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Genomic evolution and adaptation of arthropod-associated Rickettsia. Sci Rep 2022; 12:3807. [PMID: 35264613 PMCID: PMC8907221 DOI: 10.1038/s41598-022-07725-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
Rickettsia species are endosymbionts hosted by arthropods and are known to cause mild to fatal diseases in humans. Here, we analyse the evolution and diversity of 34 Rickettsia species using a pangenomic meta-analysis (80 genomes/41 plasmids). Phylogenomic trees showed that Rickettsia spp. diverged into two Spotted Fever groups, a Typhus group, a Canadensis group and a Bellii group, and may have inherited their plasmids from an ancestral plasmid that persisted in some strains or may have been lost by others. The results suggested that the ancestors of Rickettsia spp. might have infected Acari and/or Insecta and probably diverged by persisting inside and/or switching hosts. Pangenomic analysis revealed that the Rickettsia genus evolved through a strong interplay between genome degradation/reduction and/or expansion leading to possible distinct adaptive trajectories. The genus mainly shared evolutionary relationships with α-proteobacteria, and also with γ/β/δ-proteobacteria, cytophagia, actinobacteria, cyanobacteria, chlamydiia and viruses, suggesting lateral exchanges of several critical genes. These evolutionary processes have probably been orchestrated by an abundance of mobile genetic elements, especially in the Spotted Fever and Bellii groups. In this study, we provided a global evolutionary genomic view of the intracellular Rickettsia that may help our understanding of their diversity, adaptation and fitness.
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Rauch J, Barton J, Kwiatkowski M, Wunderlich M, Steffen P, Moderzynski K, Papp S, Höhn K, Schwanke H, Witt S, Richardt U, Mehlhoop U, Schlüter H, Pianka V, Fleischer B, Tappe D, Osterloh A. GroEL is an immunodominant surface-exposed antigen of Rickettsia typhi. PLoS One 2021; 16:e0253084. [PMID: 34111210 PMCID: PMC8191997 DOI: 10.1371/journal.pone.0253084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/28/2021] [Indexed: 11/26/2022] Open
Abstract
Rickettsioses are neglected and emerging potentially fatal febrile diseases that are caused by obligate intracellular bacteria, rickettsiae. Rickettsia (R.) typhi and R. prowazekii constitute the typhus group (TG) of rickettsiae and are the causative agents of endemic and epidemic typhus, respectively. We recently generated a monoclonal antibody (BNI52) against R. typhi. Characterization of BNI52 revealed that it specifically recognizes TG rickettsiae but not the members of the spotted fever group (SFG) rickettsiae. We further show that BNI52 binds to protein fragments of ±30 kDa that are exposed on the bacterial surface and also present in the periplasmic space. These protein fragments apparently derive from the cytosolic GroEL protein of R. typhi and are also recognized by antibodies in the sera from patients and infected mice. Furthermore, BNI52 opsonizes the bacteria for the uptake by antigen presenting cells (APC), indicating a contribution of GroEL-specific antibodies to protective immunity. Finally, it is interesting that the GroEL protein belongs to 32 proteins that are differentially downregulated by R. typhi after passage through immunodeficient BALB/c CB17 SCID mice. This could be a hint that the rickettsia GroEL protein may have immunomodulatory properties as shown for the homologous protein from several other bacteria, too. Overall, the results of this study provide evidence that GroEL represents an immunodominant antigen of TG rickettsiae that is recognized by the humoral immune response against these pathogens and that may be interesting as a vaccine candidate. Apart from that, the BNI52 antibody represents a new tool for specific detection of TG rickettsiae in various diagnostic and experimental setups.
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Affiliation(s)
- Jessica Rauch
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Barton
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Malte Wunderlich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Pascal Steffen
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Stefanie Papp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Katharina Höhn
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hella Schwanke
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Susanne Witt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ulricke Richardt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ute Mehlhoop
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Verena Pianka
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Dennis Tappe
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anke Osterloh
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Identification of rickettsial immunoreactive proteins using a proximity ligation assay Western blotting and the traditional immunoproteomic approach. Comp Immunol Microbiol Infect Dis 2018; 58:17-25. [DOI: 10.1016/j.cimid.2018.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/16/2018] [Accepted: 06/10/2018] [Indexed: 11/23/2022]
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El Karkouri K, Kowalczewska M, Armstrong N, Azza S, Fournier PE, Raoult D. Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp. Front Microbiol 2017; 8:1363. [PMID: 28775717 PMCID: PMC5517468 DOI: 10.3389/fmicb.2017.01363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/05/2017] [Indexed: 11/13/2022] Open
Abstract
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 massiliae 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 Dermacentor 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.
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Affiliation(s)
- Khalid El Karkouri
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Malgorzata Kowalczewska
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Nicholas Armstrong
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Said Azza
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Pierre-Edouard Fournier
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
| | - Didier Raoult
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, UM63, Centre National De La Recherche Scientifique 7278, IRD 198, Institut National De La Santé Et De La Recherche Médicale U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille UniversitéMarseille, France
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Comparative Proteomic Profiling of Ehrlichia ruminantium Pathogenic Strain and Its High-Passaged Attenuated Strain Reveals Virulence and Attenuation-Associated Proteins. PLoS One 2015; 10:e0145328. [PMID: 26691135 PMCID: PMC4686967 DOI: 10.1371/journal.pone.0145328] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/01/2015] [Indexed: 11/19/2022] Open
Abstract
The obligate intracellular bacterium Ehrlichia ruminantium (ER) causes heartwater, a fatal tick-borne disease in livestock. In the field, ER strains present different levels of virulence, limiting vaccine efficacy, for which the molecular basis remains unknown. Moreover, there are no genetic tools currently available for ER manipulation, thus limiting the knowledge of the genes/proteins that are essential for ER pathogenesis and biology. As such, to identify proteins and/or mechanisms involved in ER virulence, we performed the first exhaustive comparative proteomic analysis between a virulent strain (ERGvir) and its high-passaged attenuated strain (ERGatt). Despite their different behaviors in vivo and in vitro, our results from 1DE-nanoLC-MS/MS showed that ERGvir and ERGatt share 80% of their proteins; this core proteome includes chaperones, proteins involved in metabolism, protein-DNA-RNA biosynthesis and processing, and bacterial effectors. Conventional 2DE revealed that 85% of the identified proteins are proteoforms, suggesting that post-translational modifications (namely glycosylation) are important in ER biology. Strain-specific proteins were also identified: while ERGatt has an increased number and overexpression of proteins involved in cell division, metabolism, transport and protein processing, ERGvir shows an overexpression of proteins and proteoforms (DIGE experiments) involved in pathogenesis such as Lpd, AnkA, VirB9 and B10, providing molecular evidence for its increased virulence in vivo and in vitro. Overall, our work reveals that ERGvir and ERGatt proteomes are streamlined to fulfill their biological function (maximum virulence for ERGvir and replicative capacity for ERGatt), and we provide both pioneering data and novel insights into the pathogenesis of this obligate intracellular bacterium.
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Fotso Fotso A, Mediannikov O, Nappez C, Azza S, Raoult D, Drancourt M. Monoclonal Antibodies for the Diagnosis of Borrelia crocidurae. Am J Trop Med Hyg 2015; 94:61-67. [PMID: 26598566 DOI: 10.4269/ajtmh.15-0436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/02/2015] [Indexed: 11/07/2022] Open
Abstract
Relapsing fever borreliae, produced by ectoparasite-borne Borrelia species, cause mild to deadly bacteremia and miscarriage. In the perspective of developing inexpensive assays for the rapid detection of relapsing fever borreliae, we produced 12 monoclonal antibodies (MAbs) against Borrelia crocidurae and characterized the two exhibiting the highest titers. P3A10 MAb reacts with the 35.6-kDa flagellin B (flaB) of B. crocidurae while P6D9 MAb recognizes a 35.1-kDa variable-like protein (Vlp) in B. crocidurae and a 35.2-kDa Vlp in Borrelia duttonii. Indirect immunofluorescence assay incorporating relapsing fever and Lyme group borreliae and 11 blood-borne organisms responsible for fever in West Africa confirmed the reactivity of these two MAbs. Combining these two MAbs in indirect immunofluorescence assays detected relapsing fever borreliae including B. crocidurae in ticks and the blood of febrile Senegalese patients. Both antibodies could be incorporated into inexpensive and stable formats suited for the rapid point-of-care diagnosis of relapsing fever. These first-ever MAbs directed against African relapsing fever borreliae are available for the scientific community to promote research in this neglected field.
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Kowalczewska M, Vellaiswamy M, Nappez C, Vincentelli R, Scola BL, Raoult D. Protein candidates for the serodiagnosis of rickettsioses: 1. ACTA ACUST UNITED AC 2012; 64:130-3. [DOI: 10.1111/j.1574-695x.2011.00906.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/20/2011] [Accepted: 10/31/2011] [Indexed: 11/30/2022]
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Bechah Y, El Karkouri K, Mediannikov O, Leroy Q, Pelletier N, Robert C, Médigue C, Mege JL, Raoult D. Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities. Genome Res 2010; 20:655-63. [PMID: 20368341 PMCID: PMC2860167 DOI: 10.1101/gr.103564.109] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 02/11/2010] [Indexed: 11/24/2022]
Abstract
Rickettsia prowazekii, the agent of epidemic typhus, is an obligate intracellular bacterium that is transmitted to human beings by the body louse. Several strains that differ considerably in virulence are recognized, but the genetic basis for these variations has remained unknown since the initial description of the avirulent vaccine strain nearly 70 yr ago. We use a recently developed murine model of epidemic typhus and transcriptomic, proteomic, and genetic techniques to identify the factors associated with virulence. We identified four phenotypes of R. prowazekii that differed in virulence, associated with the up-regulation of antiapoptotic genes or the interferon I pathway in the host cells. Transcriptional and proteomic analyses of R. prowazekii surface protein expression and protein methylation varied with virulence. By sequencing a virulent strain and using comparative genomics, we found hotspots of mutations in homopolymeric tracts of poly(A) and poly(T) in eight genes in an avirulent strain that split and inactivated these genes. These included recO, putative methyltransferase, and exported protein. Passage of the avirulent Madrid E strain in cells or in experimental animals was associated with a cascade of gene reactivations, beginning with recO, that restored the virulent phenotype. An area of genomic plasticity appears to determine virulence in R. prowazekii and represents an example of adaptive mutation for this pathogen.
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Affiliation(s)
- Yassina Bechah
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
| | - Khalid El Karkouri
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
| | - Oleg Mediannikov
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
| | - Quentin Leroy
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
| | - Nicolas Pelletier
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
| | - Catherine Robert
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
| | - Claudine Médigue
- Genoscope, Centre National de Séquençage, Laboratoire de Génomique Comparative, 91057 Evry cedex, France
| | - Jean-Louis Mege
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
| | - Didier Raoult
- Unit for Research on Emergent and Tropical Infectious Diseases (URMITE), Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement, Faculty of Medicine, University of the Mediterranean, 13005 Marseille, France
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Hajem N, Weintraub A, Nimtz M, Römling U, Påhlson C. A study of the antigenicity of Rickettsia helvetica proteins using two-dimensional gel electrophoresis. APMIS 2009; 117:253-62. [PMID: 19338513 DOI: 10.1111/j.1600-0463.2009.02435.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rickettsia helvetica is an obligate intracellular Gram-negative microorganism found in Ixodes ricinus ticks. When R. helvetica was first discovered in 1979, little was known about its physiology and it fell into oblivion until it recently was suspected of being pathogenic to humans. However, all efforts to isolate R. helvetica from patients have been unsuccessful, although serological responses against R. helvetica can be demonstrated. The aim of our study was to investigate the protein profile of R. helvetica and study the antigenicity of its proteins using two-dimensional (2D) immunoblot in order to characterize the immunological response against R. helvetica infection. Our results show that in addition to the known PS120 and OmpB antigenic R. helvetica proteins, three other antigens exist: a 60 kDa GroEL protein, a 10 kDa GroES protein and a hitherto unknown 35 kDa hypothetical protein that has similarities with ORF-RC0799 of Rickettsia conorii. Furthermore, the lipopolysaccharide showed strong antigenicity. In this study, we present the first proteome map and the first 2D immunoblot profile of R. helvetica and finally we present the 35 kDa R. helvetica as an additional antigen to the previously known rickettsial antigens.
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Affiliation(s)
- Nedaa Hajem
- School of Sustainable Development of Society and Technology, Mälardalens University, Eskilstuna, Sweden
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Ogawa M, Renesto P, Azza S, Moinier D, Fourquet P, Gorvel JP, Raoult D. Proteome analysis ofRickettsia felis highlights the expression profile of intracellular bacteria. Proteomics 2007; 7:1232-48. [PMID: 17385819 DOI: 10.1002/pmic.200600721] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The proteome of Rickettsia felis, an obligate intracellular bacterium responsible for spotted fever, was analyzed using two complementary proteomic approaches: 2-DE coupled with MALDI-TOF, and SDS-PAGE with nanoLC-MS/MS. This strategy allowed identification of 165 proteins and helped to answer some questions raised by the genome sequence of this bacterium. We successfully identified potential virulence factors including two putative adhesins, four proteins of the type IV secretion system, four Sca autotransporters, four components of ABC transporters, some R. felis-specific proteins, and one antitoxin of the toxin-antitoxin system. Notably, the antitoxin was the first to be identified in intracellular bacteria. Only one protein containing rickettsia palindromic repeats was found, whereas none of the split genes, transposases, or tetratricopeptide/ankyrin repeats were detectably expressed. Comparison of the protein expression profiles of R. felis and 23 other bacterial species according to functional categories showed that intracellular bacteria express more proteins related to translation, especially ribosomal proteins. However, the remaining bacteria express more proteins related to energy production and carbohydrate/amino acid metabolism. In conclusion, this study reveals R. felis virulence factor expression and highlights the unique protein expression profile of intracellular bacteria.
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Affiliation(s)
- Motohiko Ogawa
- Unité des Rickettsies, CNRS-UMR 6020, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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