Recent advances in genomics and genome sequencing projects hightlight a striking paradox. Living organisms, despites their apparent diversity and complexity, actually share many genetic similarities from a limited repertoire of a thousand gene families. For instance, as many as 70 percent of the baker's yeast genes are similar to human genes, despite the striking difference between this unicellular fungi and the human body and its 10^14 cells.
In fact, the diversity and complexity of living organisms result from the combinatorial expression of their genes which cooperate to produce a virtually infinite number of specific cellular responses and functions. Indeed, small variations in the regulation of multiple genes can collectively induce large differences in cellular functions and developments.
The concept of biomolecular networks was introduced to describe, with simple graph representations, some aspects of this combinatorial gene expression. Major biomolecular networks include, for instance, protein-protein interactions, metabolic reactions or regulatory interactions from the cell. Hence, virtually any biological process participates in at least one biomolecular network. But, beyond the molecular specifics they encapsulate, biomolecular networks are also interesting biological "objects" of their own, that evolve and can be studied.
Our own research concerns the properties and adaptation of biomolecular networksat different scales, from their simple local structures to their more complex global organization.
1- Synthetic RNA regulatory networks and self-assembly of bacterial RNA.
We study the properties of small regulatory circuits primary based on RNAs and their interactions. In particular, we have used synthetic biology approaches coupled to advanced RNA dynamics simulations (movies 1 & 2) to design efficient RNA-based repressor (Fig.1A) and activator modules (Fig.1B). These modules control RNA transcription "on the fly" through simple RNA-RNA antisense interactions, Fig1.
Fig. 1
We also discovered that a small bacterial RNA of Escherichia coli could self-assemble, like many proteins do, to form long filaments (Fig.2A) and large physical networks (Fig2B). This finding further extends the already great versality of natural RNA functions.
Fig. 2
2- Evolution of large biomolecular networks
We are also interested in the properties of large biomolecular networks and their evolution due to genomic duplication-divergence processes at the level of individual gene or whole genome duplications, Fig.3.
Fig. 3
Our theoretical approach relies on a general duplication-divergence model, based on the necessary deletions of some functional interactions arising from stochastic duplications, Fig.4. We have shown that duplication-divergence processes bring not only genetic novelty but also evolutionary constraints that restrict by construction the emerging properties of biomolecular networks, regardless of any specific cellular functions. In particular, we could demonstrate that networks with conserved genes, which are networks of prime biological relevance, are also necessary scale-free by construction, irrespective of any evolutionary variations or fluctuations of the model parameters.
Fig. 4
By contrast, we found that conservation of network motifs including at least one interaction cannot be indefinitely preserved under general duplication-divergence evolution, Fig.5, in broad agreement with empirical evidences between phylogenetically distant species.
Fig. 5
Finally, we are also interested in the evolution of transcription networks and study the regulatory conflicts that arise through duplication of trancription factors and autoregulators. All in all, it appears that evolutionary constraints, inherent to duplication-divergence processes, have largely controlled the overall topology and scale-dependent conservation of biomolecular networks.
Last update: October 2008
Key publications
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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