2. Brains affinely normalized to Talairach space. 3. Right sulci flipped to allow left/right comparison. 4. A cross-species scaling performed by applying a species-specific homothetic transformation to all sulci of the subset. 5. Pairwise shape similarity matrices computed after rigid alignment (from Sun et al., 2012). 6. Isomap to project high dimensional space spanned by the sulci to one single dimension. 7. All sulci rigidly aligned to the sulcus with the minimum average distance to the set. -However major features are stable within species and even between species like the central sulcus (CS), dividing the motor cortex from the somatosensory cortex in primates [3].

We examined here the morphological variability of the central sulcus in hominids, with a focus on the motor hand region, significant issue of human evolution.

Comparison of the shape of the Central Sulcus in Hominids

Ophelie Foubet 1 , Zhong Yi Sun 1 , William Hopkins 2 , Jean-François Mangin 1 1 Neurospin, CEA Saclay, Gif-sur-Yvette, Ile de France, 2 University of Texas MD Anderson Cancer Center, Bastrop, TX

INTRODUCTION METHODS

Poster n°WTh748

[1] Fischl B ( 2008 -Shift between the two parts of the SC, dorsal and ventral to the knob, at the level of humans and which develops towards the orangutans: development of a more ventral somatosensory knob rather than a real second motor knob ?

RESULTS

DISCUSSION

INTRA-SPECIES VARIABILITY:

Comparison of moving averages (M.A) along the isomap axes for each species.

Humans: -similar to previous results on large human databases [5,6] -shape variability trait ranging from a single motor hand knob (*) configuration to a double knob (**) configuration: the hand knob is shifted dorsally while a second knob appears ventrally.

Chimpanzees: -single to a double knob configuration -hand knob larger, deeper and more ventral than that of humans Gorillas: shape of CS and variability trait described on their isomap axis very similar to that of chimpanzees.

Orangutans: -very specific shape of CS -seem to share the single vs double knob variability trait -dorsal shift of the hand knob seems to allow for the development of a somatosensory knob rather than a real second motor knob. -This could explain the similarity in shape of their hand-knob -It could also explain the appearance of a knob in their somato-sensory cortex on the axis common to all 4 species. Their better sensory-motor integration could reflect an increase in hand and digits use for bipedal humans and an increase in hand and foot grasping for tree-dwelling orangutans.

CONCLUSION 1: Inter-individual variability within all hominids: characterized primarily by a shape variation ranging from a single to a double knob configuration.

CONCLUSION 2: The four species together: "single-to-double-knob" no longer enough to describe all the variability. differences in overall sulci shape between species prevail; but not for chimpanzees and gorillas together. Chimpanzees and gorillas were compared on an axis of their own. -> Although the two species are close when compared to humans and orangutans, one would think that a shape specificity would distinguish them -> but the two species are not separated on their isomap axis (U1=1733; p=0.72).

  8. Moving local average shapes computed at regular coordinates 1. Morphologist 2012 pipeline [4] labelisation of the chimpanzee brain based on the human nomenclature C. Central Sulcus B. Sulci and labels A. Cortical mesh and MRI -Gyrification of the neocortex -Folding rich and complex in large brains, high inter-individual variability in humans [1,2].

  ), 'Cortical folding patterns and predicting cytoarchitecture.', Cereb Cortex 18:1973-1980. [2] Welker W (1988), 'Why does cerebral cortex fissure and fold?', Cereb Cortex 8B:3-135. [3] Hopkins W.D. (2014), 'Evolution of the Central Sulcus Morphology in Primates', Brain, behavior and evolution 84.1 (2014): 19-30. [4] Fischer C (2012), 'Morphologist 2012: the new morphological pipeline of BrainVISA.', In. HBM. Beijing. [5] Sun Z. Y. (2012), 'The Effect of Handedness on the Shape of the Central Sulcus', Neuroimage, 60(1):332-9 [6] Sun Z. Y. (2016), 'Linking morphological and functional variability in hand movement and silent reading.', Brain Structure and Function 221(7):3361how different species are organised on the same isomap axis ? 1° FOUR SPECIES -Chimpanzee and gorilla populations share the same variation in CS shape -Humans and orangutans appear to have their own variability trait -Trait along the axis: single knob to a double knob, addition of a rotation of the sulcus on the orangutan side.

  M.A of orangutans somap axis M.A of gorillas isomap axis M.A of chimpanzees isomap axis M.A of humans isomap axis Humans and orangutans: buried gyrus in the central region of the CS, suggesting greater sensory-motor connectivity and integration between their motor and somato-sensory cortices [3].


Eugen Pfeifer

Jorge De Sousa

Marie Touchon

Eduardo Pc Rocha
email: erocha@pasteur.fr

Jorge M Sousa

When bacteria are phage playgrounds: interactions between

Keywords:

des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Introduction

Bacteriophages (phages) are viruses of bacteria. Their diverse virulence strategies shape the duration, impact, and complexity of the interactions they have with the bacterial host. Virulent phages follow infection cycles that end with cell lysis and liberation of progeny. Occasionally, for reasons not fully understood, these phages can remain in cells in a non-replicative state, called pseudolysogeny, before the onset of the lytic cycle. Temperate phages can either follow the same type of lytic cycle or integrate the genome as prophages, in which case they are effectively part of the bacterial genome. They are found in at least half of the bacterial genomes and can account for a substantial part of bacterial gene repertoires [START_REF] Touchon | Genetic and life-history traits associated with the distribution of prophages in bacteria[END_REF]. Other phages have peculiar alternative lifecycles. For example, filamentous phages continuously produce viral particles that they export to the outside of the living cell (chronic life cycle without cell lysis) [START_REF] Hay | Filamentous phages: masters of a microbial sharing economy[END_REF].

Phages are very abundant predators that influence the dynamics of bacterial populations and provide the host with adaptive traits. The type and duration of the interactions between viruses and the cell are thus determinant for the success of phage infections and for bacterial survival. These interactions vary with the type of phage and the host genetic background. Some phages develop multiple different genetic programs (temperate phages), some function continuously in living cells (filamentous), and others quickly kill their hosts (virulent). The costs and opportunities provided by the lifecycle of the phage affect the evolution of these interactions. For example, one expects cells to systematically evolve defenses against virulent phages because they tend to be deadly. In contrast, temperate phages may kill the host upon inducing the lytic cycle or integrate its genome and eventually increase its fitness by providing it with novel phenotypes (lysogenic conversion). Therefore, interactions between temperate phages and the bacterial host may be more subtle and varied. Beyond these pairwise phage-bacterium interactions one must consider that phages are not alone within cells. Bacterial genomes have many other mobile genetic elements (MGEs) with whom phages may establish relations of competition, antagonism, or parasitism. In this context, cells can be regarded as playgrounds for interactions between MGEs that impact the outcome of phage infections and the rate of horizontal gene transfer between bacteria [START_REF] Haudiquet | Selfish, promiscuous, and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations[END_REF]. Here, we focus on three types of molecular interactions faced by phages upon injecting their DNA in host cells: defense systems, regulatory interactions, and recombination. These interactions have typically been studied independently, but there is increasing evidence that their interplay can have unexpected outcomes.

Defense systems: conflict and cooperation

All of life's evolution is a history of incessant conflict between hosts and parasites. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to defend themselves from phages [START_REF] Doron | Systematic discovery of antiphage defense systems in the microbial pangenome[END_REF][START_REF] Tesson | Systematic and quantitative view of the antiviral arsenal of prokaryotes[END_REF]. These mechanisms, whose complexity and diversity are quickly being unraveled, target each step of the phage reproduction cycle, from blocking its attachment to the cell, to cleaving phage nucleic acids, to spurring metabolic arrest or even cell suicide [START_REF] Egido | Mechanisms and clinical importance of bacteriophage resistance[END_REF]. They either protect cells from phage infection or stop epidemic waves by inducing cell death [START_REF] Lopatina | Abortive infection: bacterial suicide as an antiviral immune strategy[END_REF]. Surprisingly, recent results suggest that many, or even most, such so-called bacterial defenses rely on MGEs.

The rapid evolution of the antagonistic interaction between phages and bacteria drives rapid change of defense and anti-defense systems. This may occur by sequence evolution, e.g. change of CRISPR spacers to match novel phages, but in most defense systems it requires frequent acquisition of novel systems by horizontal gene transfer, which are usually co-transferred by MGEs or encoded in the MGEs themselves. In marine Vibrio, MGEs encode most of the cell defense systems. The turnover of MGEs in genomes, and their anti-phage systems, explains much of the differences in susceptibility of closely related strains to different phages [START_REF] Hussain | Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages[END_REF][START_REF] Piel | Genetic determinism of phage-bacteria coevolution in natural populations[END_REF]. MGEs encode many anti-phage systems presumably because when phages are killing the bacteria, they are also eliminating the MGEs. By defending bacterial cells, most MGEs are defending themselves.

Many of the anti-phage systems are encoded in temperate phages, that, as prophages, defend bacteria from other phages [START_REF] Hussain | Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages[END_REF][START_REF] Bondy-Denomy | Prophages mediate defense against phage infection through diverse mechanisms[END_REF][START_REF] Dedrick | Prophage-mediated defence against viral attack and viral counter-defence[END_REF][START_REF] Piel | Phage-host coevolution in natural populations[END_REF][START_REF] Owen | Prophages encode phage-defense systems with cognate self-immunity[END_REF][START_REF] Rousset | Phages and their satellites encode hotspots of antiviral systems[END_REF]. These phage-encoded bacterial defense systems have interesting characteristics. For example, their CRISPR-Cas systems are extremely compact [START_REF] Pausch | CRISPR-CasPhi from huge phages is a hypercompact genome editor[END_REF]. Sometimes they even lack cas genes and consist only of CRISPR mini-arrays that use the cas machinery from the host [START_REF] Faure | CRISPR-Cas in mobile genetic elements: counter-defence and beyond[END_REF]. Such simple systems are implicated in competition between phages [START_REF] Medvedeva | Virusborne mini-CRISPR arrays are involved in interviral conflicts[END_REF]. They fit the 'guns for hire' model whereupon phages acquire anti-phage systems through recombination with their bacterial hosts [START_REF] Koonin | Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire[END_REF], or with other MGEs, thus blurring the boundaries between defense and counter-defense systems. This frequent transfer and co-option of defense and anti-defense systems highlights the importance of gene flow, which we will expand on below, in the evolution of phage-bacteria interactions.

Phages have their own parasites. Phage satellites exploit "helper" phages by hijacking their viral particles to ensure their own horizontal transfer [START_REF] Frigols | Virus Satellites Drive Viral Evolution and Ecology[END_REF]. Recent studies suggest they are very abundant [START_REF] Chen | Intra-and intergeneric transfer of pathogenicity island-encoded virulence genes by cos phages[END_REF][START_REF] De Sousa | To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites[END_REF]. Certain satellites completely block phage reproduction, e.g. the PLE satellite of Vibrio cholerae aborts the production of ICP1 phages [START_REF] Hays | Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite[END_REF]. Its activity still kills the cell, but benefits the bacterial population by preventing the epidemic spread of the phage. In other cases, the ecological interactions between phages and their satellites are more subtle. The P4-like satellites of enterobacteria have only a small impact on the "helper" phage reproduction and encode numerous anti-phage systems that protect them, the "helper" phage, and the cell from other phages [START_REF] Rousset | Phages and their satellites encode hotspots of antiviral systems[END_REF]. Hence, satellites are hyper-parasites (parasites of parasites) that can defend bacteria from the "helper" phage or defend the cell and the "helper" phage from other phages.

Phages have evolved numerous tools to protect themselves from the cell defense systems. These anti-defense strategies may depend on cooperative interactions with other phages [START_REF] Dimitriu | Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems[END_REF]. For example, the presence of multiple infecting phages producing anti-CRISPR proteins improves the chances of neutralization of the host CRISPR-Cas activity by increasing the number of such proteins in the cell cytoplasm [START_REF] Borges | Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity[END_REF][START_REF] Landsberger | Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity[END_REF]. These anti-anti-phage proteins are thus a sort of intracellular public good. As a result, they can be used, and even exploited, by other phages or MGEs that benefit from the associated immunosuppression without paying its cost [START_REF] Chevallereau | Exploitation of the cooperative behaviors of anti-CRISPR phages[END_REF]. This opens the opportunity for dynamic, complex, and multi-layered social interactions within the cell.

The key role of MGEs in bacteria-phage interactions raises intriguing questions around the real roles of defense systems in cells and whether selection for their presence is always in the host's interest [START_REF] Rocha | Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?[END_REF]. For example, the presence of anti-phage systems in integrative conjugative elements of Vibrio cholerae decreases the likelihood of acquisition of phages carrying virulence factors [START_REF] Legault | Temporal shifts in antibiotic resistance elements govern viruspathogen conflicts[END_REF]. For a better understanding of the raison d'être of these defense systems, one thus needs to better characterize both the mechanisms of defense systems and the costs and benefits of the MGEs encoding them. It's also important to note that once the phage passes cell defenses, its fate will still depend heavily on its regulatory interactions with other MGEs and with the host. We will go through these below.

Gene regulation for the control of ecological associations

The regulation of gene expression has a key role in phage-bacteria interactions. Phages must regulate the expression of their own genes, which may be particularly complex for temperate phages that must manage different programs of gene expression (lysis/lysogeny). But phages can also regulate host functions using their DNA, RNA, or regulatory proteins. Temperate phages may act as genetic switches by interrupting/re-establishing a gene when integrating the chromosome, a process termed "active lysogeny". This strategy may co-evolve with the host to regulate gene expression in specific niches, e.g. intracellular survival [START_REF] Pasechnek | Active Lysogeny in Listeria Monocytogenes Is a Bacteria-Phage Adaptive Response in the Mammalian Environment[END_REF]. Phage-integration was shown to re-program Escherichia coli's anaerobic respiratory system through transcription of neighboring chromosomal genes initiated from a phage promotor [START_REF] Carey | Phage integration alters the respiratory strategy of its host[END_REF]. Phage encoded small RNAs can also contribute to phage-bacteria cross-regulation, e.g. by affecting the regulation of bacterial core genome transcripts [START_REF] Altuvia | Cross-Regulation between Bacteria and Phages at a Posttranscriptional Level[END_REF]. Recently, it was shown that prophage-encoded quorum sensing (QS) regulators allow phages to eavesdrop on bacterial communication systems to sense host cell-densities and eventually switch to the lytic cycle [START_REF] Silpe | A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision[END_REF]. Phage protein regulators may also activate expression of virulence genes in the bacterial host [START_REF] Hernandez-Doria | Bacteriophage Transcription Factor Cro Regulates Virulence Gene Expression in Enterohemorrhagic Escherichia coli[END_REF], or down-regulate its SOS response [START_REF] Azulay | A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response[END_REF].

Bacteria can also regulate the expression of phage genes. The transcription termination factor Rho silences phage genes by acting as a transcription termination factor. In E. coli it maintains prophages in that state by preventing their excision from the chromosome [START_REF] Menouni | Transcription termination controls prophage maintenance in Escherichia coli genomes[END_REF]. Bacteria also encode small nucleoid-associated proteins that bind and downregulate the expression of the AT-rich phage genes. These proteins are collectively referred to as xenogeneic silencers (XS) and their mode of action contrasts to that of other bacterial defense mechanisms in that it is not destructive of its targets. The ability to silence and stabilize prophages gives the cell an opportunity to benefit from lysogenic conversion (reviewed in [START_REF] Pfeifer | Impact of xenogeneic silencing on phagehost interactions[END_REF]). The impact of XSs may span multiple regulatory levels. The Shewanella oneidensis host-encoded H-NS protein represses or derepresses prophage excision depending on post-translational modifications. Under low-temperature, this XS favors prophage excision which ultimately results in the expression of cold-shock survival genes [START_REF] Liu | Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella[END_REF]. When temperature rises, the prophage reintegrates the chromosome. In this case, the host regulates the excision of a prophage that works for the host as a genetic switch.

Phages and other MGEs can also encode XS. The first of these were initially identified in plasmids, where they stabilize the presence of plasmids by decreasing their fitness cost [START_REF] Doyle | An H-NS-like stealth protein aids horizontal DNA transmission in bacteria[END_REF]. XS homologs were found in the genomes of actinophages [START_REF] Pfeifer | Impact of xenogeneic silencing on phagehost interactions[END_REF] and through metagenomics in phages infecting other bacterial clades [START_REF] Skennerton | Phage encoded H-NS: a potential achilles heel in the bacterial defence system[END_REF]. For instance, the XS encoded in a cryptic prophage of Corynebacterium glutamicum silences various AT-rich host genes (beyond regulating the prophage itself). The interference caused by this XS activity could be counter-acted by foreign XSs (H-NS from E. coli) and by truncated variants of the XS itself [START_REF] Pfeifer | Silencing of cryptic prophages in Corynebacterium glutamicum[END_REF]. This means that truncated variants of XSs can act as anti-XS proteins [START_REF] Williamson | Free A: A truncated H-NS-like protein from enteropathogenic Escherichia coli acts as an H-NS antagonist[END_REF]. Such proteins could easily evolve from existing XS, allowing phages to interfere with the XS activity of the host. Other proteins used by phages to control bacterial XS are not homologous to XS and use alternative mechanisms [START_REF] Bdira | Novel anti-repression mechanism of H-NS proteins by a phage protein[END_REF]. Overall, this paves the way for competition for the genetic control of phagebacteria interactions based on XS and anti-XS functions, which has striking parallels with that of defense and counter-defense systems.

Of all the intracellular interactions between MGEs, those of resident prophages are amongst the most vital for infecting phages. The presence of prophages in bacteria may protect the ensemble from virulent phages because of the defense systems they encode (see above). But prophages also interact with incoming phages in other ways, which are sometimes poorly understood. For example, prophages may provide protection from pseudolysogeny of virulent phages [START_REF] Markwitz | Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness[END_REF]. They may also protect the cell from closely related temperate phages by repressing them. The lytic cycle of prophages is usually actively repressed to avoid its untimely induction. The presence of these repressors in the cell precludes super-infection by the same phage, but can also repress incoming phages with similar regulatory sequences [START_REF] Thomas | Control of development in temperate bacteriophages: I. Induction of prophage genes following hetero-immune super-infection[END_REF]. Such mechanisms have been poorly studied and their relevance to control a broad range of phages is yet unclear. The study of repressor-mediated immunity in a panel of Pseudomonas strains revealed that this mechanism was responsible for a small number of cases of resistance to different temperate phages [START_REF] Bondy-Denomy | Prophages mediate defense against phage infection through diverse mechanisms[END_REF]. The relatively minor role of super-infection exclusion on cell defense may be due to the rapid evolution of regulatory systems that could rapidly make native repressors incompatible with distinct incoming phages. Nevertheless, repression of incoming phages is a relevant component of prophage-encoded mechanisms that protect the bacterial host (and thus the prophages themselves). Albeit very different from the double stranded DNA phages that are the focus of this review, filamentous phages and microvirus also encode multiple superinfection exclusion systems, which influence the infection dynamics of unrelated co-infecting viruses [START_REF] Roux | Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes[END_REF][START_REF] Kirchberger | Defensive hypervariable regions confer superinfection exclusion in microviruses[END_REF].

Since some strains have up to 20 prophages, there is a potential for complex regulatory interactions between resident prophages. It has been shown that the presence of two phages in the cell has deleterious consequences for their productivity [START_REF] Refardt | Within-host competition determines reproductive success of temperate bacteriophages[END_REF], even if the mechanisms are poorly understood. The complexity of the underlying interactions is illustrated by two pairs of Salmonella enterica prophages [START_REF] Lemire | Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors[END_REF]. Prophages Gifsy-1 and Gifsy-3 do not repress each other, but their repressors can be cross-targeted by the other prophages' anti-repressor proteins. Hence, de-repression of one leads to the induction of the other. The other pair shows a more complex mechanism. The repressor of prophage Gifsy-2 is sensitive to the anti-repressor of Fels-1, but Fels-1 induction does not depend on its own anti-repressor. This suggests that Fels-1 anti-repressor is only used by the prophage to manipulate other prophages. Another striking example of cross-regulation was identified in Listeria monocytogenes, where a prophage encoded gene has two functions resulting from two different protein domains. One of the domains regulates the expression of the prophage [START_REF] Azulay | A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response[END_REF]. The other domain downregulates the SOS response by inhibiting RecA. Since many MGEs are induced by the SOS response, this dual-function regulator can regulate the induction of the phage and of many other elements in the cell, including other prophages. These examples show that the presence of regulators in bacteria, phages and other MGEs generates a complex network of regulatory interactions that shapes the presence and activity of phages in their bacterial hosts. This network keeps changing because of the rapid turnover of phages and other MGEs in cells and of genetic exchanges between them.

Recombination drives gene flow

Many phages have mosaic genomes, i.e. interspersed regions with high similarity to distinct phages, that are the result of multiple independent events of recombination with other phages. Because the phage genome is isolated from other genomes within the viral particle, these recombination events must result from interactions taking place within the bacterial cell. Recombination is expected to be more frequent between temperate phages than between virulent phages, because the former have very long periods of co-existence as prophages providing opportunity for recombination with infecting phages or other resident prophages [START_REF] De Paepe | Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases[END_REF]. Recombination between phages is facilitated by their modular genome organization, where closely related functions tend to be encoded together, allowing the exchange of complete functional modules in a single event [START_REF] Botstein | A theory of modular evolution for bacteriophages[END_REF]. For example, lambdoid phages have similar genetic maps and recombination between these phages, which are sometimes highly divergent, can provide viable hybrids.

A few recent studies attempted to quantify genetic flux between phages. The analysis of pairs of phages in terms of nucleotide distance versus gene content similarity shows two modes of phage evolution that are consistent with high or low gene flux [START_REF] Mavrich | Bacteriophage evolution differs by host, lifestyle and genome[END_REF]. Recombination between temperate phages is frequent and associated with high gene flow. Accordingly, evolution experiments in the lab uncovered recombinants between prophages of Bacillus subtilis that resulted in the generation of virulent phages [START_REF] Dragoš | Pervasive prophage recombination occurs during evolution of spore-forming Bacilli[END_REF]. But recombination between virulent phages is not rare. The follow-up of a lineage of virulent Siphoviridae for over 29 years revealed a constant rate of five recombination events per year that caused ca. 24 times more changes to genomes than point mutations [START_REF] Kupczok | Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades[END_REF]. Hence, even virulent phages interact frequently enough within cells to exchange DNA many times in a relatively short period of time. Some of these genetic exchanges may be caused by defense systems that target the DNA sequences of phages. For example, restriction-modification systems produce recombinogenic linear double stranded DNA that might promote recombination.

On the other edge of the evolutionary scale, some very dissimilar phages, including pairs of virulent and temperate, have almost identical genes, a hallmark of gene flow [START_REF] De Sousa | Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa[END_REF]. Such processes presumably take advantage of the peculiar molecular mechanisms of recombination encoded by phages that allow exchanges between more dissimilar DNA sequences than is possible by bacterial homologous recombination [START_REF] Martinsohn | The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism[END_REF]. Accordingly, recombination is more frequently observed in phages encoding such mechanisms [START_REF] De Sousa | Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa[END_REF]. Since other MGEs, e.g. ICEs of Vibrio [START_REF] Garriss | Mobile antibiotic resistance encoding elements promote their own diversity[END_REF], encode similar recombinases, it is tempting to speculate that the recombination mechanisms themselves can be transmitted between phages and other MGEs. Recombination between unrelated phages have consequences for the transfer of genes across phage families or between phages infecting distant bacterial taxa. Even if virulent phages recombine more rarely than temperate phages, they can recombine with phages infecting more distant bacterial clades [START_REF] De Sousa | Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa[END_REF]. This suggests that virulent phages have a broader host range and could shuttle genes between temperate phages infecting distantly related bacteria.

The genes transferred between phages include defense systems, anti-defense systems, regulators, and recombinases, which are often like those of bacteria or other MGEs [START_REF] Rousset | Phages and their satellites encode hotspots of antiviral systems[END_REF][START_REF] De Sousa | Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa[END_REF]. Other functions reported to be transferred to and from phages include integrases [START_REF] Köstlbacher | Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria[END_REF] and tRNAs to compensate differences in codon usage [START_REF] Bailly-Bechet | Causes for the intriguing presence of tRNAs in phages[END_REF][START_REF] Yang | Degradation of host translational machinery drives tRNA acquisition in viruses[END_REF]. This suggests that genetic exchanges between phages, hosts, and other MGEs are common. Such functions find a novel context in the recipient genome and may end up providing novel phenotypes and even novel functions [START_REF] Randich | Origin of a Core Bacterial Gene via Cooption and Detoxification of a Phage Lysin[END_REF]. Unfortunately, there has been little work on the systematic identification of these exchanges.

Genetic exchanges between phages and other MGEs could also be at the origin of new types of MGEs such as phage-plasmids or phage satellites. Phage-Plasmids (P-Ps) are temperate phages that replicate autonomously as plasmids within bacterial cells. A recent systematic screening for these elements in bacterial genomes found that ˜6% of all plasmids and phages are P-Ps [START_REF] Pfeifer | Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires[END_REF]. These P-Ps form large, presumably ancient, families of mobile elements that may have originated from events of recombination between phages and plasmids or may represent vestiges of a period when such elements were less distinct than they tend to be today. Interestingly, while phages have few transposable elements and antibiotic resistance genes, P-Ps have many of these, sometimes grouped in integrons, just like plasmids [START_REF] Pfeifer | Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion[END_REF]. Hence, the similarities of P-Ps with both phages and plasmids may allow them to drive gene flow between the two types of elements.

Phage-inducible chromosomal islands (PICI) are phage satellites found in Proteobacteria and Firmicutes that encode DNA packaging machineries homologous to those of phages [START_REF] Fillol-Salom | Phage-inducible chromosomal islands are ubiquitous within the bacterial universe[END_REF]. While there is little information on their evolution, such genes could have been acquired from phages a long time ago, when PICI emerged. In contrast, other phage satellites such as P4 [START_REF] De Sousa | To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites[END_REF] or the PLE of Vibrio [START_REF] Netter | A phage satellite tunes inducing phage gene expression using a domesticated endonuclease to balance inhibition and virion hijacking[END_REF] have few phage homologs. Yet, even some of the hijacking mechanisms of the latter may have been acquired from phages. For example, the capR gene of PLE encodes a DNA-binding protein thought to be derived from a phage homing endonuclease. This protein represses the "helper" phage capsid morphogenesis operon [START_REF] Netter | A phage satellite tunes inducing phage gene expression using a domesticated endonuclease to balance inhibition and virion hijacking[END_REF]. Hence, a satellite obtained by genetic exchange (recombination) a gene of the "helper" phage that it uses to control the genetic expression of the latter, thereby defending the cell from this virulent phage. This nicely sums up the interplay between the three different types of interactions described in this review.

Conclusion and perspectives

The last few years revealed numerous cases of interactions between phages and the host or other MGEs in the cell. These discoveries are ongoing at an ever faster pace [START_REF] Millman | An expanding arsenal of immune systems that protect bacteria from phages[END_REF]. While it is tempting to regard defense systems as primarily anti-phage systems, this may not always be the case. For example, the Vibrio cholerae El Tor strain responsible for the seventh cholera pandemic lacks plasmids because it encodes two defense systems that cooperate to eliminate small multi-copy plasmids [START_REF] Jaskólska | Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae[END_REF]. One of the two systems also targets phages and we are tempted to speculate that phages may in this case be collateral victims of a bacteria-plasmid antagonistic interaction. Likewise, some of the regulatory interactions acting upon phages in cells may also be side effects of interactions between the large network of MGEs present in bacterial genomes.

As we saw above, phages may develop mechanisms to evade deleterious interactions with the cell or other MGEs. Some phages encode proteinaceous nucleus-like compartments that encapsulate processes such as DNA replication, recombination, and transcription [START_REF] Chaikeeratisak | Assembly of a nucleus-like structure during viral replication in bacteria[END_REF], and protect its DNA from certain anti-phage systems [START_REF] Mendoza | A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases[END_REF][START_REF] Malone | A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity[END_REF]. These compartments may protect the phage from regulatory interactions with the host, but could also decrease its ability to engage in genetic exchanges.

The existence of numerous interactions between phage and MGEs opens the possibility of their manipulation by other biological agents. We discussed above how satellites can manipulate phages. Interestingly, prophages can also be manipulated by other bacteria. Streptococcus pneumoniae displaces Staphylococcus aureus lysogens from the nasopharynx by producing peroxide hydrogen that kills the latter by inducing the lytic cycle of its prophages [START_REF] Selva | Killing niche competitors by remote-control bacteriophage induction[END_REF]. Given that prophages are "molecular timebombs", their exploitation by competitor bacteria might be common. This could occur by manipulation of the quorum-sensing mechanisms that prophages use to sense conditions favorable for prophage induction [START_REF] Bruce | Regulation of prophage induction and lysogenization by phage communication systems[END_REF][START_REF] Brady | The arbitrium system controls prophage induction[END_REF]. It is tempting to speculate that bacteria could induce the prophages of competitors by interfering with such signals. This could result in alleviation of prophage repression, induction of the lytic cycle, and cell death.

Phage-bacteria antagonistic interactions have led to the continuous evolution of strategies by which one partner aims at inactivating or controlling the other. Since both partners evolve very fast, this results in rapid turnover of the gene repertoires associated with these interactions. When interactions with the host and its MGEs are systematically negative, as is the case for virulent phages, one may expect strong selection for inactivating defense systems. But when interactions oscillate between parasitism and symbiosis, as in temperate phages, the destruction of the partner may be disadvantageous. This has led to the development of mechanisms that aim at controlling gene expression of the other partner instead of destroying it. In both situations, the molecular mechanisms used by phages and bacteria are often homologous, which is the result of frequent recombination between them.

Hence, within bacterial cells, networks of interactions between bacteria, phages, and other mobile genetic elements keep evolving and shaping their rates of adaptation.

Figure 1 : 1 .

 11 Figure 1: Genetic interactions of phages with other MGEs inside the host.1. Bacteria encode defense mechanisms against phages (such as CRISPR-Cas or restriction modifications systems) to prevent viral reproduction. MGEs can encode anti-CRISPR proteins (Acr) that inactivate the hosts Cas proteins promoting the fitness of themselves and the incoming phage. Phage satellites usually hijack the assembly/packaging machinery of the helper phage and can block the production of new infectious viruses. 2. Temperate phages have regulatory pathways to downregulate the expression of lytic genes and maintain lysogeny. They can co-repress related phages and prophages, preventing superinfection. XS proteins of different types, phage and host-encoded, bind and downregulate expression of phage AT-rich DNA. Incompatible XS functions may cause interference (de-repression), whereas similar XS can co-regulate plasmids, prophages, and phages. 3. Defense systems, regulatory pathways and other genes can be exchanged by recombination between phages, plasmids, phage-plasmids, prophages, ICE, or satellites.

(• 5 )(•• 8 )(•• 10 )(•• 24 )(• 26 )(•• 28 )(• 29 )

 581024262829 Systematic and quantitative view of the antiviral arsenal of prokaryotes-A novel bioinformatic tool that detects anti-viral defense systems in prokaryotic genomes, it was used to analyse thousands of bacterial genomes, detecting a large diversity of anti-viral defense systems between and also within species. Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages -A genome-resolved cross-infection network of marine Vibrio identifies the genetic determinants of phage resistance. Resistance is encoded on putative MGEs that show fast evolutionary turnover and are akin to genomic defense islands. Such elements constitute >90% of the flexible genome and explain most of the differences in phage susceptibility among closely related bacterial strains. Prophages mediate defense against phage infection through diverse mechanisms -In this landmark work, the authors describe a variety of mechanisms through which prophages can prevent infection of their bacterial host by other phages. This study showed that repression of phage replication genes by resident prophages is not the most frequent mechanism of anti-phage defence, and other mechanisms, including modifications of the cell surface, represent more frequent molecular strategies of phage exclusion.(••14) Phages and their satellites encode hotspots of antiviral systems -Phage satellites are often regarded as parasites of phages. However, they can provide an advantage to their helper phages if they are able to increase its survivability. This is the case of the P4-like phage satellites of E. coli that, as discovered in this study, carry diverse anti-phage systems that target the phage competitors of their P2-like helpers. Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity -This study, together with Landsberger et al. (2018), shows that the inactivation of CRISPR-Cas immunity requires phage cooperation. This is one of the first documented examples of viral altruism where the production of Acr proteins by phage genomes that fail to replicate leave the cell immunosuppressed, which predisposes the cell for successful infection by other phages in the population. (••25) Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity. Exploitation of the Cooperative Behaviors of Anti-CRISPR Phages -This study demonstrates that Anti-CRISPR (Arc) phages can be exploited by cheater non-Arc phages and illustrates how the strength of Arc proteins shape the evolutionary dynamics and social interactions of phage populations in natural communities. Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts -Using time-shift experiments, this study uncovered fluctuations in Vibrio cholerae's resistance to phages in clinical samples. They show that diverse STX integrative and conjugative elements (ICEs) carrying both antibiotic resistance genes and anti-phage systems determine epidemic Vibrio cholerae susceptibility to phages. Remarkably, this study links phage and antibiotic resistances together on a single mobile genetic element, whose transfer is stimulated by phage infection. Active Lysogeny in Listeria Monocytogenes Is a Bacteria-Phage Adaptive Response in the Mammalian Environment -Unusual partnership between a pathogen and a prophage, where prophage integration/excision provides a genetic switch of a virulence program. (•32) A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision

Acknowledgements

We thank the Microbial Evolutionary Genomics members across the years for numerous discussions on these topics. We thank Julia Frunzke and Aude Bernheim for comments and suggestions on earlier versions of this manuscript. We thank the INCEPTION project (PIA/ANR-16-CONV-0005), Equipe Fondation pour la Recherche Médicale (EQU201903007835) and the Laboratoire d'Excellence IBEID Integrative Biology of Emerging Infectious Diseases (ANR-10-LABX-62-IBEID) for funding.

Questions for further research

How many of the unknown function genes are dedicated to interactions between phages and MGEs? What are the networks of interactions of phages in cells? How much of phage host range is defined by intracellular interactions? Which processes favor gene exchanges between phages, the cellular genome and other MGEs? How do phage interactions within a bacterium contribute to the fate of infection? Is there a regulation of cell defenses? Can the regulatory cross-talk within cells be systematically subverted by phages and competitor bacteria?

Highlights

• Phages and bacteria have hyper-variable defense and counter-defense systems • Extensive regulatory cross-talk between phages, MGEs and the bacterial host.

• Defenses and regulators are frequently exchanged by recombination.

• Interactions between phages and bacteria are affected by other MGEs.

• Phages may sometimes be victims of collateral damage of other interactions.

-Receptors of bacterial communication systems can be encoded by phages, which can use this to eavesdrop bacterial hosts and induce the lytic cycle at optimal host densities.

(••34) A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response

-This study explores the mechanisms involved in the cross-regulation of two prophages on the same bacterium (Listeria monocytogenes). A regulator, AriS, has two domains that either regulate the phage genes or it downregulates the bacterial SOS response.

(•53) Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades

-Recombination is thought to be pervasive in phages, but there is a lack of proper quantification of this phenomenon. This study provides estimates for substitution and recombination rates in a Siphoviridae phage over a 30-year period, showing that, relative to mutations, recombination contributes with much more polymorphism.

(•54) Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

-By looking at pairwise gene similarity across thousands of phage genomes, this study quantified gene flow as a function of (and across) phage lifestyle, as well as the presence of molecular mechanisms potentially responsible for such changes.

(•60) Origin of a Core Bacterial Gene via Co-option and Detoxification of a Phage Lysin

-This study details the domestication of a phage lysin as part of a bacterial morphogenesis gene, SpmX.

(•61) Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires

-Phages and plasmids are typically regarded as distinct entities. This study shows that phage-plasmids resemble both. It quantifies for the first time the abundance of these elements and suggests they may act as a genetic hub for exchanges between phages and plasmids.

(•64) A phage satellite tunes inducing phage gene expression using a domesticated endonuclease to balance inhibition and virion hijacking

-Recombination involving phages is not always beneficial. This study shows that an important component of the hijacking machinery of the PLE phage satellite, resulted from the acquisition and repurpose of a phage gene. Thus, recombination between mobile elements can actively contribute to their interactions.

(•66) Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae -Multiple defence systems can cooperate to protect against mobile elements and can have widespread effects across multiple MGEs. That is the case for a defence system in Vibrio that prevents the spread of plasmids through bacterial populations and also the spread of phages.

(•71) Regulation of prophage induction and lysogenization by phage communication systems -Both this study and another in the same issue [START_REF] Brady | The arbitrium system controls prophage induction[END_REF] show how communication between prophages in different cells can allow them to coordinate their induction in conditions that are favourable for it.

(•72) The arbitrium system controls prophage induction -See [START_REF] Bruce | Regulation of prophage induction and lysogenization by phage communication systems[END_REF]