energy into carbohydrates that serve as carbon skeleton for
several building blocks. Although a plethora of metabolites and pathways has
been investigated, little is known about metabolite signaling, interaction with
growth and development as well as their role in genotype-phenotype
interactions.Currently,effortstoelucidateplantbiomassproduction,aprocess
closed link to metabolism, are booming due to the great potential to generate
bioenergy and alternative products (e.g., cosmetics, biopolymers or bioisoprene). In this context, my group has been working on two strategies to
explore the metabolic regulatory network controlling plant growth and
development. First, we are combining genetics, metabolomics and expression
profilestodissectthegeneticbasisofmetabolicdiversityinsugarcanebiomass
productionusingabiparentalpopulationandanassociationpanelforenhancing
ourknowledgeofboththefunctionalgenomicsandmetabolisminthisimportant
bioenergycropasapowerfulstrategytopredictplantperformance.Second,we
are investigating the potential of the master growth regulator, the Target Of
Rapamycin (TOR) kinase pathway, as a potent metabolic switch that offers a
novel route for biotechnological optimization of plant carbon partition. In my
presentation,Iwillprovideanoverviewofhowthoseapproachescouldenable
theunderstandingofplantmetabolismanditsimportanceforhumannutrition,
sustainableagricultureandresourceconservation.
Page 21 of 21