DYGEVO
The genomics
journey
Professor Bernard Dujon discusses his research on yeasts
and the usefulness of this family as model organisms in
cutting-edge genetic manipulation experiments
With such hypotheses, detailed knowledge has
been gained about the effect of population
size. But yeasts are unicellular fungi adapted
to phases of very rapid clonal expansion under
favourable conditions, intermingled with phases
of massive cell death. A glass of beer contains
more yeast individuals than the world’s human
population. This abundance allows us to work
on rare genetic events without having to wait
very long periods of time.
For what reasons do unicellular eukaryotic
genomes often prefer clonal expansions
over regular reproduction cycles?
Could you provide some context to your
current project examining yeast genome
diversity – DYGEVO? What are your
main objectives?
I started sequencing DNA in 1978. Back then,
people were sequencing pieces of genes, not
genomes! I was interested in the dynamics
of genomes from my early years of research,
and always applied the newest methods
to study these questions (what a change in
three decades!).
The complete sequencing of the genome of
Saccharomyces cerevisiae back in 1996 was
regarded as a scientific milestone, and I was
involved in this achievement. At that time,
nearly all scientists were moving to what
they called ‘post-genomics’. Very few like
myself were interested in exploring genome
diversity. The DYGEVO project emerged in this
context – I have always been keen to explore
unconventional routes.
The general functional organisation of
eukaryotic genomes indicates that common
mechanistic and evolutionary principles are
shared. Yet unicellular eukaryotic genomes
are largely diverse, with different origins.
Could you explain the effects of population
size and modes of reproduction on aetiology?
Classical population genetics usually considers
sexual populations, and in many cases assume
that they are panmictic and at equilibrium.
Many organisms seem to favour clonal
expansion over sexual reproduction as
soon as conditions are appropriate. During
the sunny season, some insects engage in
parthenogenesis, and many plants propagate
clonally. But it is true that unicellular organisms
do employ clonal expansion widely. The
reasons are probably numerous. One of them is
that they have a hard time identifying cells of
the same species. Therefore, if they participate
in genetic exchange, they cannot easily limit
those exchanges to their own species.
Unicellular fungi are highly viable models
for laboratory experiments. What is your
trial methodology and why you have
chosen to examine the basic mechanism of
eukaryotic genome dynamics?
There are many advantages of yeasts for genetic
experimentations. They are eukaryotic cells and
phylogenetically related to the animal world,
including ourselves. Any genetic manipulation
can be controlled with extreme precision by
complete resequencing of the entire genome.
Over 85 per cent of the S. cerevisiae genes have
been functionally characterised, offering an
unparalleled wealth of information for genetic
analysis. There are no ethical constraints (except
keeping our genetically engineered yeasts
strictly within the laboratory).
indicate that structural genome alterations
(segmental duplications, inversions, segmental
insertion and deletion, gene loss) occur much
more rapidly than anticipated by classical
methods. They tend to create more genetic
variations on a limited timescale than the
classically considered changes based on
sequence evolution. In addition, structural
genome alterations create an abrupt, stepwise
pattern of evolution instead of a seemingly
continuous spectrum of variation, more in line
with original Hugo de Vries principles proposed
back in 1909 than with neo-Darwinian ideas on
gradual, permanent optimisation of the fittest.
How can the flexibility of yeast genomes
be exploited to increase cell fitness when
simple nucleotide changes have a low
probability of accomplishing such a task?
Both mechanisms can, in principle, contribute
to evolutionary changes, but we did not
observe simple nucleotide changes in our
experiments. This is in agreement with the
now precisely established mutation rates in
yeast. To obtain a sufficient number of single
nucleotide changes to expect that one would,
by chance, alter fitness would take a much
larger number of generations. Changing gene
copy number is much more rapid.
Do you intend to continue your research on
eukaryotic unicellular models?
My lab is ageing, like myself, but during the
time left we will continue to work in parallel
on comparisons of as large a number of yeast
species as possible to learn from nature, and
to simultaneously run experiments on our
developed model systems to check hypotheses.
What role is played by eukaryotic genome
dynamics in the evolution of these
unicellular organisms?
Our present data, based on comparative
genomics of many distinct yeast species,
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DYGEVO
Insights from yeasts
Yeast continues to be one of the most important model organisms in modern biology. Today, a group at the
Institut Pasteur in Paris, France, is using yeast to conduct a trio of novel experiments designed to deepen our
understanding of the eukaryotic genome and possibly even challenge the accepted model of speciation
SINCE WATSON AND CRICK first described
the structure of DNA, the field of genetics
has expanded exponentially. Today, scientists
have sequenced the entire human genome,
cloned animals and illustrated the fundamental
principles of molecular evolution. Alongside
these milestones was one of the most important
feats in modern biology – the sequencing of the
Saccharomyces cerevisiae genome in 1996, an
achievement in which Professor Bernard Dujon
from the Institut Pasteur in Paris, France, was
heavily involved.
Dujon, who began his biological career in the
late 1960s, now heads the Yeasts Molecular
Genetics Unit at the Institut and is Professor of
Molecular Genetics both there and at Université
Pierre et Marie Curie. Throughout his career,
Dujon has focused on some of the central
questions of genetics and evolutionary biology.
THE BENEFITS OF YEAST
Yeast has been and continues to be one of
the most important experimental subjects in
biology – it is a unicellular eukaryote capable of
rapid population expansion, fits of evolutionary
change
and
subsequent
adaptation:
“Theoretically, a single yeast cell placed under
favourable conditions would be able to produce,
in a week, a clonal progeny capable of covering
the globe with a crust several kilometres thick,”
highlights Dujon. These characteristics have
made yeast such a popular model organism
54INTERNATIONAL INNOVATION
that over 100,000 published research papers
concern its biology.
Despite the huge amount of attention it has
received, Dujon is confident that yeast still
has information to reveal: “I believe that this
is a topic in which much has yet to be learned,
given the power of novel technologies”. With
the development of genomic techniques,
scientists now have the ability to artificially
engineer yeast genomes. Dujon’s current work
utilises this ability to explore how the dynamics
of genomic change affect evolution and
population dynamics.
Dujon and his colleagues to experimentally
simulate genetic events which would be very
rare in a wild population. The challenge for the
Pasteur team is to then ascertain the abundance
and importance of these laboratory-simulated
behaviours in the real world.
DYGEVO
Dujon has recently embarked upon a new project
called DYGEVO consisting of three distinct
research objectives: to quantify the impact of
flexibility in the yeast genome on cell fitness
and survival; to analyse the function of the
TO CLONE OR NOT TO CLONE?
One of the most interesting behaviours observed
in yeasts is the ability to switch between sexual
and clonal reproduction. This behaviour is not
unique to yeasts – also being seen in other
organisms such as aphids – but remains rare.
Given the correct environmental conditions,
yeast is capable of cloning itself, allowing one
cell to form the basis of an entire colony.
In many species, this type of reproduction
would render a population genetically ‘poor’
and extremely susceptible to environmental
change, but not yeast: “Yeasts have developed
mechanisms to produce diversified populations
even after clonal expansion from a unique cell,”
explains Dujon. This ability to undergo selfmotivated genetic diversification has inspired
Colonies of yeast cells with normal (large) and
genetically altered (small) genomes after incubation
on a rich medium. Size difference illustrates the severe
growth rate reduction due to controlled genetic
alterations used for experiments.
Yeast has been and continues
to be one of the most
important experimental
subjects in biology
– it is a unicellular
eukaryote capable of
rapid population
expansion, fits of
evolutionary change
and subsequent
adaptation
BEYOND SACCHAROMYCETACEAE
Flocculating yeast cells obtained after experimental
evolution of engineered repeat-containing genes.
curious exchange of genetic material between
different species and the implications this has
for understanding what constitutes a species;
and finally, to assess the origin and function,
if any, of long tandem repeats seen in proteincoding sequences of some yeast species.
The DYGEVO team’s approach to genomics
is somewhat novel: “Studying spontaneous
evolution of artificially disabled genomes under
the best possible environmental conditions
looked more attractive to me than studying
adaptation to limiting environments, as done
by nearly all other researchers”. Following this
approach has allowed the Pasteur team to
make new discoveries and challenge traditional
biology. For instance, the group has preliminary
evidence indicating that hybrids between
distantly related yeasts can form spontaneously
and then rapidly evolve. Unfortunately, previous
experiments had not elucidated the parental
genomes. Dujon now plans to re-run these
experiments, having identified the parental
genomes, enabling him to reconstruct the
hybridisation event and track subsequent
evolutionary changes. Work on the formation
of hybrids in yeast may one day shift current
understanding of the model for speciation.
Although the future for the DYGEVO project
is exciting in the context of speciation, the
team’s short-term objective is concerned with
understanding the role and implications of
large segmental changes in yeast genomes:
“Our immediate goal is to establish the role
of the various aspects of genome dynamics
(segmental change) compared to classical
mutational changes (sequence variation),”
explains Dujon. This work has academic value,
but given the conserved nature of eukaryotic
genomes, it may also one day shed light on
human genetic diseases such as cancer. In this
context, the utility and benefits of yeast as a
model organism should not be underestimated.
Almost half of all sequenced yeast species today
belong to the Saccharomycetaceae family,
meaning their genomes share a common global
architecture with that of S. cerevisiae. Not only
attractive for fermenting alcohol and leavening
bread, S. cerevisiae is also extremely well-suited
for experimental studies.
Because of this success, researchers have been
slow to explore and sequence other types of
yeasts. Hence, there is a need to explore other
branches in order to gain a more comprehensive
and balanced picture of the actual diversity and
evolution of their genomes.
Targeting
such
under-researched yeasts,
Dikaryome is a collaborative programme separate
from DYGEVO, in which Dujon’s lab is also engaged.
Specifically, the researchers are sequencing
representatives of the unexplored or poorly studied
phylogenetic branches from both ascomycetous
and basidiomycetous yeasts. As an example of this
work, in a paper published in Genome Biology and
Evolution in 2013, Dujon and colleagues presented
the complete genome sequence of the haploidtype strain of Kuraishia capsulate, a nitrateassimilating Saccharomycetales of uncertain
taxonomy, isolated from tunnels of insect larvae
underneath coniferous barks and characterised
by its copious production of extracellular
polysaccharides. The researchers confirmed that
its many similarities and differences with other
sequenced Saccharomycotina warranted further
long-range evolutionary genomic investigations of
other family members.
EXPANDING UNDERSTANDING
Despite being the focus of many thousands of
hours of work and subsequent publications,
yeasts continue to be extremely useful model
organisms for biologists. These eukaryotic
organisms
retain
conserved
genomic
characteristics similar to their multicellular
counterparts and as such act as a tool for
understanding genome dynamics across all
eukaryotes. Dujon and his colleague’s work
should yield a better understanding of the true
variety of genomic change in the process of
adaptation and reproduction. Importantly, if
proved correct, the hypotheses developed by
the team may change the traditional view of
processes such as speciation and significantly
broaden the horizon for modern genetics.
INTELLIGENCE
DYNAMICS AND EVOLUTION OF THE
GENOMES OF YEAST, UNICELLULAR
EUKARYOTIC MODELS
OBJECTIVES
To combine the power of yeast genetics with
new results from comparative genomics
to study the mechanisms underlying
the spontaneous changes or alteration
of eukaryotic genomes, with the goal to
understand their role in biological evolution
as well as in the emergence of human
diseases, and to eventually control them.
KEY COLLABORATORS
DYGEVO team: Guy-Frank Richard, Chargé
de recherches • Agnès Thierry; Varun
Khanna; Cyril Saguez, Research engineers •
Lucia Morales, Postdoctoral fellow, Institut
Pasteur, Paris, France
Past team members: Cécile Fairhead; Gilles
Fischer; Romain Koszul
External collaborators: André Goffeau,
Université Catholique de Louvain la Neuve,
Belgium • Jean Weissenbach, Director,
Génoscope sequencing center, Evry, France
FUNDING
Institut Pasteur
Centre national de la recherche
scientifique (CNRS)
Université Pierre et Marie Curie
Agence Nationale de la Recherche (ANR)
Association de recherche contre
le cancer (ARC)
CONTACT
Bernard Dujon
Professor of Molecular Genetics
Unité de Génétique moléculaire des levures
Department of Genomes and Genetics,
Institut Pasteur 25, rue du Docteur Roux,
F75724 Paris, Cedex 15, France
T +33 145 688 482
E [email protected]
www.agence-nationale-recherche.
fr/projet-anr/?tx_lwmsuivibilan_
pi2%5BCODE%5D=ANR-11-BSV6-0001
www.pasteur.fr/recherche/unites/Gmlev/
en/accueil-en.html
BERNARD DUJON is Professor of Molecular
Genetics at Université Pierre et Marie Curie
and the Institut Pasteur, Paris, France. He
has published over 190 research articles on
the architecture, dynamics and evolution
of eukaryotic genomes using primarily
yeasts as models. He is a member of EMBO,
Academia Europaea and the French Academy
of Sciences, and is Chevalier of Légion
d’Honneur.
DNA molecules of yeast chromosomes, separated
by pulsed field gel electrophoresis (left) and
hybridised with specific probes (right). Cartoons
symbolise normal and altered chromosomes
obtained after experimental evolution.
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