Awa Diop

Didier Raoult

Pierre-Edouard Fournier
email: pierre-edouard.fournier@univ-amu.fr

Pierre-Edouard Pr

Fournier

Paradoxical evolution of rickettsial genomes

Keywords: Rickettsia, genomics, evolution, virulence, genome rearrangement, non-coding DNA, gene loss, DNA repeats

Rickettsia species are strictly intracellular bacteria that evolved approximately 150 million years ago from a presumably free-living common ancestor from the order Rickettsiales that followed a transition to an obligate intracellular lifestyle. Rickettsiae are best known as human pathogens vectored by various arthropods causing a range of mild to severe human diseases. As part of their obligate intracellular lifestyle, rickettsial genomes have undergone a convergent evolution that includes a strong genomic reduction resulting from progressive gene degradation, genomic rearrangements as well as a paradoxical expansion of various genetic elements, notably small RNAs and short palindromic elements whose role remains unknown. This reductive evolutionary process is not unique to members of the Rickettsia genus but is common to several human pathogenic bacteria. Gene loss, gene duplication, DNA repeat duplication and horizontal gene transfer all have shaped rickettsial genome evolution. Gene loss mostly involved amino-acid, ATP, LPS and cell wall component biosynthesis and transcriptional regulators, but with a high preservation of toxin-antitoxin (TA) modules, recombination and DNA repair proteins. Surprisingly the most virulent Rickettsia species were shown to have the most drastically reduced and degraded genomes compared to closely related species of milder pathogenesis. In contrast, the less pathogenic species harbored the greatest number of mobile genetic elements. Thus, this distinct evolutionary process observed in Rickettsia species may be correlated with the differences in virulence and pathogenicity observed in these obligate intracellular bacteria. However, future investigations are needed to provide novel insights into the evolution of genome sizes and content, for that a better understanding of the balance between proliferation and elimination of genetic material in these intracellular bacteria is required.

Introduction

The genus Rickettsia (order Rickettsiales, family Rickettsiaceae) comprises strictly intracellular α-proteobacteria mostly associated with diverse arthropod vectors around the world [START_REF] Raoult | Rickettsioses as paradigms of new or emerging infectious diseases[END_REF][START_REF] Stothard | Ancestral divergence of Rickettsia bellii from the spotted fever and typhus groups of Rickettsia and antiquity of the genus Rickettsia[END_REF]. Rickettsia species evolved approximately 150 million years ago from a common ancestor of Rickettsiales that was presumably free-living, and progressively followed a transition to an obligate intracellular lifestyle that occurred 775-525 million years ago and then to primarily infecting arthropod lineages approximately 525-425 million years ago [START_REF] El Karkouri | Genome sequence of the tick-borne pathogen Rickettsia raoultii[END_REF][START_REF] Merhej | Rickettsial evolution in the light of comparative genomics[END_REF]Lucy A Weinert et al., 2009). These bacteria are also well known to infect mammalian hosts, mostly through arthropod bites or arthropod feces infecting scratching lesions. On the basis of their phenotypic properties, vector hosts and phylogenetic organization, Rickettsia species were split into three to four groups by different authors (Figure 1): i) the spotted fever group (SFG, Figure 1) contains many spotted fever-causing species as well as numerous species of as-yet unknown pathogenicity. SFG rickettsiae are mostly associated with ticks, but also fleas and mites [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF]; ii) the second phylogenetic group, the typhus group (TG, Figure 1) is only made of R. prowazekii and R. typhi that cause epidemic and murine typhus, and are associated with human body lice and rat fleas, respectively [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF]; iii) the ancestral group includes R. bellii and R. canadensis. These species diverged early from SFG and TG rickettsiae, are associated with ticks but do not cause human disease (Figure 1) [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF]; iv) a fourth group, named transitional group, was proposed by Gillespie et al. to include SFG species phylogenetically close to R. felis [START_REF] Gillespie | Plasmids and rickettsial evolution: insight from Rickettsia felis[END_REF]. However, as these species do not exhibit significant differences with other SFG species except their phylogenetic position, several authors discussed the validity of this latter group [START_REF] Shpynov | New approaches in the systematics of rickettsiae[END_REF].

Rickettsia species cause a range of illnesses, from mild and self-limiting to severe and life-threatening diseases [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF]. Currently, the most common rickettsioses are African tick-bite fever caused by R. africae, scalp eschar and neck lymphadenopathy (SENLAT) caused by R. slovaca, Mediterranean spotted fever (MSF) caused by R. conorii, Rocky Mountain spotted fever (RMSF) caused by R. rickettsii and murine typhus caused by R. typhi. [START_REF] El Karkouri | Multiomics analysis sheds light on the evolution and the intracellular lifestyle strategies of spotted fever group Rickettsia spp[END_REF][START_REF] Parola | Update on tick-borne rickettsioses around the World: a geographic approach[END_REF][START_REF] Sahni | Recent molecular insights into rickettsial pathogenesis and immunity[END_REF]. Rickettsia prowazekii, the historical agent of epidemic typhus, is only rarely encountered currently but has a strong epidemic potential [START_REF] Parola | Update on tick-borne rickettsioses around the World: a geographic approach[END_REF]. Furthermore, recent studies have reported the association of other Rickettsia lineages with other reservoirs including protozoa, algae, leeches, plants or insects [START_REF] Merhej | Rickettsial evolution in the light of comparative genomics[END_REF][START_REF] Munson | Buchnera aphidicola (a prokaryotic endosymbiont of aphids) contains a putative 16S rRNA operon unlinked to the 23S rRNA-encoding gene: sequence determination, and promoter and terminator analysis[END_REF]Weinert et al., 2009).

In 1998, the first complete Rickettsia genome, that of R. prowazekii strain Madrid E, was sequenced (Andersson et al., 1998). It was the seventh bacterial genome to be sequenced.

Subsequently, the genomes of many Rickettsia species have been fully sequenced, allowing a better knowledge of the molecular mechanisms involved in their pathogenicity [START_REF] Balraj | Advances in Rickettsia pathogenicity[END_REF]. Genome sequencing also appeared as a potential tool to revolutionize the phylogenetic and evolutionary investigations of prokaryotes, especially endosymbiotic bacteria. Hence, deciphering rickettsial genomes appeared as an efficient tool to understand the evolution of these obligate intracellular bacteria.

General features of rickettsia genomes

Rickettsia species have small genome sizes and low G+C contents. SFG and TG rickettsiae exhibit genome sizes of 1.25 to 2.3 Mb, and 1.11 Mb, respectively. They also exhibit G+C contents ranging from 32.2 to 33.0% and 28.9 to 29.0%, respectively. Rickettsia species have numbers of predicted protein-coding genes varying between 817 and 2,479 and most of them maintain a near perfect chromosomal synteny [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF], which enabled the identification of an ongoing and progressive genome degradation [START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF]. Rickettsial genomes contain many functional or unfunctional pseudogenes and possess a high percentage of non-coding DNA (Blanc et al., 2007;[START_REF] Mcleod | Complete Genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae[END_REF]) (Fig. 2). This percentage of non-coding DNA ranges from 16.2% for R. felis to 31% for R. massiliae. Rickettsia prowazekii, the most reduced rickettsial genome contains 24% of non-coding sequence. By comparison, Chlamydia trachomatis, another strictly intracellular bacterium, possesses only 10% non-coding DNA (Andersson et al., 1998;[START_REF] Holste | Are noncoding sequences of Rickettsia prowazekii remnants of ``neutralized'' genes?[END_REF][START_REF] Rogozin | Congruent evolution of different classes of non-coding DNA in prokaryotic genomes[END_REF].This pseudogenization progressively leads to a genome downsizing and results from a switch from a free-living to an obligate intracellular lifestyle. This progressive reductive evolution has allowed rickettsiae to purge unnecessary and redundant genes mainly involved in metabolisms supplied by eukaryotic host cells [START_REF] Georgiades | Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules[END_REF][START_REF] Merhej | Massive comparative genomic analysis reveals convergent evolution of specialized bacteria[END_REF]. Paradoxically to this ongoing genomic reduction, rickettsial genomes exhibit another marker of convergent evolution, i. e., the expansion of genetic elements including small RNAs, tandem repeats, short palindromic elements named rickettsia palindromic elements (RPEs) [START_REF] Ogata | Protein coding palindromes are a unique but recurrent feature in Rickettsia[END_REF], ankyrin and tetratricopeptide repeats and gene family duplication mainly ADP-ATP translocases, toxin-antitoxin modules and type IV secretion system (T4SS).

Another unexpected property of rickettsial genomes is the presence of plasmids, the first described in obligate intracellular bacteria. The first plasmid was identified in R. felis (Ogata et al., 2005a). To date, at least 20 rickettsial plasmids have been described in 11 species. Their number varies from 1 to 4 per species/strain [START_REF] Baldridge | Transposon insertion reveals pRM, a plasmid of Rickettsia monacensis[END_REF]G. Blanc et al., 2007;[START_REF] El Karkouri | Genome sequence of the tick-borne pathogen Rickettsia raoultii[END_REF]. These findings suggest possible exchanges of genetic material by conjugation, a mechanism that was thought to be absent in obligate intracellular and allopatric bacteria [START_REF] Georgiades | Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules[END_REF][START_REF] Merhej | Massive comparative genomic analysis reveals convergent evolution of specialized bacteria[END_REF]Ogata et al., 2005a).

Rickettsia genome in an ongoing convergent evolution

Ongoing reductive evolution of Rickettsial genomes

Following their adaptation from a free-living to an obligate intracellular lifestyle in eukaryotic cells, rickettsiae underwent genomic changes to fit their specific bottleneck ecosystem, resulting not only in a reducing genome size but also in a specific genomic architecture [START_REF] Keeling | Archaebacterial genomes: eubacterial form and eukaryotic content[END_REF][START_REF] Sicheritz-Pontén | GRS: a graphic tool for genome retrieval and segment analysis[END_REF]. Comparative genomics revealed that rickettsiae, by taking advantage of host cell metabolites, underwent a genome reductive evolution [START_REF] Georgiades | Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules[END_REF][START_REF] Merhej | Massive comparative genomic analysis reveals convergent evolution of specialized bacteria[END_REF] that occurred through a progressive pseudogenization (Fig. 2) and gene loss of selected biosynthetic pathway components (Andersson et al., 1998;[START_REF] Audia | Study of the five Rickettsia prowazekii proteins annotated as ATP/ADP translocases (Tlc): only Tlc1 transports ATP/ADP, while Tlc4 and Tlc5 transport other ribonucleotides[END_REF][START_REF] Fournier | Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction[END_REF][START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF][START_REF] Sakharkar | Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis[END_REF][START_REF] Walker | Progress in rickettsial genome analysis from pioneering of Rickettsia prowazekii to the recent Rickettsia typhi[END_REF][START_REF] Wolf | Genome reduction as the dominant mode of evolution: prospects & overviews[END_REF]. In addition, genomic degradation was detrimental for the G+C content, as it led to an enrichment in A+T, in particular in the high proportion of non-coding DNA [START_REF] Sakharkar | Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis[END_REF]. However, a great variation in chromosome size, ranging from 1.1 to 2.3 Mb, is observed in rickettsiae [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF], indicating that some species are at a more advanced stage of reductive genomic evolution (TG rickettsiae) than others (SFG rickettsiae) [START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF]. In ehrlichiae, a similar genomic reduction is observed, but the G+C content may remain as high as 49.8% in Anaplasma species [START_REF] Dunning Hotopp | Comparative genomics of emerging human ehrlichiosis agents[END_REF], suggesting that the reductive process in these bacteria had a lesser impact on the G+C content degradation. Rickettsial genomes are characterized by a high rate of accumulation of slightly harmful deletions, mutations and insertions [START_REF] Brynnel | Evolutionary rates for tuf genes in endosymbionts of aphids[END_REF]. Alternatively, gene loss can also result from the accumulations of small mutations. The formation of internal stop codons within intact genes can occur through the creation of a frameshit by single base mutation, insertion or deletion [START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF]. This induces the genome degradation resulting from fragmented gene accumulation or gene remnants. An unexpected finding of rickettsial genomics was that the most virulent species had the most reduced genomes [START_REF] Fournier | Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction[END_REF]. Such a finding is not an isolated phenomenon as in Mycobacterium, Streptococcus spp., Corynebacterium spp. and other genera, the highest degree of gene loss is observed in the most virulent species when compared to closely related and milder or nonpathogenic species (Blanc et al., 2007;[START_REF] Merhej | Postgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factors[END_REF][START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF]. Many of the genes required by free-living bacteria are absent in Rickettsia [START_REF] Bechah | Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities[END_REF] and degraded genes include mostly those involved in the biosynthesis of nutrients [START_REF] Blanc | Molecular evolution of Rickettsia surface antigens: evidence of positive selection[END_REF][START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF][START_REF] Renesto | Some lessons from Rickettsia genomics[END_REF]. For example, Rickettsia exhibits few genes for de novo nucleotide synthesis, i. e., only those for conversion of nucleoside monophosphates into all other nucleotides, implying that they take up nucleoside monophosphates from the host [START_REF] Wixon | Featured organism: reductive evolution in bacteria: Buchnera sp., Rickettsia prowazekii and Mycobacterium leprae[END_REF]. Analysis of R. conorii and R. prowazekii genomes [START_REF] Dunning Hotopp | Comparative genomics of emerging human ehrlichiosis agents[END_REF][START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF] revealed that genes coding glycolytic enzymes and those required for nucleotide or cofactor biosynthesis are totally absent in R. conorii and R. prowazekii when compared to most genera in the order Rickettsiales that have complete glycolytic pathways. Nevertheless, rickettsiae must obtain glycerol-3-phosphate from the host via a glycerol-3-phosphate transporter [START_REF] Dunning Hotopp | Comparative genomics of emerging human ehrlichiosis agents[END_REF]. This ATP production profile is similar for Rickettsia and mitochondria, as they possess a high number of ATP/ADP translocases, suggesting that they have both evolved from a common ancestor (Andersson et al., 1998;[START_REF] Renesto | Some lessons from Rickettsia genomics[END_REF]. In addition, the genome sequencing of R. prowazekii revealed a lack of amino acid metabolism such as those for glutamate metabolism (Andersson et al., 1998;[START_REF] Fuxelius | The genomic and metabolic diversity of Rickettsia[END_REF]. The enzymes involved in the aspartate and alanine metabolism pathways, and those playing a role in the biosynthesis of leucine, valine, isoleucine and aromatic amino acids (tryptophan, tyrosine, phenylalanine) are similarly missing in Rickettsia species [START_REF] Renesto | Some lessons from Rickettsia genomics[END_REF], suggesting the use of host-derived amino acids for their growth, survival and replication. Additionally, all Rickettsia species except R. belli have a reduced set of folate biosynthesis genes (Fuxelius et al., 2007). In TG rickettsiae all five genes required for the de novo folate biosynthesis are lacking [START_REF] Hunter | The Rickettsia endosymbiont of Ixodes pacificus contains all the genes of de novo folate biosynthesis[END_REF]. Furthermore, a limited set of genes for LPS and cell wall component biosynthesis, including lipid-A and peptidoglycan, respectively, were identified in Rickettsia species [START_REF] Fuxelius | The genomic and metabolic diversity of Rickettsia[END_REF]. The rickettsial surface protein-coding genes rickA and sca2 are another example of genes that were degraded or eliminated by Rickettsia species during their specialization. The RickA protein participates in actin polymerization through the activation of Arp2/3 similar to that found in Listeria monocytogenes and Shigella spp. (Balraj et al., 2008b;[START_REF] Gouin | The RickA protein of Rickettsia conorii activates the Arp2/3 complex[END_REF][START_REF] Gouin | A comparative study of the actin-based motilities of the pathogenic bacteria Listeria monocytogenes, Shigella flexneri and Rickettsia conorii[END_REF]. While lacking in the TG, rickA is present in all AG and SFG rickettsial genomes avalaible [START_REF] Baldridge | Analysis of fluorescent protein expression in transformants of Rickettsia monacensis, an obligate intracellular tick symbiont[END_REF]Balraj et al., 2008aBalraj et al., , 2008b;;[START_REF] Heinzen | Directional actin polymerization associated with spotted fever group Rickettsia infection of vero cells[END_REF][START_REF] Jeng | A Rickettsia WASP-like protein activates the Arp2/3 complex and mediates actinbased motility: Rickettsia RickA activates the Arp2/3 complex[END_REF][START_REF] Mcleod | Complete Genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae[END_REF][START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF][START_REF] Ogata | Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens[END_REF]Ogata et al., , 2005a)). The absence of rickA in R. prowazekii is not surprising if we consider its lack of actin motility. In contrast, R. typhi exhibits a unique and erratic actin-based motility despite having a nonfunctional RickA protein [START_REF] Mcleod | Complete Genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae[END_REF][START_REF] Reed | Rickettsia actin-based motility occurs in distinct phases mediated by different actin nucleators[END_REF]. In addition, R. canadensis expresses RickA but does not exhibit actin-based motility [START_REF] Heinzen | Directional actin polymerization associated with spotted fever group Rickettsia infection of vero cells[END_REF]. These data suggest the possible involvement of other actin polymerization mechanisms and that RickA alone may not be sufficient or required for actin-based rickettsial motility.

Nevertheless, it was proposed that RickA originated early in rickettsial evolution and may have been lost during the divergence of the TG. Recent research suggests that Rickettsia spp. use also Sca2 for actin-based motility with a distinct mechanism compared to RickA. Sca2 was found to be intact in R. conorii, absent in R. prowazekii and pseudogenized in R. typhi [START_REF] Mcleod | Complete Genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae[END_REF]. In R. typhi, Sca2 lacks the FH1 (formin homology 1) domain and contains only a proline-rich tract and a series of five WH2 domains (β-domains) in different locations with a divergence in sequences [START_REF] Sears | Surface proteome analysis and characterization of surface cell antigen (Sca) or autotransporter family of Rickettsia typhi[END_REF]. The evolutionary process of genome degradation in rickettsiae led to loss of transcriptional regulator genes with a decreased translational capacity as observed in R. prowazekii (Andersson and Kurland, 1998), despite conserved gene sets coding for toxins, toxin-antitoxin (TA) modules and recombination and DNA repair proteins most likely needed for protection against host immune response [START_REF] Moran | Microbial minimalism: genome reduction in bacterial pathogens[END_REF].

The reductive evolution of rickettsial genomes is not only the consequence of gene degradation or loss, but it is also linked to a differential expression level of genes [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF]. Some genes under the influence of evolutionary forces are dormant or repressed while others under this effect are overexpressed. Recent research involving two virulent and two milder SFG rickettsiae demonstrated that the two virulent agents R. conorii (MSF) and R. slovaca (SENLAT) have the most reduced genome and displayed less up-regulated than down-regulated genes than the milder R. massiliae and R. raoultii causing MSF and SENLAT, respectively [START_REF] El Karkouri | Multiomics analysis sheds light on the evolution and the intracellular lifestyle strategies of spotted fever group Rickettsia spp[END_REF], that have less reduced genomes.

Consequently, to adapt to their specific intracellular environment, Rickettsia species were shaped by distinct evolutionary processes. The most pathogenic species are characterized by a strong reductive genomic evolution, with a higher genome degradation rate and accumulation of non-coding DNA than less pathogenic species. These findings suggest that reductive genomic evolution, resulting in protein structural variations, is associated to the emergence of virulence [START_REF] El Karkouri | Multiomics analysis sheds light on the evolution and the intracellular lifestyle strategies of spotted fever group Rickettsia spp[END_REF]. It was speculated that the loss of regulator genes, as observed in several intracellular pathogens, is a critical cause of virulence [START_REF] Darby | Intracellular pathogens go extreme: genome evolution in the Rickettsiales[END_REF]. This reductive genomic evolution appears to have occurred in several other human pathogens that have no common intracellular ancestor with Rickettsia such as Treponema spp., Mycobacterium spp. or Yersinia spp [START_REF] Merhej | Massive comparative genomic analysis reveals convergent evolution of specialized bacteria[END_REF][START_REF] Walker | Progress in rickettsial genome analysis from pioneering of Rickettsia prowazekii to the recent Rickettsia typhi[END_REF][START_REF] Wixon | Featured organism: reductive evolution in bacteria: Buchnera sp., Rickettsia prowazekii and Mycobacterium leprae[END_REF].

Overall, during the course of evolution, rickettsial genomes exhibit a trend toward gene loss rather than acquisition, but strong selective effects co-exist with functional duplication required for survival.

Gene order, recombination events and ''junk DNA'' in rickettsial genomes

A comparison of 13 rickettsial genomes [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF] demonstrated that they exhibit a highly conserved synteny and present few genomic rearrangements, except for R. bellii that exhibits little colinearity with other genomes, and R. felis that underwent several inversions.

In addition, R. typhi, underwent a 35-kb inversion close to the replication terminus and a specific 124-kb inversion nearby the origin of replication when compared to R. prowazekii and R. conorii [START_REF] Mcleod | Complete Genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae[END_REF]. As in other bacteria, inversions that occured in the origin of replication region are also found in R. australis, R. helvetica and R. honei (X. Dong et al., 2012;Xin Dong et al., 2012;[START_REF] Xin | Genomic comparison of Rickettsia honei strain RBT and other Rickettsia Species[END_REF], indicating that this region constitutes a hotspot for genomic rearrangement [START_REF] Eisen | Evidence for symmetric chromosomal inversions around the replication origin in bacteria[END_REF]. Homologous intra-chromosomal recombination, the principal mechanism for genomic rearrangement in rickettsiae, occured between repeated sequences or by site-specific recombination. Consequently, duplications, deletions and inversions arose through these structures (Andersson and Kurland, 1998;[START_REF] Krawiec | Organization of the bacterial chromosome[END_REF]). Such events have been observed in Rickettsia spp., in the so-called super-ribosomal protein gene operon. Highly conserved in a broad range of bacteria and archaea, this operon consists of about 40 genes located in seven operons in the same order [START_REF] Sicheritz-Pontén | GRS: a graphic tool for genome retrieval and segment analysis[END_REF]. Despite their conserved order in many bacteria including E. coli and Bacillus subtilis, genes in the ribosomal protein gene operon are scattered around the genomes of Haemophilus influenzae, Mycoplasma genitalium and R.

prowazeki (Andersson and Kurland, 1998;[START_REF] Fraser | The minimal gene complement of Mycoplasma genitalium[END_REF]. Ribosomal RNA genes in bacterial genomes are normally organized into an operon with a conserved order 16S-23S-5S, and tRNA genes are often found in the spacer between the 16S and the 23S rRNA genes [START_REF] Krawiec | Organization of the bacterial chromosome[END_REF]. However, an unusual arrangement of rRNA genes has been observed in all avalaible Rickettsia genomes, as the 16S rRNA gene is separated from the 23S and 5S rRNA gene cluster (Andersson et al., 1999;[START_REF] Munson | Buchnera aphidicola (a prokaryotic endosymbiont of aphids) contains a putative 16S rRNA operon unlinked to the 23S rRNA-encoding gene: sequence determination, and promoter and terminator analysis[END_REF]. A similar organization is observed in all members of the order Rickettsiales [START_REF] Dunning Hotopp | Comparative genomics of emerging human ehrlichiosis agents[END_REF]. The upstream spacer of the rearranged 23S rRNA gene in some Rickettsia species contains short repetitive sequences that have been eliminated in other related species, suggesting that the rearrangement of rRNA genes occurred by intra-chromosomal recombination prior to speciation in Rickettsia spp. Rickettsial genome analysis highlighted a second major genomic rearrangement in rickettsiae, the elongation factor proteins (tuf and fus) being present in more than one copy in Rickettsia genomes [START_REF] Syvänen | A chimeric disposition of the elongation factor genes in Rickettsia prowazekii[END_REF]. These genes can serve as repeat sequences, and initiate a rapid gene loss through intra-chromosomal recombination [START_REF] Krawiec | Organization of the bacterial chromosome[END_REF]. In addition, the degree and positions of deletions caused by intra-chromosomal recombination in Rickettsia is different among the species, which suggests that the homologous recombination is an ongoing process that may result in an ongoing genes loss under weak or no selection pressure.

When compared to other bacterial genomes, rickettsial genomes have a high percentage of non-coding DNA sequences which also contains many DNA repeat sequences [START_REF] Holste | Are noncoding sequences of Rickettsia prowazekii remnants of ``neutralized'' genes?[END_REF][START_REF] Rogozin | Congruent evolution of different classes of non-coding DNA in prokaryotic genomes[END_REF]. Non-coding DNA in rickettsial genomes is traditionally considered as "junk DNA" resulting from gene degradation. R. prowazekii and R. typhi, the most reduced rickettsial genomes, harbor high rates of non-coding DNA with 24.6 and 23.7%, respectively. However, R. bellii exhibits the lowest rickettsial level of non-coding DNA with 14.8% [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF].

Paradoxical genomic expansions

From a general point of view, rickettsial genomes are typical of those of symbiotic bacteria, in which the reductive trend is the dominant mode of evolution (Andersson and Andersson, 1999;[START_REF] Georgiades | Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules[END_REF][START_REF] Merhej | Massive comparative genomic analysis reveals convergent evolution of specialized bacteria[END_REF][START_REF] Ogata | Rickettsia felis, from culture to genome sequencing[END_REF]. However, despite this reductive evolution, a paradoxical expansion of genetic elements can still occur in rickettsial genomes [START_REF] Ogata | Protein coding palindromes are a unique but recurrent feature in Rickettsia[END_REF]. Genome sequence analysis revealed that rickettsial genome expansion may occur through proliferation of selfish DNA (small non coding RNAs (sRNAs) and rickettsia palindromic elements (RPEs)), gene duplications and horizontal gene transfer [START_REF] Merhej | Rickettsial evolution in the light of comparative genomics[END_REF]. Bacterial non-coding RNAs, whose biogenesis is predominantly attributed to either the intergenic regions (trans-acting) or to the antisense strand of an open reading frame (cis-acting) [START_REF] Schroeder | Bacterial small RNAs in the genus Rickettsia[END_REF], were well documented in many bacterial taxa including Enterobacteriaceae, Listeria monocytogenes, Clostridium perfringens, Staphylococcus aureus, Pseudomonas aeruginosa and Mycobacterium tuberculosis [START_REF] Papenfort | Target activation by regulatory RNAs in bacteria[END_REF]. sRNAs are classified among the most important post-transcriptional regulators involved in virulence and adaptation depending on the host niche, through transcriptomic regulation [START_REF] Schroeder | Bacterial small RNAs in the genus Rickettsia[END_REF]. [START_REF] Schroeder | Bacterial small RNAs in the genus Rickettsia[END_REF] were the first to identify sRNAs in Rickettsia species. Twenty to 30% of intergenic regions presumably encode for trans-acting sRNAs (14 to 191 sRNAs, depending on species). These findings may explain the highly conserved intergenic spacers identified by early comparative studies in Rickettsia [START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF]. More than 1,700 trans-acting sRNAs were predicted in 16 genomes of 13 species spanning all rickettsial groups [START_REF] Schroeder | Bacterial small RNAs in the genus Rickettsia[END_REF].

Rickettsia prowazekii was shown to possess stem loop structures after homopolymeric poly(T) stretches in the termination sites where the expression of sRNAs occurs [START_REF] Woodard | Analysis of convergent gene transcripts in the obligate intracellular bacterium Rickettsia prowazekii[END_REF]. Rickettsia palindromic elements (RPEs) were identified in 2002 by Ogata et al. [START_REF] Ogata | Protein coding palindromes are a unique but recurrent feature in Rickettsia[END_REF]. These genetic elements are more abundant in SFG than TG rickettsiae (Figure 2). In the R. conorii genome, a total of 656 RPEs, classified into 8 families, were identified (RPE-1 to RPE-8) and represent 3.2% of the entire genome [START_REF] Ogata | Protein coding palindromes are a unique but recurrent feature in Rickettsia[END_REF]. By comparison, only 10 of the 44 RPE-1 copies described in R. conorii were found in the R. prowazekii genome. Surprisingly, nine of these 10 RPE-1 copies that are present in R. prowazekii are inserted in protein-coding genes, versus 19/44 in R. conorii. In addition, the RPE-1s inserted into protein-coding genes have a position compatible with the 3-dimentional fold and function of proteins [START_REF] Ogata | Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens[END_REF]. This process of genomic evolution by inserting RPEs within protein-coding genes was initially thought to be unique to Rickettsia species but is also encountered in the Wolbachia genus (Ogata et al., 2005b;[START_REF] Riegler | Tandem repeat markers as novel diagnostic tools for high resolution fingerprinting of Wolbachia[END_REF]. Bacteria may use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. The presence of a mobile element inserted in many unrelated genes also suggests the potential role of selfish DNA in rickettsial genome for de novo creation of new protein sequences during the course of evolution, suggesting an implication in the dynamics of genome evolution [START_REF] Claverie | The insertion of palindromic repeats in the evolution of proteins[END_REF]. Moreover, genomic comparison also enabled the identification of several copies of Ankyrin and Tetratricopeptide (TPR)-repeats in rickettsiae. Such repeated elements are frequently found in endosymbionts and assumed to play a role in host-pathogen interaction [START_REF] Caturegli | ankA: an Ehrlichia phagocytophila group gene encoding a cytoplasmic protein antigen with ankyrin repeats[END_REF][START_REF] Felsheim | Genome sequence of the endosymbiont Rickettsia peacockii and comparison with virulent Rickettsia rickettsii: identification of virulence factors[END_REF][START_REF] Seshadri | Complete genome sequence of the Q-fever pathogen Coxiella burnetii[END_REF][START_REF] Wu | Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: A streamlined genome overrun by mobile genetic elements[END_REF]. Twenty-two copies of ankyrinand 11 copies of TPR-repeats were found in R. felis (Ogata et al., 2005a). In both species, they were proposed to be linked to pathogenicity. In Legionella pneumophila, which exhibits 20 Ankyrin-repeat copies and numerous TPR-repeat copies, these elements are suspected to play a modulatory role in the interactions with the host cytoskeleton and in interferences with the host cell trafficking events, respectively [START_REF] Cazalet | Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity[END_REF].

In addition to DNA repeat sequences, various gene families are duplicated in rickettsial genomes. Gene duplication was considered as an important source of bacterial adaptation to environmental changes in the host [START_REF] Hooper | On the nature of gene innovation: duplication patterns in microbial genomes[END_REF]. Following duplication, gene copies can evolve by conserving the same functions or undergoing mutations and becoming nonfunctional or assuming new functions, thus providing a putative new selective advantage in a new environment [START_REF] Greub | History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago[END_REF][START_REF] Walsh | How often do duplicated genes evolve new functions?[END_REF]. Rickettsia prowazekii, the most reduced and degraded rickettsial genome that lacks the genes encoding the biosynthesis of purines and pyrimidines (Andersson et al., 1998), exhibits five copies of tlc1 genes. These genes encode ADP/ATP translocases responsible of energy exploitation from host cells [START_REF] Greub | History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago[END_REF][START_REF] Renesto | Some lessons from Rickettsia genomics[END_REF]. Similar sequences were found in R. typhi, R. rickettsii and R. montanensis. Thus, the duplication of the tlc genes in Rickettsia is most likely explained by their important role in maintaining an efficient uptake and transport system of host cytoplasmic. ATP Four to 14 copies of spoT genes, involved in stringent response and the adaptation to intracellular environment, were also found in rickettsiae (Ogata et al., 2005a;[START_REF] Renesto | Some lessons from Rickettsia genomics[END_REF][START_REF] Rovery | Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation[END_REF]. The R. conorii genome has multiple copies of ampG agent encoding β-lactamase, which may explain the resistance of these bacteria to βlactam antibiotics [START_REF] Ogata | Mechanisms of evolution in Rickettsia conorii and R. prowazekii[END_REF]. The T4SS, a multiple component, membrane-spanning transporter system containing eight distinct classes such as the MPF-T class (P-T4SSs), is largely found in many rickettsial genomes. Rickettsiae possess an incomplete P-T4SS system (related to systems of the IncP group conjugative plasmid) that is characterized by the lack of virB5 but the duplication of the virB4, virB6, virB8 and virB9 genes [START_REF] Gillespie | The Rickettsia type IV secretion system: unrealized complexity mired by gene family expansion[END_REF].

The R. prowazekii genome has six Vir components (virB4, virB8-virB11, virD4), and the virB4 and virB9 were duplicated [START_REF] Gillespie | An Anomalous type IV secretion system in Rickettsia Is evolutionarily conserved[END_REF]. Seventeen orthologous surface cell antigen-coding genes (sca) were identified in rickettsial genomes [START_REF] Blanc | Molecular evolution of Rickettsia surface antigens: evidence of positive selection[END_REF]. SCA proteins autotransporter proteins that were demonstrated to play roles in mammalian cell infection as well as infection of their arthropod host cells, notably by promoting actin-based motility [START_REF] Sears | Surface proteome analysis and characterization of surface cell antigen (Sca) or autotransporter family of Rickettsia typhi[END_REF]. The R. bellii genome possesses a set of complete conjugation genes, and pilli like-filaments were observed on the bacterial surface [START_REF] Ogata | Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens[END_REF]. Among 13 tested Rickettsia collection strains, 11 got positive conjugation gene detection. This suggests that the conjugation elements are widely present among Rickettsia spp (88), and that horizontal gene transfer (HGT) occured at a high rate (Weinert et al., 2009). Within amoebae, HGTs have given the Rickettsia ancestor the access to novel gene pools, with possibility to acquire foreign DNA from other intracellular bacteria, thus, in capability of adaptation environment [START_REF] Ogata | Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens[END_REF]. In addition, a RAGE module, considered as a genetic exchange facilitator, was found in multiple copies in the genome from Rickettsia endosymbiont of Ixodes scapularis (REIS), the largest rickettsial genome described to date [START_REF] Gillespie | Secretome of obligate intracellular Rickettsia[END_REF][START_REF] Gillespie | A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle[END_REF].

Finally, a large number of mobile genetic elements (MGEs) referred to as mobilome are found in rickettsiae despite their reduced genome size. This mobilome, mostly consisting of plasmids, may ensure DNA movement within and between genomes. To date, at least 20 known rickettsial plasmids have been described in 11 species despite their allopatric lifestyle [START_REF] Diop | Rickettsial genomics and the paradigm of genome reduction associated with increased virulence[END_REF]. Recent phylogenomic analysis revealed that rickettsial plasmids are undergoing reductive evolutionary events similar to those affecting their co-residing chromosomes [START_REF] El Karkouri | Genome sequence of the tick-borne pathogen Rickettsia raoultii[END_REF]. Rickettsial plasmids were thus shaped by a biphasic model of convergent evolution including a strong reductive evolution as well as an increased complexity via horizontal gene transfer and gene duplication and genesis [START_REF] El Karkouri | Genome sequence of the tick-borne pathogen Rickettsia raoultii[END_REF]. The most reduced and virulent rickettsial genomes have probablely lost plasmid(s) during their evolution when compared to the related milder or non pathogenic species [START_REF] Darby | Intracellular pathogens go extreme: genome evolution in the Rickettsiales[END_REF][START_REF] El Karkouri | Multiomics analysis sheds light on the evolution and the intracellular lifestyle strategies of spotted fever group Rickettsia spp[END_REF]Ogata et al., 2005a).

Conclusions and Perspectives

Rickettsia species are strictly intracellular bacteria that are likely to have evolved from a presumably free-living ancestor and followed a transition to an obligate intracellular lifestyle.

To adapt to such a bottleneck lifestyle associated with genetic drift, Rickettsia species have been shaped by distinct evolutionary processes resulting not only in differences in genome size, but also in genomic architecture. Generally, rickettsial genomes are small and contain a high ratio of non-coding DNA, which suggests that the reductive trend is their dominant mode of evolution. Comparative sequence analysis has provided important clues on the mechanisms driving the genome-reduction process of Rickettsia spp. This phenomenon is marked by a selected loss of genes such as those associated with amino-acid, ATP, LPS and cell wall component biosynthesis with a loss of regulatory genes and a high preservation of toxinassociated proteins and toxin-antitoxin modules. Homologous intra-chromosomal recombination, principal mechanism for genomic rearrangement structures seems play a role in rapid gene loss. Consequently, rickettsiae have evolved under a distinct process including a strong reductive evolution as well as a paradoxical expansion of genetic elements acquired by horizontal gene transfer and gene duplication and genesis. Thus, during the course of evolution, rickettsial genomes had a trend of gene loss rather than gene acquisition or duplication, but these strong selective effects co-exist with functional duplications required for survival. In order to understand the evolution of genome size and content, it is necessary to understand the balance between proliferation and elimination of genetic material in these intracellular bacteria. (downloaded from GenBank), gene prediction was obtained using the Prokka software [START_REF] Seemann | Prokka: rapid prokaryotic genome annotation[END_REF]. The core genome was identified using the ProteinOrtho software [START_REF] Lechner | Proteinortho: detection of (co-) orthologs in large-scale analysis[END_REF]. Then, the amino acid sequences of 591 proteins (Supplementary Table )     conserved in all studied genomes were concatenated for each species and multiple alignment was performed using the Mafft software (Katoh and Standley, 2013, p. 2). Gapped positions were removed. The phylogenetic inferences were obtained using the Maximum Likelihood method and the MEGA software version 6 [START_REF] Tamura | MEGA6: Molecular evolutionary genetics analysis version 6.0[END_REF]. Branching support was evaluated using the bootstrap method with 1000 replications. Bootstrap values greater than 90% are shown at the nodes. Properties of each species were extracted from the following references (Andersson et al., 1998;G. Blanc et al., 2007;Guillaume Blanc et al., 2007b;[START_REF] El Karkouri | Multiomics analysis sheds light on the evolution and the intracellular lifestyle strategies of spotted fever group Rickettsia spp[END_REF], 2016;[START_REF] Fournier | Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction[END_REF][START_REF] Mcleod | Complete Genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae[END_REF]Ogata, 2001b;[START_REF] Ogata | Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens[END_REF]Ogata et al., , 2005a)). NA = data not available; RPEs = Rickettsia palindromic elements.

Supplementary Table: List of protein sequences used for inferring the phylogenomic relationshiops of ten

Figure 1 :

 1 Figure 1: Phylogenomic tree of 29 Rickettsia species based on whole-genome sequence

Figure 2 :

 2 Figure 2: Phylogenomic tree based on 591 core proteins and pathogenic and genomic

Rickettsia species exhibiting various degrees of pathogenesis and presented in Figure 2.

	cRIG00043 cRIG00091 cRIG00138 cRIG00186 cRIG00234 cRIG00282 cRIG00330 cRIG00378 cRIG00426 cRIG00474 cRIG00522 cRIG00569	iscU FeS cluster assembly scaffold IscU ftsZ Cell division protein ftsZ Putative metal-dependent hydrolase Iojap-related protein lipB Putative lipoate-protein ligase B abcTABC transporter ATP-binding protein hflK Protease activity modulator HflK coxC Cytochrome c oxidase subunit III pdhA Pyruvate dehydrogenase e1 component, alpha subunit precursor tdpX1 Thioredoxin peroxidase murG UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-ftsL Cell division protein FtsL	isc fts -lojap lip abcT hfl cox pdh tdpX mur fts
	Clusters ID cRIG00001 cRIG00002 cRIG00003 cRIG00004 cRIG00005 cRIG00006 cRIG00007 cRIG00008 cRIG00009 cRIG00010 cRIG00011 cRIG00012 cRIG00013 cRIG00014 cRIG00015 cRIG00016 cRIG00017 cRIG00018 cRIG00019 cRIG00020 cRIG00021 cRIG00022 cRIG00023 cRIG00024 cRIG00025 cRIG00026 cRIG00027 cRIG00028 cRIG00029 cRIG00030 cRIG00031 cRIG00032 cRIG00033 cRIG00034 cRIG00035 cRIG00036 cRIG00037 cRIG00038 cRIG00039 cRIG00040 cRIG00041 cRIG00042 cRIG00044 cRIG00045 cRIG00046 cRIG00047 cRIG00048 cRIG00049 cRIG00050 cRIG00051 cRIG00052 cRIG00053 cRIG00054 cRIG00055 cRIG00056 cRIG00057 cRIG00058 cRIG00059 cRIG00060 cRIG00061 cRIG00062 cRIG00063 cRIG00064 cRIG00065 cRIG00066 cRIG00067 cRIG00068 cRIG00069 cRIG00070 cRIG00071 cRIG00072 cRIG00073 cRIG00074 cRIG00075 cRIG00076 cRIG00077 cRIG00078 cRIG00079 cRIG00080 cRIG00081 cRIG00082 cRIG00083 cRIG00084 cRIG00085 cRIG00086 cRIG00087 cRIG00088 cRIG00089 cRIG00090 cRIG00092 cRIG00093 cRIG00094 cRIG00095 cRIG00096 cRIG00097 cRIG00098 cRIG00099 cRIG00100 cRIG00101 cRIG00102 cRIG00103 cRIG00104 cRIG00105 cRIG00106 cRIG00107 cRIG00108 cRIG00109 cRIG00110 cRIG00111 cRIG00112 cRIG00113 cRIG00114 cRIG00115 cRIG00116 cRIG00117 cRIG00118 cRIG00119 cRIG00120 cRIG00121 cRIG00122 cRIG00123 cRIG00124 cRIG00125 cRIG00126 cRIG00127 cRIG00128 cRIG00129 cRIG00130 cRIG00131 cRIG00132 cRIG00133 cRIG00134 cRIG00135 cRIG00136 cRIG00137 cRIG00139 cRIG00140 cRIG00141 cRIG00142 cRIG00143 cRIG00144 cRIG00145 cRIG00146 cRIG00147 cRIG00148 cRIG00149 cRIG00150 cRIG00151 cRIG00152 cRIG00153 cRIG00154 cRIG00155 cRIG00156 cRIG00157 cRIG00158 cRIG00159 cRIG00160 cRIG00161 cRIG00162 cRIG00163 cRIG00164 cRIG00165 cRIG00166 cRIG00167 cRIG00168 cRIG00169 cRIG00170 cRIG00171 cRIG00172 cRIG00173 cRIG00174 cRIG00175 cRIG00176 cRIG00177 cRIG00178 cRIG00179 cRIG00180 cRIG00181 cRIG00182 cRIG00183 cRIG00184 cRIG00185 cRIG00187 cRIG00188 cRIG00189 cRIG00190 cRIG00191 cRIG00192 cRIG00193 cRIG00194 cRIG00195 cRIG00196 cRIG00197 cRIG00198 cRIG00199 cRIG00200 cRIG00201 cRIG00202 cRIG00203 cRIG00204 cRIG00205 cRIG00206 cRIG00207 cRIG00208 cRIG00209 cRIG00210 cRIG00211 cRIG00212 cRIG00213 cRIG00214 cRIG00215 cRIG00216 cRIG00217 cRIG00218 cRIG00219 cRIG00220 cRIG00221 cRIG00222 cRIG00223 cRIG00224 cRIG00225 cRIG00226 cRIG00227 cRIG00228 cRIG00229 cRIG00230 cRIG00231 cRIG00232 cRIG00233 cRIG00235 cRIG00236 cRIG00237 cRIG00238 cRIG00239 cRIG00240 cRIG00241 cRIG00242 cRIG00243 cRIG00244 cRIG00245 cRIG00246 cRIG00247 cRIG00248 cRIG00249 cRIG00250 cRIG00251 cRIG00252 cRIG00253 cRIG00254 cRIG00255 cRIG00256 cRIG00257 cRIG00258 cRIG00259 cRIG00260 cRIG00261 cRIG00262 cRIG00263 cRIG00264 cRIG00265 cRIG00266 cRIG00267 cRIG00268 cRIG00269 cRIG00270 cRIG00271 cRIG00272 cRIG00273 cRIG00274 cRIG00275 cRIG00276 cRIG00277 cRIG00278 cRIG00279 cRIG00280 cRIG00281 cRIG00283 cRIG00284 cRIG00285 cRIG00286 cRIG00287 cRIG00288 cRIG00289 cRIG00290 cRIG00291 cRIG00292 cRIG00293 cRIG00294 cRIG00295 cRIG00296 cRIG00297 cRIG00298 cRIG00299 cRIG00300 cRIG00301 cRIG00302 cRIG00303 cRIG00304 cRIG00305 cRIG00306 cRIG00307 cRIG00308 cRIG00309 cRIG00310 cRIG00311 cRIG00312 cRIG00313 cRIG00314 cRIG00315 cRIG00316 cRIG00317 cRIG00318 cRIG00319 cRIG00320 cRIG00321 cRIG00322 cRIG00323 cRIG00324 cRIG00325 cRIG00326 cRIG00327 cRIG00328 cRIG00329 cRIG00331 cRIG00332 cRIG00333 cRIG00334 cRIG00335 cRIG00336 cRIG00337 cRIG00338 cRIG00339 cRIG00340 cRIG00341 cRIG00342 cRIG00343 cRIG00344 cRIG00345 cRIG00346 cRIG00347 cRIG00348 cRIG00349 cRIG00350 cRIG00351 cRIG00352 cRIG00353 cRIG00354 cRIG00355 cRIG00356 cRIG00357 cRIG00358 cRIG00359 cRIG00360 cRIG00361 cRIG00362 cRIG00363 cRIG00364 cRIG00365 cRIG00366 cRIG00367 cRIG00368 cRIG00369 cRIG00370 cRIG00371 cRIG00372 cRIG00373 cRIG00374 cRIG00375 cRIG00376 cRIG00377 cRIG00379 cRIG00380 cRIG00381 cRIG00382 cRIG00383 cRIG00384 cRIG00385 cRIG00386 cRIG00387 cRIG00388 cRIG00389 cRIG00390 cRIG00391 cRIG00392 cRIG00393 cRIG00394 cRIG00395 cRIG00396 cRIG00397 cRIG00398 cRIG00399 cRIG00400 cRIG00401 cRIG00402 cRIG00403 cRIG00404 cRIG00405 cRIG00406 cRIG00407 cRIG00408 cRIG00409 cRIG00410 cRIG00411 cRIG00412 cRIG00413 cRIG00414 cRIG00415 cRIG00416 cRIG00417 cRIG00418 cRIG00419 cRIG00420 cRIG00421 cRIG00422 cRIG00423 cRIG00424 cRIG00425 cRIG00427 cRIG00428 cRIG00429 cRIG00430 cRIG00431 cRIG00432 cRIG00433 cRIG00434 cRIG00435 cRIG00436 cRIG00437 cRIG00438 cRIG00439 cRIG00440 cRIG00441 cRIG00442 cRIG00443 cRIG00444 cRIG00445 cRIG00446 cRIG00447 cRIG00448 cRIG00449 cRIG00450 cRIG00451 cRIG00452 cRIG00453 cRIG00454 cRIG00455 cRIG00456 cRIG00457 cRIG00458 cRIG00459 cRIG00460 cRIG00461 cRIG00462 cRIG00463 cRIG00464 cRIG00465 cRIG00466 cRIG00467 cRIG00468 cRIG00469 cRIG00470 cRIG00471 cRIG00472 cRIG00473 cRIG00475 cRIG00476 cRIG00477 cRIG00478 cRIG00479 cRIG00480 cRIG00481 cRIG00482 cRIG00483 cRIG00484 cRIG00485 cRIG00486 cRIG00487 cRIG00488 cRIG00489 cRIG00490 cRIG00491 cRIG00492 cRIG00493 cRIG00494 cRIG00495 cRIG00496 cRIG00497 cRIG00498 cRIG00499 cRIG00500 cRIG00501 cRIG00502 cRIG00503 cRIG00504 cRIG00505 cRIG00506 cRIG00507 cRIG00508 cRIG00509 cRIG00510 cRIG00511 cRIG00512 cRIG00513 cRIG00514 cRIG00515 cRIG00516 cRIG00517 cRIG00518 cRIG00519 cRIG00520 cRIG00521 cRIG00568 cRIG00567 cRIG00566 cRIG00565 cRIG00564 cRIG00563 cRIG00562 cRIG00561 cRIG00560 cRIG00559 cRIG00558 cRIG00557 cRIG00556 cRIG00555 cRIG00554 cRIG00553 cRIG00552 cRIG00551 cRIG00550 cRIG00549 cRIG00548 cRIG00547 cRIG00546 cRIG00545 cRIG00523 cRIG00570 cRIG00524 cRIG00571 cRIG00525 cRIG00572 cRIG00526 cRIG00573 cRIG00527 cRIG00574 cRIG00528 cRIG00575 cRIG00529 cRIG00576 cRIG00530 cRIG00577 cRIG00531 cRIG00578 cRIG00532 cRIG00579 cRIG00533 cRIG00580 cRIG00534 cRIG00581 cRIG00535 cRIG00582 cRIG00536 cRIG00583 cRIG00537 cRIG00584 cRIG00538 cRIG00585 cRIG00539 cRIG00586 cRIG00540 cRIG00587 cRIG00541 cRIG00588 cRIG00542 cRIG00589 cRIG00543 cRIG00590 cRIG00544 cRIG00591	Protein function rnpA Ribonuclease P rplT 50S ribosomal protein L nrdG Organic radical activating enzymes rplY 50S ribosomal protein L ychF GTP-binding protein YchF murE UDP-N-acetylmuramoylalanyl-D-glutamate--, 2,6-diaminopimelate ligase murF UDP-N-acetylmuramoylalanyl-D-glutamyl-, 2,6-diaminopimelate--D-alanyl-D-alanyl ligase mraY1 Phospho-N-acetylmuramoyl-pentapeptide-transferase recG ATP-dependent DNA helicase RecG traX F pilin acetylation protein TraX mviN Integral membrane protein MviN ppa Inorganic pyrophosphatase ccmE Cytochrome c-type biogenesis protein ccmE Sco2 protein precursor secD Protein-export membrane protein secD yajC Preprotein translocase YajC subunit gyrB DNA gyrase subunit B murA UDP-N-acetylglucosamine -1-carboxyvinyltransferase surA Parvulin-like peptidyl-prolyl isomerase secA Preprotein translocase secA subunit Unknown uvrC Excinuclease ABC subunit C cmk Cytidylate kinase rpsA 30S ribosomal protein S1 clpP ATP-dependent Clp protease proteolytic subunit glmU UDP-N-acetylglucosamine pyrophosphorylase Unknown Unknown lpdA2 Dihydrolipoamide dehydrogenase 5 -Formyltetrahydrofolate cyclo-ligase rnd Ribonuclease D gcvT Glycine cleavage T-protein putP Na+/proline symporter and signal transduction histidine kinase hemC Porphobilinogen deaminase trpS Tryptophanyl-tRNA synthetase plsC 1-acyl-sn-glycerol--phosphate acyltransferase ampG1 AmpG tlc3 ATP/ADP translocase Unknown ispB Octaprenyl-diphosphate synthase potE Putrescine-ornithine antiporter iscA2 Iron-sulfur cluster assembly accessory protein iscS Cysteine desulfurase IscS spl1 NifS-like protein Unknown ntrY Nitrogen regulation protein NtrY rpsU 30S ribosomal protein S Unknown ileS Isoleucyl-tRNA synthetase accC Acetyl-CoA carboxylase, biotin carboxylase pccB Propionyl-CoA carboxylase beta chain precursor aas2 -acylglycerophosphoethanolamine acyltransferase znuB Zinc/manganese ABC transporter permease protein ubiG Ubiquinone biosynthesis O-methyltransferase gltX Glutamyl-tRNA synthetase groEL 60 kD chaperonin groES 10 kD chaperonin rph Ribonuclease PH grpE GrpE protein perM Permease PerM-like protein DnaA-like protein rplQ 50S ribosomal protein L17 rpoA DNA-directed RNA polymerase alpha chain rpsK 30S ribosomal protein S11 rpsM 30S ribosomal protein S13 adk Adenylate kinase secY Preprotein translocase secY subunit rplO 50S ribosomal protein L15 rpmD 50S ribosomal protein L30 rpsE 30S ribosomal protein S5 rplR 50S riboSomal protein L18 rplF 50S riboSomal protein L6 rp30SH 30S riboSomal protein S8 rp30SN 30S riboSomal protein S14 rplE 50S riboSomal protein L5 rplX 50S riboSomal protein L24 rplN 50S ribosomal protein L14 rpsQ 30S ribosomal protein S17 rpmC 50S ribosomal protein L29 rplP 50S ribosomal protein L16 rpsC 30S ribosomal protein S3 rplV 50S ribosomal protein L22 rpsS 30S ribosomal protein S19 rplB 50S ribosomal protein L2 rplW 50S ribosomal protein L23 rplD 50S ribosomal protein L4 rpsJ 30S ribosomal protein S10 tuf Elongation factor EF-Tu fumC Fumarate hydratase NifU-like protein ampG2 AmpG rhlE ATP-dependent RNA helicase RhlE cspA Cold shock-like protein ksgA Dimethyladenosine transferase Unknown ostA Organic solvent tolerance protein-like protein xseA Exodeoxyribonuclease VII, large subunit xth2 Exodeoxyribonuclease III GTP-binding protein ubiB 2-polyprenylphenol -hydroxylase ubiE Ubiquinone/menaquinone biosynthesis methlytransferase UbiE Unknown tatD Putative deoxyribonuclease TatD metG Methionyl-tRNA synthetase tmk1Thymidylate kinase proP4 Proline/betaine transporter ubiA 4-hydroxybenzoate octaprenyltransferase valS Valyl-tRNA synthetase RmuC family protein exsB Trans-regulatory protein ExsB msbA2 Multidrug resistance protein Unknown bcr2 MFS-type bicyclomycin resistance protein Lipoprotein releasing system, transmembrane protein, LolC/E family protein lolD Lipoprotein releasing system ATP-binding protein LolD Unknown Hemolysin-like protein ccmF Cytochrome c-type biogenesis protein ccmF ompB, sca5 Outer membrane protein rOmpB Beta-glucosidase lpxK Tetraacyldisaccharide 4'-kinase ligA DNA ligase, NAD-dependent tgt Queuine tRNA-ribosyltransferase ABC transporter substrate binding protein NADHubiquinone oxidoreductase 17,2 kD subunit rnhA Ribonuclease H Unknown Unknown coaE Dephospho-CoA kinase dnaQ DNA polymerase III epsilon chain surf1 Surfeit locus protein ATP-dependent helicase fabD Malonyl CoA-acyl carrier protein transacylase tlc5 ATP/ADP translocase tlyC Hemolysin C lipA Lipoic acid synthetase glyA Glycine/serine hydroxymethyltransferase Serine esterase nth Endonuclease III Putative methyltransferase ABC-type transport systems periplasmic component tatA Twin-arginine translocation protein TatA pgpA Phosphatidylglycerophosphatase A rplU 50S ribosomal protein L21 rpmA 50S ribosomal protein L27 Unknown proP5 Proline/betaine transporter NAD-specific glutamate dehydrogenase trmE tRNA modification GTPase TrmE recA RecA fabG 3-oxoacyl reductase acpP Acyl carrier protein fabF 3-oxoacyl-mreC Rod shape-determining protein MreC mreB Rod shape-determining protein MreB Putative permeases pal Peptidoglycan-associated lipoprotein precursor rpmF 50S ribosomal protein L32 smpA tmRNA-binding protein ftsY Signal recognition particle-docking protein FtsY polA DNA polymerase I dnaE DNA polymerase III alpha chain udg UDP-glucose 6-dehydrogenase Unknown ampG3 AmpG tatC Sec-independent protein translocase protein TatC serS Seryl-tRNA synthetase virB4-2 VirB4 Unknown terC Tellurium resistance protein TerC nuoL1 NADH dehydrogenase I chain L nuoM NADH dehydrogenase I chain M ccmA Heme exporter protein A nuoI NADH dehydrogenase I chain I nuoH NADH dehydrogenase I chain H nuoG NADH dehydrogenase I chain G atpG ATP synthase gamma chain atpA ATP synthase alpha chain atpH ATP synthase delta chain lpdA1 Dihydrolipoamide dehydrogenase Unknown kefB Glutathione-regulated potassium-efflux system protein KefB bolA2 BolA-like protein infA Translation initiation factor IF-maf Nucleotide-binding protein implicated in inhibition of septum formation dksA DnaK suppressor-like protein xerC Tyrosine recombinase XerC hypothetical protein ftsK Cell division protein FtsK mraY2 Undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase Unknown Unknown Putative outer surface protein fdxA Ferredoxin ccmC Heme exporter protein C Cation diffusion facilitator family transporter omp 17 kD surface antigen precursor znuC Zinc ABC transporter ATP-binding protein uvrA Excinuclease ABC subunit A ssb Single-stranded DNA-binding protein DAP dipeptidyl aminopeptidase/acylaminoacyl-peptidase-like protein htpG Heat shock protein htpG hemA 5-aminolevulinic acid synthase tig Trigger factor obg GTP-binding protein gltA Citrate synthase I Uracil-DNA glycosylase, family Ribosomal large subunit pseudouridine synthases RluD subfamily protein hemK Methylase of polypeptide chain release factors Sua5/YciO/YrdC/YwlC family putative translation factor protein glyS Glycyl-tRNA synthetase beta chain glyQ Glycyl-tRNA synthetase alpha chain Unknown Unknown dnaG DNA primase sec59 Dolichol kinase greA Transcription elongation factor GreA pntA2 NAD(P) transhydrogenase subunit alpha pntA1 NAD(P) transhydrogenase subunit alpha lolA Outer membrane lipoprotein-sorting protein LolA Unknown Putative aspartyl protease glnQ Glutamine ABC transporter ATP-binding protein phnP Metal-dependent hydrolases of the beta-lactamase superfamily I Unknown Putative permeases holC DNA polymerase III chi subunit HolC dapE Succinyl-diaminopimelate desuccinylase Unknown rpsP 30S ribosomal protein S16 mutL DNA mismatch repair protein MutL proP7 Proline/betaine transporter hemF Coproporphyrinogen III oxidase precursor Putative membrane protein hemH Putative ferrochelatase hemE Uroporphyrinogen decarboxylase Unknown trxA Thioredoxin rfbE O-antigen export system ATP-binding protein RfbE rfbA O-antigen export system permease protein RfbA gltD NADPH-dependent glutamate synthase beta chain and related oxidoreductases lpxA Acyl-fabZ (3R)-hydroxymyristoyl-lpxD UDP-3-O-Putative P-loop hydrolase znuA Zinc/manganese ABC transporter substrate binding protein pcnB Poly(A) polymerase atpF ATP synthase B chain atpX ATP synthase B chain atpE ATP synthase C chain atpB ATP synthase A chain Unknown dsbG Protein-disulfide isomerase Transcriptional regulator Unknown cvpA Putative colicin V production membrane protein clpB ClpB hypothetical protein rpsF 30S ribosomal protein S6 rpsR30 S ribosomal protein S18 rplI 50S ribosomal protein L9 tilS, mesJ tRNA(Ile)-lysidine synthetase ftsH ATP-dependent metalloprotease FtsH sdhB Succinate dehydrogenase iron-sulfur protein Unknown lgt Prolipoprotein diacylglyceryl transferase Putative membrane protein yidC Preprotein translocase subunit YidC pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase Unknown tlc1 ATP/ADP translocase uhpC Sugar phosphate permease ndk Nucleoside diphosphate kinase gidA Glucose-inhibited division protein A soj ATPase involved in chromosome partitioning ParB-like partition proteins Unknown kdsA -deoxy--phosphooctulonate synthase iscAIron-sulfur cluster assembly accessory protein dgt Deoxyguanosinetriphosphate triphosphohydrolase argS Arginyl-tRNA synthetase Unknown parC Topoisomerase IV subunit A Unknown dcd Deoxycytidine triphosphate deaminase secB Protein-export protein secB czcR Transcriptional activator protein CzcR GTP cyclohydrolase I Unknown pntB NAD(p) transhydrogenase subunit beta ompW OmpW family outer-membrane protein sam S-adenosylmethionine transporter proP1 Proline/betaine transporter cysS Cysteinyl-tRNA synthetase rpsB 30S ribosomal protein S2 tsf Elongation factor EF-Ts kdtA 3-deoxy-D-manno-octulosonic-acid transferase Unknown aatA Aspartate aminotransferase A Unknown vacJ VacJ lipoprotein precursor ABC-type transporter related to toluene tolerance alr Alanine racemase ABC transporter permease protein mkl Ribonucleotide ABC transporter ATP-binding protein rpmB 50S ribosomal protein L28 rpmE 50S ribosomal protein L31 Hypothetical GTP-binding protein virB3 VirB3 virB4-1 VirB4 virB6-3 VirB6 virB6-4 VirB6 virB6-5 VirB6 trmD tRNA (guanine-n1)-methyltransferase rplS 50S ribosomal protein L19 Unknown secF Protein-export membrane protein secF nuoF NADH dehydrogenase I chain F lepB Signal peptidase I era GTP-binding protein Era ruvC Crossover junction endodeoxyribonuclease RuvC Putative nucleoside-diphosphate-sugar epimerase mrp Mrp hflC2 Membrane protease subunit, stomatin/prohibitin-like protein htrA Periplasmic serine protease Putative sulfurtransferase sdhC Succinate dehydrogenase cytochrome b-556 subunit yqiY Amino acid ABC transporter permease protein rpsL 30S ribosomal protein S12 rpsG 30S ribosomal protein S7 fusA Elongation factor EF-G nusG Transcription antitermination protein NusG rplK 50S ribosomal protein L11 rplA 50S ribosomal protein L1 rplJ 50S ribosomal protein L10 rplL 50S ribosomal protein L7/L12 rpoB DNA-directed RNA polymerase beta chain rpoC DNA-directed RNA polymerase beta prime chain pepA Aminopeptidase A Chromosome partitioning protein-like protein aspS Aspartyl-tRNA synthetase Integral membrane protein, interacts with FtsH yqiX Amino acid ABC transporter substrate binding protein gatA Glutamyl-tRNA(Gln) amidotransferase subunit A gatC Glutamyl-tRNA(Gln) amidotransferase subunit C rrf Ribosome recycling factor pyrH Uridylate kinase mnhE Multisubunit Na+/H+ antiporter, MnhE subunit emrB MFS-type multidrug resistance protein B (SPLIT GENE) omp1 Outer membrane protein omp Putative membrane-associated zinc metalloprotease nusB N utilization substance protein B rrmJ Ribosomal RNA large subunit methyltransferase J Oligoketide cyclase/lipid transport protein Unknown hupA DNA-binding protein HU holB DNA polymerase III delta subunit ffh Signal recognition particle protein gltP Na+/H+-dicarboxylate symporters Putative 6-pyruvoyl tetrahydropterin synthase sucB Dihydrolipoamide acetyltransferase component sucA2 -oxoglutarate dehydrogenase Ecomponent recN DNA repair protein RecN comL DNA uptake lipoprotein dnaJ DnaJ dnaK DnaK Heat shock protease Unknown holA DNA polymerase III, delta subunit coq7 Ubiquinone biosynthesis protein coq virB2 VirB2-like protein RafdapD 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase uspA Universal stress protein UspA and related nucleotide-binding proteins imp TRAP-type uncharacterized transport system, periplasmic component Unknown hscA Heat shock protein hscA rnhB Ribonuclease HII uvrB Excinuclease ABC subunit B grxC1 Glutaredoxin, GrxC family atm1 Multidrug resistance protein Atm gyrA DNA gyrase subunit A def1 Polypeptide deformylase fmt Methionyl-tRNA formyltransferase abcT3 Multidrug resistance ABC transporter ATP-binding protein Unknown cydA Cytochrome d ubiquinol oxidase subunit I thrS Threonyl-tRNA synthetase Unknown tolC Type I secretion outer membrane protein TolC Unknown Ankyrin repeat parE DNA topoisomerase IV, B subunit ctp Carboxyl-terminal protease barA Histidine kinase sensor protein Unknown Unknown WD40-like repeat rplM 50S ribosomal protein L13 rpsI 30S ribosomal protein S9 nudH (Di)nucleoside polyphosphate hydrolase Regulatory components of sensory transduction system efp Translation elongation factor EF-P suhB Extragenic suppressor protein suhB Unknown psd Phosphatidylserine decarboxylase pssA CDP-diacylglycerol--serine O-phosphatidyltransferase hypothetical protein Unknown bolA1 BolA-like protein EAL domain containing protein murC UDP-N-acetylmuramate--alanine ligase murB UDP-N-acetylenolpyruvoylglucosamine reductase ddlB D-alanine--D-alanine ligase Membrane protein implicated in regulation of membrane protease activity cycM Cytochrome c lpxC UDP-3-O-xth1 Exodeoxyribonuclease III pdhB Pyruvate dehydrogenase E1 component, beta subunit precursor typA GTP-binding protein TypA hlpA Outer membrane protein icd Isocitrate dehydrogenase, NADP-dependent Monovalent cation/proton antiporter, MnhG/PhaG subunit mnhB Multisubunit Na+/H+ antiporter, MnhB subunit ccmB Heme exporter protein B Unknown petA Ubiquinol-cytochrome c reductase, iron-sulfur subunit petB Cytochrome b fbcH Cytochrome c1, heme protein precursor nuoL2 NADH dehydrogenase I chain L nuoN2 NADHubiquinone oxidoreductase subunit (chain N) mnhC Multisubunit Na+/H+ antiporter, MnhC subunit virB8-1VirB8 virB8-2 VirB8 virB9-2 VirB9 virD4 VirD4 gppA Guanosine pentaphosphate phosphohydrolase Unknown Unknown cysQ 3'(2'),'5-bisphosphate nucleotidase mutS DNA mismatch repair protein MutS lacA Ribose-5-phosphate isomerase nlpD1 Membrane-bound metallopeptidase thyX Thymidylate synthase, flavin-dependent tolB TolB protein precursor hypothetical protein cox11, ctaG Cytochrome c oxidase assembly protein cox 11 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase atrC1 Cationic amino acid transporter-1 hisS Histidyl-tRNA synthetase tolQ TolQ tolR TolR Periplasmic protein TonB, links inner and outer membranes proP10 Proline/betaine transporter HlyD family secretion protein aprD Alkaline protease secretion ATP-binding protein AprD asd Aspartate-semialdehyde dehydrogenase Unknown hslV Heat shock protein HslV hslU Heat shock protein HslVU, ATPase subunit HslU lpxB Lipid-A-disaccharide synthase Aminodeoxychorismate lyase cyaY CyaY gltX1 Glutamyl-tRNA synthetase topA DNA topoisomerase I hflC1 Membrane protease subunit, stomatin/prohibitin-like protein Putative membrane-associated metal-dependent hydrolase Efflux transporter, RND family, MFP subunit Putative hydrolase/acyltransferase Glycosyltransferase rpsD 30S ribosomal protein S4 cyoB, ctaB Protoheme IX farnesyltransferase rimM 16S rRNA processing protein RimM Unknown xseB Exodeoxyribonuclease VII small subunit mpg DNA-3-methyladenine glycosidase nuoE NADH dehydrogenase I chain E nuoD NADH dehydrogenase I chain D nuoC NADH dehydrogenase I chain C nuoA NADH dehydrogenase I chain A cutE Apolipoprotein N-acyltransferase lysS Lysyl-tRNA synthetase Putative permease tme Malate oxidoreductase proP3 Proline/betaine transporter mdh Malate dehydrogenase tlc2 ATP/ADP translocase pyrG CTP synthase kdsB 3-deoxy-manno-octulosonate cytidylyltransferase folE GTP cyclohydrolase I proS Prolyl-tRNA synthetase ruvB Holliday junction DNA helicase RuvB msbA1 Multidrug resistance protein dacF Penicillin-binding protein dacF precursor rlpA Rare lipoprotein A precursor osmY Putative periplasmic or secreted lipoprotein ispZ Intracellular septation protein A FTR1 family protein Unknown Unknown Protocatechuate-3,4-dioxygenase, beta subunit tlpA Thioldisulfide interchange protein tlpA sppA1 Signal peptide peptidase SppA, 36K type dut Deoxyuridine 5'-triphosphate nucleotidohydrolase mltESoluble lytic murein transglycosylase precursor mccF Microcin C7 self-immunity protein RecB family exonuclease Putative glutamine amidotransferase coxA Cytochrome c oxidase polypeptide I coxB Cytochrome c oxidase polypeptide II nlpD2 Membrane-bound metallopeptidase ftsW Cell division protein ftsW mraW S-adenosyl-methyltransferase MraW mraZ MraZ protein rho Transcription termination factor birA Biotin-(acetyl-CoA carboxylase) ligase rssA Putative esterase of the alpha/beta hydrolase superfamily protein sodB Superoxide dismutase folC Folylpolyglutamate synthase Glutathione S-transferase ppdK Pyruvate,phosphate dikinase precursor Unknown glnA Glutamine synthetase sca Cell surface antigen Sca tlc4 ATP/ADP translocase truB tRNA pseudouridine synthase B rpsO 30S ribosomal protein S15 pnp Polyribonucleotide nucleotidyltransferase kpsF KpsF Unknown nrdB Ribonucleoside-diphosphate reductase beta chain nrdA Ribonucleoside-diphosphate reductase alpha chain trxB2 Thioredoxin reductase folD Methylenetetrahydrofolate dehydrogenase yhbH Putative sigma(54) modulation protein lon1 ATP-dependent protease La undecaprenol N-acetylglucosamine transferase Unknown pbpA2 Penicillin-binding protein Glycosyltransferase pbpA1 Penicillin-binding protein dapF Diaminopimelate epimerase Unknown MiaB-like tRNA modifying enzyme Unknown pheS Phenylalanyl-tRNA synthetase alpha chain ntrX Nitrogen assimilation regulatory protein NtrX pheT Phenylalanyl-tRNA synthetase beta chain ubiH 2-polyprenyl-6-methoxyphenol 4-hydroxylase dnaN DNA polymerase III beta chain nusA N utilization substance protein A, transcription termination factor NusA Unknown infB Translation initiation factor IF-2 rbfA Ribosome-binding factor A Putative glycoprotein endopeptidase Putative membrane protein Unknown RDD family protein N6-adenine-specific methylase recR Recombination protein RecR rluA2 Ribosomal large subunit pseudouridine synthase ppnK Putative inorganic polyphosphate/ATP-NAD kinase dnaB Replicative DNA helicase Putative hydrolase of the metallo-beta-lactamase superfamily ubiX 3-octaprenyl-4-hydroxybenzoate carboxy-lyase gpsA Glycerol--phosphate dehydrogenase priA Primosomal protein N' Putative permease hemB Delta-aminolevulinic acid dehydratase Putative hydrolase/acyltransferase Unknown trxB1 Thioredoxin reductase nuoN1 NADHubiquinone oxidoreductase subunit (chain N) lgtD Glycosyl transferase proP6 Proline/betaine transporter uvrD DNA helicase II dus Putative dihydrouridine synthase Dus Unknown phbC Poly-beta-hydroxybutyrate polymerase tdcB Threonine dehydratase Unknown	Genes rnpA rpl nrd rpl ychF mur mur mraY rec tra mviN ppa ccm Sco2 sec yajC gyr mur surA sec -uvr cmk rps clp glmU --lpdA -rnd gcvT putP hemC trpS plsC ampG tlc -isp potE isc isc spl1 -ntr rps -ileS accC pccB aas znuB ubi gltX groEL groES rph grpE perM DnaA rpl rpo rps rps adk sec rpl rpm rps rpl rpl rps rps rpl rpl rpl rps rpm rpl rps rpl rps rpl rpl rpl rps tuf fumC NifU ampG rhlE cspA ksgA -ostA xse xth -ubi ubi -tat metG tmk1 proP4 ubi valS RmuC exsB msbA -bcr2 Lol Lol --ccm sca -lpx lig tgt --rnh --coaE dna surf1 -fab tlc tlyC lip gly -nth --tat pgpA rpl rpm -proP NAD trm rec fab acpP fab mre mre -pal rpm smpA fts pol dna udg -ampG tat serS virB -terC nuo nuo ccm nuo nuo nuo atp atp atp lpdA -kefB bolA inf maf dksA xerC -fts mraY --sca fdxA ccm -Sca znu uvr ssb dap htpG hemA tig obg gltA Uracil RluD hemK Sua5 gly gly --dna sec greA pnt pnt Lol --gln phnP --holC dap -rps mut proP hemF -hemH hemE -trx rfb rfb gltA lpx fab lpx -znu pcnB atp atp atp atp -dsbG --cvpA clp -rps rps rpl tilS fts sdh -lgt -yidC pgsA -tlc uhpC ndk gid soj ParB -kds isc dgt arg -Par -dcd sec czcR GTP -pnt Sca sam proP cysS rps tsf kdtA -aatA -vacJ -alr -mkl rpm rpm -virB virB virB virB virB trm rpl -sec nuo lepB era ruvC -mrp hfl htrA -sdh yqi rps rps fusA nus rpl rpl rpl rpl rpo rpo pepA -aspS fts yqi gat gat rrf pyr mnh emrB Sca -nus rrmJ --hupA hol ffh glt -suc suc rec comL dna dna hsl -hol coq7 virB dap uspA imp -hsc rnh uvr grxC1 atm1 gyr def fmt abcT -cyd thrS -tol --Par ctp barA ---rpl rps nudH -efp suhB -psd pssA --bolA EAL mur mur ddlB -cycM lpx xth pdh typ hlp icd MnhG mnh ccm -pet pet fbcH nuo nuo mnh virB virB virB virD gppA --cysQ mut lacA nlpD thy tol -cox trm atrC hisS tol tol Ton proP HlyD aprD asd -hsl hsl lpx -cyaY glt top hfl -rnd --rps cyoB rimM -xse mpg nuo nuo nuo nuo cut lys -tme proP mdh tlc fts mra nlpD mra cox rho cox birA -rssA rec sodB mccF fol mltE -dut ppdk sppA -tlpA gln -Sca -tlc -truB FTR1 rps isp pnp osmY kpsF rlpA -dac nrd msbA nrd ruv trx proS fol fol yhbH kds lon1 pyr pbpA -pbpA --dap -Mia ntr phe ubi phe nus dna inf --rbf --N6 rdd rluA rec dna ppnk ubi -priA pgsA hemB ---nuo trx proP lgt dus uvr phb -tdcB -

a cRIG = Rickettsial orthologous cluster