Les récentes avancées de la génomique et des projets de séquencage de génomes mettent en lumière un étonnant paradoxe. Les organismes vivants, malgré leurs apparentes diversité et complexité, partagent en fait de nombreuses similarités génétiques à partir d'un répertoire limité d'un millier de familles de gènes. Par exemple, près de 70 pourcents des gènes de la levure du boulanger sont similaires à des gènes humains, malgré les différences frappantes entre ce champignon unicellulaire et un organisme humain et ses 1014 cellules.
En fait, la diversité et complexité des organismes vivants résultent de la combinatoire de l'expression de leurs gènes qui coopèrent pour produire un nombre quasi infini de réponses et fonctions cellulaires spécifiques. En effet, de petites variations de régulation pour de multiples gènes peuvent collectivement induire de larges différences de fonctions et développements cellulaires.
Le concept de réseaux biologiques a été introduit pour décrire, à l'aide de simples graphes, certains aspects de la combinatoire de l'expression génétique. Les principaux réseaux biomoléculaires incluent, par exemple, des interactions protéine-protéine, des réactions métaboliques ou des interactions de régulation cellulaire. Ainsi, n'importe quel processus biologique participe à au moins un réseau biomoléculaire. Mais, au-delà des détails moléculaires qu'ils englobent, les réseaux biomoléculaires sont aussi des "objets" biologiques, intéressants en tant que tel, qui évoluent et peuvent être étudiés.
Notre recherche concerne les propriétés et l'adaptation des réseaux biologiques à différentes échelles, depuis leurs structures locales les plus simples jusqu'à leur organisation globale plus complexe.
1- Modules de régulation ARN synthétiques et auto-assemblage d'ARN bactérien
Nous étudions les propriétés de petits circuits de régulation principalement basés sur l'ARN et leurs interactions. En particulier, nous avons utilisé des approches de biologie synthétique couplées à des simulations avancées de dynamique de l'ARN (film1, film2) pour concevoir des modules de répression (Fig.1A) ou d'activation (Fig.1B) efficaces basés sur l'ARN. Ces modules de régulation contrôlent le repliement de l'ARN au cours de sa propre transcription, à l'aide de simples interactions antisenses ARN-ARN, Fig.1 et films 1&2.
Fig. 1
Nous avons aussi découvert qu'un petit ARN bactérien d'Escherichia coli pouvait s'auto-assembler, comme de nombreuses protéines le font, pour former de longs filaments (Fig.2A) et de grands réseaux physiques (Fig.2B). Ce résultat élargit encore l'étendue déjà très variée des fonctions des ARN naturels.
Fig. 2
2- Evolution de grands réseaux biomoléculaires
Nous nous sommes aussi intéressés aux propriétés des grands réseaux biologiques et à leur évolution sous l'effet des processus de duplication-divergence au niveau de gènes individuels ou de génomes entiers, Fig.3.
Fig. 3
Notre approche théorique se fonde sur un modèle de duplication-divergence, basé sur le nécessaire effacement d'interactions fonctionnelles apparaissant avec les duplications, Fig.4. Nous avons montré que les processus de duplication-divergence apportent non seulement de la nouveauté génétique mais aussi des contraintes d'évolution qui limitent par construction les propriétés émergeantes des réseaux biomoléculaires, indépendamment d'aucune fonction cellulaire spécifique. En particulier, nous avons pu démontrer que les réseaux dont les gènes étaient conservés, qui sont de première importance biologique, étaient aussi nécessairement sans échelle par construction, indépendamment de toutes variations ou fluctuations des paramètres du modèle au cours de l'évolution.
Fig. 4
A l'inverse, nous avons montré que la conservation des motifs réseaux incluant au moins une interaction ne peut pas être indéfiniment préservée par une évolution par duplication-divergence, Fig.5, en large accord avec les évidences observées entre espèces phylogénétiquement distantes.
Fig. 5
Enfin, nous intéressons aussi à l'évolution des réseaux de transcription et étudions les conflits de régulation apparaissant par duplication des facteurs de transcription et autorégulateurs. Globalement, il apparaît que les contraintes de l'évolution, inhérentes aux processus de duplication-divergence, ont largement contrôlé la topologie globale et la conservation dépendante d'échelle des réseaux biomoléculaires.
Dernière mise à jour : octobre 2008
Publications clés
2009
Cayrol B, Nogues C, Dawid A, Sagi I, Silberzan P, Isambert H A nanostructure made of a bacterial non-coding RNA J Am Chem Soc, 2009; 131(47): 17270-17276 - Abstract
Natural RNAs, unlike many proteins, have never been reported to form extended nanostructures, despite their wide variety of cellular functions. This is all the more striking as synthetic DNA and RNA forming large nanostructures have long been successfully designed. Here, we show that DsrA, a 87-nt non-coding RNA of Escherishia coli, selfassembles into a hierarchy of nanostructures through antisense interactions of three contiguous self-complementary regions. Yet, the extended nanostructures, observed using atomic force microscopy (AFM) and fluorescence microscopy, are easily disrupted into >100nm long helical bundles of DsrA filaments, including hundreds of DsrA monomers and surprisingly resistant to heat and urea denaturation. Molecular modeling demonstrates that this structural switch of DsrA nanostructures into filament bundles results from the relaxation of stored torsional constraints and suggests possible implications for DsrA regulatory function.
Isambert H, Stein RR. On the need for widespread horizontal gene transfers under genome size constraint Biol Direct., 2009;4:28 - Abstract
BACKGROUND: While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery. HYPOTHESIS: We propose that the abundance of horizontal gene transfers in free-living prokaryotes is a simple but necessary consequence of two opposite effects: i) their apparent genome size constraint compared to typical eukaryote genomes and ii) their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss. IMPLICATIONS: This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene recovery mechanisms, must have ultimately favored the emergence of more complex life styles and ecological integration of many eukaryotes
H. Isambert The jerky and knotty dynamics of RNA Methods, 2009; 49:189-196 - Abstract
RNA is known to exhibit a jerky dynamics, as intramolecular thermal motion, on <0.1 μs time scales, is punctuated by infrequent structural rearrangements on much longer time scales, i.e. from >10 μs up to a few minutes or even hours. These rare stochastic events correspond to the formation or dissociation of entire stems through cooperative base pairing/unpairing transitions. Such a clear separation of time scales in RNA dynamics has made it possible to implement coarse grained RNA simulations, which predict RNA folding and unfolding pathways including kinetically trapped structures on biologically relevant time scales of seconds to minutes. RNA folding simulations also enable to predict the formation of pseudoknots, that is, helices interior to loops, which mechanically restrain the relative orientations of other non-nested helices. But beyond static structural constraints, pseudoknots can also strongly affect the folding and unfolding dynamics of RNA, as the order by which successive helices are formed and dissociated can lead to topologically blocked transition intermediates. The resulting knotty dynamics can enhance the stability of RNA switches, improve the efficacy of co-transcriptional folding pathways and lead to unusual self-assembly properties of RNA.
Dawid A, Cayrol B, Isambert H RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation Phys. Biol., 2009; 6(2):25007 - Abstract
Among all biopolymers, ribonucleic acids or RNA have a unique functional versatility, which lead to the early suggestion that RNA alone (or a closely related biopolymer) might have once sustained a primitive form of life based on a single type of biopolymer. This has been supported by the demonstration of processive RNA-based replication and the discovery of “riboswitches” or RNA switches, that directly sense their metabolic environment. In this paper, we further explore the plausibility of this “RNA world” scenario and show, through synthetic molecular design guided by advanced RNA simulations, that RNA can also perform elementary regulation tasks on its own. We demonstrate that RNA synthetic regulatory modules directly inspired from bacterial transcription attenuators can efficiently activate or repress the expression of other RNAs by merely controlling their folding paths “on the fly” during transcription through simple RNA-RNA antisense interaction. Factors, such as NTP concentration and RNA synthesis rate, affecting the efficiency of this kinetic regulation mechanism are also studied and discussed in the light of evolutionary constraints. Overall, this suggests, that direct coupling between synthesis, folding and regulation of RNAs may have enabled the early emergence of autonomous RNA-based regulation networks in absence of both DNA and protein partners.
Evlampiev K, Isambert H Conservation and topology of protein interaction networks under duplication-divergence evolution Proc Natl Acad Sci USA, 2008; 105 (29) : 9863-9868 - Abstract
Genomic duplication-divergence processes are the primary source of new protein functions and thereby contribute to the evolutionary expansion of functional molecular networks. Yet, it is still unclear to what extent such duplication-divergence processes also restrict by construction the emerging properties of molecular networks, regardless of any specific cellular functions. We address this question, here, focusing on the evolution of protein-protein interaction (PPI) networks. We solve a general duplication-divergence model, based on the statistically necessary deletions of protein-protein interactions arising from stochastic duplications at various genomic scales, from single-gene to whole-genome duplications. Major evolutionary scenarios are shown to depend on two global parameters only: (i) a protein conservation index (M), which controls the evolutionary history of PPI networks, and (ii) a distinct topology index (M') controlling their resulting structure. We then demonstrate that conserved, nondense networks, which are of prime biological relevance, are also necessarily scale-free by construction, irrespective of any evolutionary variations or fluctuations of the model parameters. It is shown to result from a fundamental linkage between individual protein conservation and network topology under general duplication-divergence evolution. By contrast, we find that conservation of network motifs with two or more proteins cannot be indefinitely preserved under general duplication-divergence evolution (independently from any network rewiring dynamics), in broad agreement with empirical evidence between phylogenetically distant species. All in all, these evolutionary constraints, inherent to duplication-divergence processes, appear to have largely controlled the overall topology and scale-dependent conservation of PPI networks, regardless of any specific biological function.
Sellerio AL, Bassetti B, Isambert H, Cosentino Lagomarsino M A comparative evolutionary study of transcription networks. The global role of feedback and hierachical structures Mol BioSyst., 2009; 5(2):170-9. Epub 2008 Nov 25 - Abstract
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species: the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the global aspects of feedback and hierarchy in transcriptional regulatory pathways. While confirming that gene duplication has a significant impact on the shaping of all the analyzed transcription networks, our results point to distinct trends between the bacteria, which display a hierarchical network structure with short transcription cascades, and yeast, which seems able to sustain a higher wiring complexity, including larger feedback, longer transcription cascades, and the combinatorial use of heterodimers made of duplicate transcription factors, absent in E. coli.
Cosentino-Lagomarsino M, Jona P, Bassetti B, Isambert H Hierarchy and feedback in the evolution of the E. coli transcription network Proc Natl Acad Sci USA., 2007; 104 (13) : 5516-20 - Abstract
The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of gene duplication based on protein domain architecture shows that (i) transcriptional autoregulators have mostly arisen through duplication, while (ii) the expected feedback loops stemming from their initial cross-regulation are strongly selected against. This requires a divergent coevolution of the transcription factor DNA-binding sites and their respective DNA cis-regulatory regions. Moreover, we find that the network tends to grow by expansion of the existing hierarchical layers of computation, rather than by addition of new layers. We also argue that rewiring of regulatory links due to mutation/selection of novel transcription factor/DNA binding interactions appears not to significantly affect the network global hierarchy, and that horizontally transferred genes are mainly added at the bottom, as new target nodes. These findings highlight the important evolutionary roles of both duplication and selective deletion of crosstalks between autoregulators in the emergence of the hierarchical transcription network of E.coli.
Xayaphoummine A, Viasnoff V, Harlepp S, Isambert H Encoding folding paths of RNA switches Nucleic Acids Res., 2007; 35(2):614-622 - Abstract
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and intermolecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.
Evlampiev K, Isambert H Modeling protein network evolution under genome duplication and domain shuffling BMC Systems Biology, 2007; 1:49 - Abstract
Background
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. Such exponential evolutionary processes must have largely contributed to shape the topology of protein-protein interaction (PPI) networks by outweighing, in particular, all time-linear network growths modeled so far.
Results
We propose and solve a mathematical model of PPI network evolution under successive genome duplications. This demonstrates, from first principles, that evolutionary conservation and scale-free topology are intrinsically linked properties of PPI networks and emerge from i) prevailing exponential network dynamics under duplication and ii) asymmetric divergence of gene duplicates. While required, we argue that this asymmetric divergence arises, in fact, spontaneously at the level of protein-binding sites. This supports a refined model of PPI network evolution in terms of protein domains under exponential and asymmetric duplication/divergence dynamics, with multidomain proteins underlying the combinatorial formation of protein complexes. Genome duplication then provides a powerful source of PPI network innovation by promoting local rearrangements of multidomain proteins on a genome wide scale. Yet, we show that the overall conservation and topology of PPI networks are robust to extensive domain shuffling of multidomain proteins as well as to finer details of protein interaction and evolution. Finally, large scale features of direct and indirect PPI networks of S. cerevisiae are well reproduced numerically with only two adjusted parameters of clear biological significance (i.e. network effective growth rate and average number of protein-binding domains per protein).
Conclusion
This study demonstrates the statistical consequences of genome duplication and domain shuffling on the conservation and topology of PPI networks over a broad evolutionary scale across eukaryote kingdoms. In particular, scale-free topologies of PPI networks, which are found to be robust to extensive shuffling of protein domains, appear to be a simple consequence of the conservation of protein-binding domains under asymmetric duplication/divergence dynamics in the course of evolution.
Viasnoff V, Meller A, Isambert H DNA nanomechanical switches under folding kinetics control Nano Letters, 2006; 6, 101-104 - Abstract
Existing DNA nanodevices operate at equilibrium under changes in solution composition. We propose an alternative DNA switch design that can be driven and maintained out of equlibrium, under fixed chemical conditions. Moderate cooling rate after heat denaturation drives the switch to its lowest energy conformation, while rapid cooling (>100 C/ms) locks the molecule in a unique alternative conformation that is retained over weeks at room temperature. This reversible process is probed using fluorescent energy transfer. DNA switches operating out of equilibrium should be more amenable to nanotechnology applications and scalable integration.
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