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10. Gene gain and loss events in Rickettsia and Orientia species

Author

Raoult Didier, El Karkouri Khalid, Merhej Vicky, Georgiades Kalliopi, and Pontarotti Pierre

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background Genome degradation is an ongoing process in all members of the Rickettsiales 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 Rickettsiales genomes. We shed light on the role played by horizontal gene transfers in the genome evolution of Rickettsiales. Results 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 Orientia and 6 to Rickettsia spp., while we also identified 3 possible horizontal gene transfer events from Rickettsia and Orientia to other bacteria. We found 17 putative genes in Rickettsia spp. that are probably the result of de novo 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-Rickettsiales" and "proto-Rickettsiaceae", which correspond to the ancestors of Rickettsiales and Rickettsiaceae, respectively. Finally, we found that 2,135 genes were lost during the evolution of the Rickettsiaceae to an intracellular lifestyle. Conclusions 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 Rickettsiales species and various prokaryotic, viral and eukaryotic species. Open peer review Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section.

Published
2011
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11. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction

Author

Audic Stéphane, Parola Philippe, Socolovschi Cristina, Renesto Patricia, Giumelli Bernadette, Robert Catherine, Leroy Quentin, El Karkouri Khalid, Fournier Pierre-Edouard, and Raoult Didier

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

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

Published
2009
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12. Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp

Author

El Karkouri, Khalid, Kowalczewska, Malgorzata, Armstrong, Nicholas, Azza, Said, Fournier, Pierre-Edouard, Raoult, Didier, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
virulence, proteomics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, evolution, lcsh:QR1-502, genomics, pathogenicity, Rickettsia, infectious diseases, Microbiology, intracellular, lcsh:Microbiology
Abstract

International audience; Arthropod-borne Rickettsia species are obligate intracellular bacteria which are pathogenic for humans. Within this genus, Rickettsia slovaca and Rickettsia conorii cause frequent and potentially severe infections, whereas Rickettsia raoultii and Rickettsia massiliac cause rare and milder infections. All four species belong to spotted fever group (SFG) rickettsiae. However, R. slovaca and R. raoultii cause scalp eschar and neck lymphadenopathy (SENLAT) and are mainly associated with Derrnacentor ticks, whereas the other two species cause Mediterranean spotted fever (MSF) and are mainly transmitted by Rhipicephalus ticks. To identify the potential genes and protein profiles and to understand the evolutionary processes that could, comprehensively, relate to the differences in virulence and pathogenicity observed between these four species, we compared their genomes and proteomes. The virulent and milder agents displayed divergent phylogenomic evolution in two major clades, whereas either SENLAT or MSF disease suggests a discrete convergent evolution of one virulent and one milder agent, despite their distant genetic relatedness. Moreover, the two virulent species underwent strong reductive genomic evolution and protein structural variations, as well as a probable loss of plasmid(s), compared to the two milder species. However, an abundance of mobilome genes was observed only in the less pathogenic species. After infecting Xenopus laevis cells, the virulent agents displayed less up-regulated than down regulated proteins, as well as less number of identified core proteins. Furthermore, their similar and distinct protein profiles did not contain some genes (e.g., ompA/B and rickA) known to be related to rickettsial adhesion, motility and/or virulence, but may include other putative virulence-, antivirulence-, and/or disease related proteins. The identified evolutionary forces herein may have a strong impact on intracellular expressions and strategies in these rickettsiae, and that may contribute to the emergence of distinct virulence and diseases in humans. Thus, the current multi-omics data provide new insights into the evolution and fitness of SFG virulence and pathogenicity, and intracellular pathogenic bacteria.

Published
2017

13. Identification of internal transcribed spacer sequence motifs in truffles: A first step toward their DNA bar coding

Author

Karkouri, Khalid El, Murat, Claude, Zampieri, Elisa, and Bonfante, Paola

Subjects
Nucleotide sequence -- Analysis, Ribosomal RNA -- Analysis, DNA microarrays -- Analysis, Biological sciences
Abstract

DNA sequence motifs from the internal transcribed spacer of the nuclear rRNA repeat unit is presented. This work provides a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies.

Published
2007

14. Rickettsia gravesii sp. nov.: a novel spotted fever group rickettsia in Western Australian Amblyomma triguttatum triguttatum ticks

Author

Abdad, Mohammad Y., primary, Abdallah, Rita Abou, additional, Karkouri, Khalid El, additional, Beye, Mamadou, additional, Stenos, John, additional, Owen, Helen, additional, Unsworth, Nathan, additional, Robertson, Ian, additional, Blacksell, Stuart D., additional, Nguyen, Thi-Tien, additional, Nappez, Claude, additional, Raoult, Didier, additional, Fenwick, Stan, additional, and Fournier, Pierre-Edouard, additional

Published
2017
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15. Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities

Author

Bechah, Yassina, Karkouri, Khalid El, Mediannikov, Oleg, Leroy, Quentin, Pelletier, Nicolas, Robert, Catherine, Medigue, Claudine, Mege, Jean-Louis, and Raoult, Didier

Subjects
Rickettsia -- Genetic aspects, Proteomics -- Usage, Virulence (Microbiology) -- Research, Gene mutations -- Analysis, Genetic transcription -- Research, Health
Published
2010

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

Author

El Karkouri, Khalid, Selosse, M.-A., Mousain, D., Interactions cellulaires et moléculaires (ICM), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-IFR140-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3)

Subjects
Mediterranean Region, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ISSR, rDNA (ITS), Agriculture, Pinus, Plant Roots, Polymerase Chain Reaction, SCAR, Species Specificity, Seedlings, Mycorrhizae, DNA, Ribosomal Spacer, ectomycorrhizae, Suillus collinitus, DNA, Fungal, inoculant survival, Biomarkers, Polymorphism, Restriction Fragment Length, DNA Primers, Environmental Monitoring
Abstract

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 ecology.

Published
2006

23. Bactrop: A platform of genomic resources to study organization and evolution of tropical crop species [S04-3]

Author

Piffanelli, Pietro, Noa-Carrazana, Juan Carlos, Clément, Didier, Ciampi, Ana, Vilarinhos, Alberto Duarte, Thibivilliers, Sandra, Lagoda, Pierre, Sabau, Xavier, Ruiz, Manuel, Karkouri, Khalid, Leroy, Thierry, Billotte, Norbert, Seguin, Marc, Safar, Jan, D'Hont, Angélique, and Glaszmann, Jean-Christophe

Subjects
ADN, Coffea, Banque de gènes, F30 - Génétique et amélioration des plantes, Pool de gènes, Theobroma cacao, Elaeis guineensis, Cocos nucifera, Sorghum, food and beverages, Musa, Saccharum, Hevea brasiliensis, RFLP, Banque de données
Abstract

BAC libraries are essential tools for assisting genome organization and evolution. Given the rapid development of genomics projects on tropical crops, we have begun the creation of a platform of BAC library resources for a number of tropical species, called BACTROP. BAC libraries for 9 tropical plant species were constructed and characterised. Efforts are now focused on three main research axes: 1)comparative analysis between the genomes of three tropical monocots (banana, oil palm and coconut) and that of rice using highly conserved cDNA and genetically anchored RFLP probes; 2)characterise linkage disequilibrium patterns in the genome of perennial (coffee, rubber tree, cocoa) and annual crops (sorghum, sugarcane) with marked differences in their domestication and pollination strategies; 3)characterisation of genetically mapped resistance gene analogs co-segregating with QTLs for important agronomic traits in tropical perennial crop species (cocoa, rubber tree). To manage the approximately 4 million BAC clones of BACTROP a database called BACTROPDB is under development and will enable to keep track of screenings, replicas, and sequencing of BAC clones belonging to different BAC libraries. We acknowledge financial support to realise BACTROP from CIRAD-AMIS, Agropolis International, INIBAP, EMBRAPA, COCOP. (Texte intégral)

Published
2003

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

Author

Fournier, Pierre-Edouard, primary, El Karkouri, Khalid, additional, Leroy, Quentin, additional, Robert, Catherine, additional, Giumelli, Bernadette, additional, Renesto, Patricia, additional, Socolovschi, Cristina, additional, Parola, Philippe, additional, Audic, Stéphane, additional, and Raoult, Didier, additional

Published
2009
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49. Tryptose phosphate broth improves R ickettsia felis replication in mammalian cells.

Author

Saisongkorh, Watcharee, Karkouri, Khalid El, Patrice, Jean-Yves, Bernard, Annick, Rolain, Jean-Marc, and Raoult, Didier

Subjects
*RICKETTSIA, *VIRAL replication, *CELL culture, *CELL lines, *AMPHIBIANS, *PHOSPHATES, *BACTERIAL growth
Abstract

In cell culture, R ickettsia felis grows only at low temperatures (< 31 °C). Therefore, its ability to enter, survive and grow in cell lines has primarily been tested in cells derived from amphibians and arthropods, which naturally grow at low temperatures, and only infrequently in mammalian cells. We subcultured R . felis in mammalian cells for more than 10 passages using media supplemented with tryptose phosphate broth ( TPB) and found that TPB is critical for optimal growth of R . felis in mammalian cells. [ABSTRACT FROM AUTHOR]

Published
2012
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50. Genome Sequence of Rickettsia conorii subsp, caspia, the Agent of Astrakhan Fever.

Author

Sentausa, Erwin, El Karkouri, Khalid, Robert, Catherine, Raoult, Didier, and Fournier, Pierre-Edouard

Subjects
*RICKETTSIAL diseases, *GENOMES, *FEVER
Abstract

Rickettsia conorii subsp. caspia is the agent of Astrakhan fever, a spotted fever group rickettsiosis endemic to Astrakhan, Russia. The present study reports the draft genome of Rickettsia conorii subsp. caspia strain A-167. [ABSTRACT FROM AUTHOR]

Published
2012
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