Gene gain and loss events in Rickettsia and Orientia species

<p>Abstract</p> <p>Background</p> <p>Genome degradation is an ongoing process in all members of the <it>Rickettsiales </it>order, which makes these bacterial species an excellent model for studying reductive evolution through interspecies variation in genome size and gene content. In this study, we evaluated the degree to which gene loss shaped the content of some <it>Rickettsiales </it>genomes. We shed light on the role played by horizontal gene transfers in the genome evolution of <it>Rickettsiales</it>.</p> <p>Results</p> <p>Our phylogenomic tree, based on whole-genome content, presented a topology distinct from that of the whole core gene concatenated phylogenetic tree, suggesting that the gene repertoires involved have different evolutionary histories. Indeed, we present evidence for 3 possible horizontal gene transfer events from various organisms to <it>Orientia </it>and 6 to <it>Rickettsia </it>spp., while we also identified 3 possible horizontal gene transfer events from <it>Rickettsia </it>and <it>Orientia </it>to other bacteria. We found 17 putative genes in <it>Rickettsia </it>spp. that are probably the result of <it>de novo </it>gene creation; 2 of these genes appear to be functional. On the basis of these results, we were able to reconstruct the gene repertoires of "proto-<it>Rickettsiales</it>" and "proto-<it>Rickettsiaceae</it>", which correspond to the ancestors of <it>Rickettsiales </it>and <it>Rickettsiaceae</it>, respectively. Finally, we found that 2,135 genes were lost during the evolution of the <it>Rickettsiaceae </it>to an intracellular lifestyle.</p> <p>Conclusions</p> <p>Our phylogenetic analysis allowed us to track the gene gain and loss events occurring in bacterial genomes during their evolution from a free-living to an intracellular lifestyle. We have shown that the primary mechanism of evolution and specialization in strictly intracellular bacteria is gene loss. Despite the intracellular habitat, we found several horizontal gene transfers between <it>Rickettsiales </it>species and various prokaryotic, viral and eukaryotic species.</p> <p>Open peer review</p> <p>Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section.</p

RickA Expression Is Not Sufficient to Promote Actin-Based Motility of Rickettsia raoultii

Background: Rickettsia raoultii is a novel Rickettsia species recently isolated from Dermacentor ticks and classified within the spotted fever group (SFG). The inability of R. raoultii to spread within L929 cells suggests that this bacterium is unable to polymerize host cell actin, a property exhibited by all SFG rickettsiae except R. peacocki. This result led us to investigate if RickA, the protein thought to generate actin nucleation, was expressed within this rickettsia species. Methodology/Principal Findings: Amplification and sequencing of R. raoultii rickA showed that this gene encoded a putative 565 amino acid protein highly homologous to those found in other rickettsiae. Using immunofluorescence assays, we determined that the motility pattern (i.e. microcolonies or cell-to-cell spreading) of R. raoultii was different depending on the host cell line in which the bacteria replicated. In contrast, under the same experimental conditions, R. conorii shares the same phenotype both in L929 and in Vero cells. Transmission electron microscopy analysis of infected cells showed that non-motile bacteria were free in the cytosol instead of enclosed in a vacuole. Moreover, western-blot analysis demonstrated that the defect of R. raoultii actin-based motility within L929 cells was not related to lower expression of RickA. Conclusion/Significance: These results, together with previously published data about R. typhi, strongly suggest that another factor, apart from RickA, may be involved with be responsible for actin-based motility in bacteria from the Rickettsi

Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction

<p>Abstract</p> <p>Background</p> <p>The <it>Rickettsia </it>genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent <it>R. prowazekii</it>, which causes epidemic typhus and kills its arthropod host, to the mild pathogen <it>R. africae</it>, the agent of African tick-bite fever, which does not affect the fitness of its tick vector.</p> <p>Results</p> <p>We evaluated the clonality of <it>R. africae </it>in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 bp including a <it>tra </it>operon and an unstable 12,377-bp plasmid. To study the genetic characteristics associated with virulence, we compared this species to <it>R. prowazekii</it>, <it>R. rickettsii </it>and <it>R. conorii</it>. <it>R. africae </it>and <it>R. prowazekii </it>have, respectively, the less and most decayed genomes. Eighteen genes are present only in <it>R. africae </it>including one with a putative protease domain upregulated at 37°C.</p> <p>Conclusion</p> <p>Based on these data, we speculate that a loss of regulatory genes causes an increase of virulence of rickettsial species in ticks and mammals. We also speculate that in <it>Rickettsia </it>species virulence is mostly associated with gene loss.</p> <p>The genome sequence was deposited in GenBank under accession number [GenBank: <ext-link ext-link-type="gen" ext-link-id="NZ_AAUY01000001">NZ_AAUY01000001</ext-link>].</p

Dominance of the mycorrhizal fungus Rhizopogon rubescens in a plantation of Pinus pinea seedlings inoculated with Suillus collinitus

We examined the below-ground mycorrhizal diversity of P. pinea seedlings inoculated with S. collinitus six years after outplanting in a disturbed site, located at La Petite-Camargue (Gard, France). This was performed using the polymerase chain reaction (PCR), the restriction fragment length polymorphism (RFLP) and the sequencing of the nuclear ribosomal internal transcribed spacer (ITS). Seven and one plants corresponding, respectively, to inoculated and non-inoculated (control) treatments were chosen randomly. Examinations were carried out directly from ectomycorrhizae. A total number of 233 root tips was examined. Five ITS RFLP taxa were detected. The ITS taxon I corresponded to the ectomycorrhizal species Rhizopogon rubescens. This fungus was abundant (55%) in the P. pinea ectomycorrhizal community. The other ITS taxa were rare and remained unidentified. The current P. pinea plantation showed a restricted diversity of the ectomycorrhizal community which is typical of ectomycorrhizal communities in young plantations established in disturbed stands.Dominance de l'espèce mycorhizienne R. rubescens dans une plantation à Pinus pinea. La diversité ectomycorhizienne de plants de P. pinea, inoculés par S. collinitus, a été examinée six années après transplantation dans un site perturbé de La Petite-Camargue (Gard, France). L'identification de cette diversité fongique a été effectuée à partir de l'espaceur interne transcrit (ITS) de l'acide désoxyribonucléique (ADN) nucléaire et ribosomal. Deux marqueurs moléculaires dérivés de la réaction de polymérase en chaîne (PCR) ont été utilisés : le polymorphisme de fragments de restriction (RFLP) et le séquençage des produits d'amplification de l'ADN. Sept et un plants correspondant, respectivement, aux plants inoculés et non inoculés (témoin) ont été choisis au hasard. Le typage moléculaire a été réalisé directement à partir des ectomycorhizes. Deux cent trente trois racines courtes mycorhizées ou non ont été examinées. Cinq types d'ITS RFLP ont été détectés. Le type I correspond à l'espèce ectomycorhizienne Rhizopogon rubescens. Cette dernière, est dominante (55 %) dans la communauté ectomycorhizienne de cette plantation. Les autres types d'ITS RFLP ont été rares et restent non identifiés. La plantation de P. pinea a montré une faible diversité ectomycorhizienne qui est typique des communautés ectomycorhiziennes des jeunes plantations établies dans des sites perturbés

MIPDB: a relational database dedicated to MIP family proteins

International audienceBACKGROUND INFORMATION: The MIPs (major intrinsic proteins) constitute a large family of membrane proteins that facilitate the passive transport of water and small neutral solutes across cell membranes. Since water is the most abundant molecule in all living organisms, the discovery of selective water-transporting channels called AQPs (aquaporins) has led to new knowledge on both the physiological and molecular mechanisms of membrane permeability. The MIPs are identified in Archaea, Bacteria and Eukaryota, and the rapid accumulation of new sequences in the database provides an opportunity for large-scale analysis, to identify functional and/or structural signatures or to infer evolutionary relationships. To help perform such an analysis, we have developed MIPDB (database for MIP proteins), a relational database dedicated to members of the MIP family. RESULTS: MIPDB is a motif-oriented database that integrates data on 785 MIP proteins from more than 200 organisms and contains 230 distinct sequence motifs. MIPDB proposes the classification of MIP proteins into three functional subgroups: AQPs, glycerol-uptake facilitators and aquaglyceroporins. Plant MIPs are classified into three specific subgroups according to their subcellular distribution in the plasma membrane, tonoplast or the symbiosome membrane. Some motifs of the database are highly selective and can be used to predict the transport function or subcellular localization of unknown MIP proteins. CONCLUSIONS: MIPDB offers a user-friendly and intuitive interface for a rapid and easy access to MIP resources and to sequence analysis tools. MIPDB is a web application, publicly accessible at http://idefix.univ-rennes1.fr:8080/Prot/index.htm

Diversity of ectomycorrhizal symbionts in a disturbed Pinus halepensis plantation in the Mediterranean region

Ectomycorrhizal diversity (ED) associated with Pinus halepensis trees was examined 1.5 years after outplanting at a fire-disturbed site of Rieucoulon (Hérault, France). ED analysis was examined on non-inoculated and Suillus collinitus-inoculated plants, and on naturally regenerated trees. A total of 461 single ectomycorrhizas was typed using PCR-RFLP analysis and sequencing of the internal transcribed spacer (ITS) of the nuclear rDNA. Twelve ITS RFLP-taxa were detected. The ectomycorrhizal fungus S. collinitus (ITS RFLP-taxon 1) was the most abundant (45.8–59.7%) species in the three treatments, suggesting that it is a strong ectomycorrhizal competitor in this site. S. mediterraneensis (ITS RFLP-taxon 2) was restricted to control and naturally regenerated trees and was unequally moderate (11.7–31.9%). The remaining below-ground ITS RFLP-taxa were uncommon and rare (0.0–9.6%). The current experimental P. halepensis plantation showed a species-poor community dominated by two Suillus species. Ecological strategies of these symbionts are discussed.Diversité ectomycorhizienne dans une plantation à Pinus halepensis. La diversité génétique des ectomycorhizes de plants de P. halepensis a été examinée une année et demie après introduction dans un site incendié de Rieucoulon (Hérault, France). Cette diversité a été caractérisée à l’aide du polymorphisme de fragments de restriction (RFLP) et du séquençage de l’espaceur interne transcrit (ITS) de l’ADN ribosomal nucléaire. Trois traitements ont été examinés : des plants témoins, des plants mycorhizés avec Suillus collinitus et des plants en régénération naturelle. Au total, 461 ectomycorhizes ont été soumises au typage moléculaire. Douze ribotypes d’ITS ont été détectés. S. collinitus (ribotype 1) est l’espèce dominante (45,8–59,7 %) dans les trois traitements suggérant une forte capacité de colonisation dans ce site. La présence de S. mediterraneensis (ribotype 2) est limitée aux plants témoins et aux autres issus de la régénération naturelle et sa fréquence est modérée (11,7–31,9 %). Les autres symbiotes ectomycorhiziens sont rares (0,0–9,6 %) et leur abondance diffère d’un traitement à l’autre. Cette étude révèle une faible diversité des symbiotes ectomycorhiziens dans la plantation à P. halepensis ; elle est dominée par deux espèces du genre Suillus. Les stratégies écologiques de ces symbiotes sont discutées

Diversity of ectomycorrhizal symbionts in a disturbed Pinus halepensis plantation in the Mediterranean region

Ectomycorrhizal diversity (ED) associated with Pinus halepensis trees was examined 1.5 years after outplanting at a fire-disturbed site of Rieucoulon (Herault, France). ED analysis was examined on non-inoculated and Suillus collinitus-inoculated plants, and on naturally regenerated trees. A total of 461 single ectomycorrhizas was typed using PCR-RFLP analysis and sequencing of the internal transcribed spacer ( ITS) of the nuclear rDNA. Twelve ITS RFLP-taxa were detected. The ectomycorrhizal fungus S. collinitus ( ITS RFLP-taxon 1) was the most abundant (45.8 - 59.7%) species in the three treatments, suggesting that it is a strong ectomycorrhizal competitor in this site. S. mediterraneensis ( ITS RFLP-taxon 2) was restricted to control and naturally regenerated trees and was unequally moderate (11.7 - 31.9%). The remaining below-ground ITS RFLP-taxa were uncommon and rare (0.0 - 9.6%). The current experimental P. halepensis plantation showed a species-poor community dominated by two Suillus species. Ecological strategies of these symbionts are discussed.Diversité ectomycorhizienne dans une plantation à Pinus halepensis. La diversité génétique des ectomycorhizes de plants de P. halepensis a été examinée une année et demie après introduction dans un site incendié de Rieucoulon (Hérault, France). Cette diversité a été caractérisée à l’aide du polymorphisme de fragments de restriction (RFLP) et du séquençage de l’espaceur interne transcrit (ITS) de l’ADN ribosomal nucléaire. Trois traitements ont été examinés : des plants témoins, des plants mycorhizés avec Suillus collinitus et des plants en régénération naturelle. Au total, 461 ectomycorhizes ont été soumises au typage moléculaire. Douze ribotypes d’ITS ont été détectés. S. collinitus (ribotype 1) est l’espèce dominante (45,8–59,7 %) dans les trois traitements suggérant une forte capacité de colonisation dans ce site. La présence de S. mediterraneensis (ribotype 2) est limitée aux plants témoins et aux autres issus de la régénération naturelle et sa fréquence est modérée (11,7–31,9 %). Les autres symbiotes ectomycorhiziens sont rares (0,0–9,6 %) et leur abondance diffère d’un traitement à l’autre. Cette étude révèle une faible diversité des symbiotes ectomycorhiziens dans la plantation à P. halepensis; elle est dominée par deux espèces du genre Suillus. Les stratégies écologiques de ces symbiotes sont discutées

Molecular markers detecting an ectomycorrhizal Suillus collinitus strain on Pinus halepensis roots suggest successful inoculation and persistence in Mediterranean nursery and plantation

Survival of the ectomycorrhizal fungal strain Suillus collinitus Sc-32 on Pinus halepensis after inoculation and outplanting was monitored in a Mediterranean plantation. Three molecular fingerprints were developed: RFLP of the internal transcribed spacer ribosomal DNA, intersimple sequence repeat, and a specific sequence-characterized amplified region marker. The inoculant was demonstrated to survive on inoculated seedlings 4 years after outplanting (56 months after inoculation), although S. collinitus was not fruiting. The designed markers set allows reliable and inexpensive monitoring of inoculated seedlings and suggests that S. collinitus is suitable for inoculation of Mediterranean Pinus. These data are discussed in the framework of suilloid population ecolog

Diversity of ectomycorrhizal fungi naturally established on containerised Pinus seedlings in nursery conditions

International audienceThe study examined the diversity of ectomycorrhizal fungi, naturally established on roots of containerised Pinus seedlings in a nursery, using PCR-RFLP and sequencing of the nuclear ribosomal. internal transcribed spacer. Seventy-two samples, including ectomycorrhizae and fruit bodies, were examined. Molecular typing assigned the fungal symbionts to four ectomycorrhizal Boletates: Rhizopogon rubescens, Suillus bovinus, S. variegatus, and R. luteolus. R. rubescens was abundant (37.5%), while Suillus and R. luteolus species were moderately established (25-26%) and rare (2.8%), respectively. In addition, Rhizopogon species colonised P nigra ssp. salzmannii seedlings, whereas Suillus species were identified on Pinus nigra ssp. nigra seedlings. The diversity and the ability of these naturally established symbionts under artificial nursery conditions were discussed. The molecular survey investigated here should contribute to successful monitoring of mycorrhizal. application under both nursery and plantation conditions