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Zhao Z, Hu Y, Hu Y, White AP, Wang Y. Features and algorithms: facilitating investigation of secreted effectors in Gram-negative bacteria. Trends Microbiol 2023; 31:1162-1178. [PMID: 37349207 DOI: 10.1016/j.tim.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Gram-negative bacteria deliver effector proteins through type III, IV, or VI secretion systems (T3SSs, T4SSs, and T6SSs) into host cells, causing infections and diseases. In general, effector proteins for each of these distinct secretion systems lack homology and are difficult to identify. Sequence analysis has disclosed many common features, helping us to understand the evolution, function, and secretion mechanisms of the effectors. In combination with various algorithms, the known common features have facilitated accurate prediction of new effectors. Ensemblers or integrated pipelines achieve a better prediction of performance, which combines multiple computational models or modules with multidimensional features. Natural language processing (NLP) models also show the merits, which could enable discovery of novel features and, in turn, facilitate more precise effector prediction, extending our knowledge about each secretion mechanism.
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Affiliation(s)
- Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Aaron P White
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen 518060, China; Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen 518060, China.
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Meyer DF, Moumène A, Rodrigues V. Microbe Profile: Ehrlichia ruminantium - stealthy as it goes. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37994906 DOI: 10.1099/mic.0.001415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Graphical abstract
Summary of
Ehrlichia ruminantium
infection.
E. ruminantium
bacterium is typically spread to ruminants by bite from infected ticks. Following adhesion of infectious elementary bodies to host cell,
E. ruminantium
establishes the depicted intracellular biphasic lifestyle by the means of secreted effector proteins that hijack host cellular pathways. Replicating bacteria (reticulate bodies) fill a large cytoplasmic vacuole named morula inside mammalian or tick cells. Formation of this vacuole is critical for bacterial development and subsequent lysis of the host cell leading to the establishment of heartwater disease. Genetic diversity is one remarkable and biologically significant feature of pathogens in the
Anaplasmataceae
family, including
E. ruminantium
. The maximum-likelihood phylogenetic tree of four representative species of
Ehrlichia
(
E. chaffeensis
str. Arkansas,
E. canis
str. Jake,
E. muris
AS145,
E. ruminantium
str. Gardel) with
Wolbachia
endosymbiont of D. melanogaster as an outgroup was reconstructed on the basis of concatenated nucleic acid alignment of proteins shared by all species (core genomes) with 100 bootstrap resamplings. Major hosts of these bacteria are indicated. Mb, megabase. ORFs, open reading frames. (All images created by S. Mateus, C. Noroy. O. Gros and D.F. Meyer.)
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Affiliation(s)
- Damien F Meyer
- CIRAD, UMR ASTRE, Centre for Research and surveillance on Vector-borne diseases in the Caribbean, WOAH Reference Laboratory for Heartwater, F- 97170 Petit-Bourg, Guadeloupe, France
- ASTRE, CIRAD, INRAE, Univ Montpellier, Montpellier, France
| | - Amal Moumène
- CIRAD, UMR ASTRE, Centre for Research and surveillance on Vector-borne diseases in the Caribbean, WOAH Reference Laboratory for Heartwater, F- 97170 Petit-Bourg, Guadeloupe, France
- ASTRE, CIRAD, INRAE, Univ Montpellier, Montpellier, France
| | - Valérie Rodrigues
- CIRAD, UMR ASTRE, Centre for Research and surveillance on Vector-borne diseases in the Caribbean, WOAH Reference Laboratory for Heartwater, F- 97170 Petit-Bourg, Guadeloupe, France
- ASTRE, CIRAD, INRAE, Univ Montpellier, Montpellier, France
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Analysis of the Type 4 Effectome across the Genus Rickettsia. Int J Mol Sci 2022; 23:ijms232415513. [PMID: 36555155 PMCID: PMC9779031 DOI: 10.3390/ijms232415513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Rickettsia are obligate intracellular bacteria primarily carried by arthropod hosts. The genus Rickettsia contains several vertebrate pathogens vectored by hematophagous arthropods. Despite the potential for disease, our understanding of Rickettsias are limited by the difficulties associated with growing and manipulating obligate intracellular bacteria. To aid with this, our lab conducted an analysis of eight genomes and three plasmids from across the genus Rickettsia. Using OPT4e, a learning algorithm-based program designed to identify effector proteins secreted by the type 4 secretion system, we generated a putative effectome for the genus. We then consolidated effectors into homolog sets to identify effectors unique to Rickettsia with different life strategies or evolutionary histories. We also compared predicted effectors to non-effectors for differences in G+C content and gene splitting. Based on this analysis, we predicted 1571 effectors across the genus, resulting in 604 homolog sets. Each species had unique homolog sets, while 42 were present in all eight species analyzed. Effectors were flagged in association with pathogenic, tick and flea-borne Rickettsia. Predicted effectors also varied in G+C content and frequency of gene splitting as compared to non-effectors. Species effector repertoires show signs of expansion, degradation, and horizontal acquisition associated with lifestyle and lineage.
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Functional Characterization of Non-Ankyrin Repeat Domains of Orientia tsutsugamushi Ank Effectors Reveals Their Importance for Molecular Pathogenesis. Infect Immun 2022; 90:e0062821. [PMID: 35435726 DOI: 10.1128/iai.00628-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Orientia tsutsugamushi is a genetically intractable obligate intracellular bacterium, causes scrub typhus, and has one of the largest known armamentariums of ankyrin repeat-containing effectors (Anks). Most have a C-terminal F-box presumed to interact with the SCF ubiquitin ligase complex primarily based on their ability to bind overexpressed Skp1. Whether all F-box-containing Anks bind endogenous SCF components and the F-box residues essential for such interactions has gone unexplored. Many O. tsutsugamushi Ank F-boxes occur as part of a PRANC (pox protein repeats of ankyrin-C-terminal) domain. Roles of the non-F-box portion of the PRANC and intervening sequence region (ISR) that links the ankyrin repeat and F-box/PRANC domains are unknown. The functional relevance of these effectors' non-ankyrin repeat domains was investigated. The F-box was necessary for Flag-tagged versions of most F-box-containing Anks to precipitate endogenous Skp1, Cul1, and/or Rbx1, while the ISR and PRANC were dispensable. Ank toxicity in yeast was predominantly F-box dependent. Interrogations of Ank1, Ank5, and Ank6 established that L1, P2, E4, I9, and D17 of the F-box consensus are key for binding native SCF components and for Ank1 and Ank6 to inhibit NF-κB. The ISR is also essential for Ank1 and Ank6 to impair NF-κB. Ectopically expressed Ank1 and Ank6 lacking the ISR or having a mutagenized F-box incapable of binding SCF components performed as dominant-negative inhibitors to block O. tsutsugamushi NF-κB modulation. This study advances knowledge of O. tsutsugamushi Ank functional domains and offers an approach for validating their roles in infection.
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Couvin D, Dereeper A, Meyer DF, Noroy C, Gaete S, Bhakkan B, Poullet N, Gaspard S, Bezault E, Marcelino I, Pruneau L, Segretier W, Stattner E, Cazenave D, Garnier M, Pot M, Tressières B, Deloumeaux J, Breurec S, Ferdinand S, Gonzalez-Rizzo S, Reynaud Y. KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies). BIOINFORMATICS ADVANCES 2022; 2:vbac010. [PMID: 36699379 PMCID: PMC9710593 DOI: 10.1093/bioadv/vbac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/28/2023]
Abstract
Summary Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a 'one health' approach, for a better comprehension and surveillance of humans, plants or animals' health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to 'omics' data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated 'Galaxy KaruBioNet' platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html. Contact dcouvin@pasteur-guadeloupe.fr. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- David Couvin
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,To whom correspondence should be addressed
| | - Alexis Dereeper
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Damien F Meyer
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe 97170, France,ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier 34000, France
| | - Christophe Noroy
- Développement, Analyse, Transfert et Application (DATA), Lamentin, Guadeloupe 97129, France
| | - Stanie Gaete
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Bernard Bhakkan
- Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Nausicaa Poullet
- URZ Recherches Zootechniques, INRAE, Petit-Bourg, Guadeloupe 97170, France
| | - Sarra Gaspard
- Laboratoire COVACHIMM2E EA3592, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Etienne Bezault
- UMR BOREA (MNHN, CNRS-7208, IRD-207, Sorbonne Université, UCN, UA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Isabel Marcelino
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Ludovic Pruneau
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Damien Cazenave
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Maëlle Garnier
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Matthieu Pot
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Benoît Tressières
- Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Jacqueline Deloumeaux
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France,Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Sébastien Breurec
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Séverine Ferdinand
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Silvina Gonzalez-Rizzo
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
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