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Abstract
Type III secretion systems (T3SSs) are utilized by Gram-negative pathogens to enhance their pathogenesis. This secretion system is associated with the delivery of effectors through a needle-like structure from the bacterial cytosol directly into a target eukaryotic cell. These effector proteins then manipulate specific eukaryotic cell functions to benefit pathogen survival within the host. The obligate intracellular pathogens of the family Chlamydiaceae have a highly evolutionarily conserved nonflagellar T3SS that is an absolute requirement for their survival and propagation within the host with about one-seventh of the genome dedicated to genes associated with the T3SS apparatus, chaperones, and effectors. Chlamydiae also have a unique biphasic developmental cycle where the organism alternates between an infectious elementary body (EB) and replicative reticulate body (RB). T3SS structures have been visualized on both EBs and RBs. And there are effector proteins that function at each stage of the chlamydial developmental cycle, including entry and egress. This review will discuss the history of the discovery of chlamydial T3SS and the biochemical characterization of components of the T3SS apparatus and associated chaperones in the absence of chlamydial genetic tools. These data will be contextualized into how the T3SS apparatus functions throughout the chlamydial developmental cycle and the utility of heterologous/surrogate models to study chlamydial T3SS. Finally, there will be a targeted discussion on the history of chlamydial effectors and recent advances in the field.
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Affiliation(s)
- Elizabeth A. Rucks
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Durham Research Center II, Omaha, Nebraska, USA
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2
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Pasternak Z, Chapnik N, Yosef R, Kopelman NM, Jurkevitch E, Segev E. Identifying protein function and functional links based on large-scale co-occurrence patterns. PLoS One 2022; 17:e0264765. [PMID: 35239724 PMCID: PMC8893610 DOI: 10.1371/journal.pone.0264765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/16/2022] [Indexed: 11/23/2022] Open
Abstract
Objective The vast majority of known proteins have not been experimentally tested even at the level of measuring their expression, and the function of many proteins remains unknown. In order to decipher protein function and examine functional associations, we developed "Cliquely", a software tool based on the exploration of co-occurrence patterns. Computational model Using a set of more than 23 million proteins divided into 404,947 orthologous clusters, we explored the co-occurrence graph of 4,742 fully sequenced genomes from the three domains of life. Edge weights in this graph represent co-occurrence probabilities. We use the Bron–Kerbosch algorithm to detect maximal cliques in this graph, fully-connected subgraphs that represent meaningful biological networks from different functional categories. Main results We demonstrate that Cliquely can successfully identify known networks from various pathways, including nitrogen fixation, glycolysis, methanogenesis, mevalonate and ribosome proteins. Identifying the virulence-associated type III secretion system (T3SS) network, Cliquely also added 13 previously uncharacterized novel proteins to the T3SS network, demonstrating the strength of this approach. Cliquely is freely available and open source. Users can employ the tool to explore co-occurrence networks using a protein of interest and a customizable level of stringency, either for the entire dataset or for a one of the three domains—Archaea, Bacteria, or Eukarya.
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Affiliation(s)
- Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police, Jerusalem, Israel
- Faculty of Management of Technology, Holon Institute of Technology, Holon, Israel
| | - Noam Chapnik
- Faculty of Management of Technology, Holon Institute of Technology, Holon, Israel
| | - Roy Yosef
- Faculty of Management of Technology, Holon Institute of Technology, Holon, Israel
| | - Naama M. Kopelman
- Faculty of Science, Holon Institute of Technology, Holon, Israel
- * E-mail:
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elad Segev
- Faculty of Science, Holon Institute of Technology, Holon, Israel
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3
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Li D, Wang X, Xu X, Gu J, Yang Y, Liu T, Wang S, Chen S, Li J. Duck Complement Factor H Binds to Outer Membrane Protein Omp24 of Riemerella anatipestifer. Avian Dis 2021; 65:261-268. [PMID: 34412457 DOI: 10.1637/0005-2086-65.2.261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 03/29/2021] [Indexed: 11/05/2022]
Abstract
The resistance to serum complement-mediated killing is a vital virulence property of microbial pathogens. Complement factor H (FH) is a key negative regulator of the complement alternative pathway (AP) that prevents formation and accelerates the decay of AP C3 convertase and acts as a cofactor in the inactivation of C3b. Pathogens can recruit host FH through their surface proteins to escape the clearance of the complement system. Riemerella anatipestifer could also evade the complement system attack to achieve host infection, but the mechanism is still unclear. In this study, the R. anatipestifer proteins that could interact with FH in host serum were screened and analyzed, and the functions were determined. Affinity chromatography with a Ni-nitrilotriacetic acid Sefinose column and mass spectrometry identified three outer membrane proteins (Omp) of R. anatipestifer, Omp54, Omp53, and Omp24, as potential FH-binding proteins. We then successfully conducted the prokaryotic expression and polyclonal antibody preparation of three candidate proteins. Indirect immunofluorescence assay showed that three candidate proteins were all present in R. anatipestifer. The affinity blotting assay, anti-serum-inhibiting assay, and serum bactericidal assay presented evidence that Omp24 could bind FH. Moreover, FH bound to Omp24 was associated with resistance to the alternative pathway and functional for R. anatipestifer survival in the normal duck serum. These results suggested that R. anatipestifer Omp24 was a FH-binding protein and the interaction with FH blocked the alternative pathway. Recruitment of complement regulatory proteins may facilitate better R. anatipestifer resistance to this vital line of host defense.
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Affiliation(s)
- Delong Li
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, People's Republic of China
| | - Xiangli Wang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Xingsheng Xu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Jiulong Gu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Yunchuan Yang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Ting Liu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Siyuan Wang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China
| | - Sihuai Chen
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, People's Republic of China
| | - Jixiang Li
- College of Veterinary Medicine, Southwest University, Chongqing 402460, People's Republic of China, .,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, People's Republic of China
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4
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Dharamshi JE, Tamarit D, Eme L, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG. Marine Sediments Illuminate Chlamydiae Diversity and Evolution. Curr Biol 2020; 30:1032-1048.e7. [PMID: 32142706 DOI: 10.1016/j.cub.2020.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/22/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Orsay 91400, France
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Felix Homa
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Steffen L Jørgensen
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, Bergen 5020, Norway
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg 1790 AB, the Netherlands
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands.
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5
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Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M. Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae. ISME JOURNAL 2017. [PMID: 28644443 PMCID: PMC5604735 DOI: 10.1038/ismej.2017.95] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Marc Mussmann
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | | | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthias Horn
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
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6
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Erhardt M, Wheatley P, Kim EA, Hirano T, Zhang Y, Sarkar MK, Hughes KT, Blair DF. Mechanism of type-III protein secretion: Regulation of FlhA conformation by a functionally critical charged-residue cluster. Mol Microbiol 2017; 104:234-249. [PMID: 28106310 DOI: 10.1111/mmi.13623] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 11/28/2022]
Abstract
The bacterial flagellum contains a specialized secretion apparatus in its base that pumps certain protein subunits through the growing structure to their sites of installation beyond the membrane. A related apparatus functions in the injectisomes of gram-negative pathogens to export virulence factors into host cells. This mode of protein export is termed type-III secretion (T3S). Details of the T3S mechanism are unclear. It is energized by the proton gradient; here, a mutational approach was used to identify proton-binding groups that might function in transport. Conserved proton-binding residues in all the membrane components were tested. The results identify residues R147, R154 and D158 of FlhA as most critical. These lie in a small, well-conserved cytoplasmic domain of FlhA, located between transmembrane segments 4 and 5. Two-hybrid experiments demonstrate self-interaction of the domain, and targeted cross-linking indicates that it forms a multimeric array. A mutation that mimics protonation of the key acidic residue (D158N) was shown to trigger a global conformational change that affects the other, larger cytoplasmic domain that interacts with the export cargo. The results are discussed in the framework of a transport model based on proton-actuated movements in the cytoplasmic domains of FlhA.
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Affiliation(s)
- Marc Erhardt
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Junior Research Group Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Inhoffenstraβe 7, Braunschweig, 38124, Germany
| | - Paige Wheatley
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Eun A Kim
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Takanori Hirano
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Toshiba Medical Service Corporation, 1385 Shimoichigami, Otawara-shi, Tochigi, 324-8550, Japan
| | - Yang Zhang
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | | | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
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7
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Elucidation of the functional role of flagella in virulence and ecological traits of Pseudomonas cichorii using flagella absence (Δ fliJ ) and deficiency (Δ fliI ) mutants. Res Microbiol 2016; 167:262-271. [DOI: 10.1016/j.resmic.2016.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 01/20/2016] [Accepted: 01/20/2016] [Indexed: 02/02/2023]
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8
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Burgess JL, Jones HB, Kumar P, Toth RT, Middaugh CR, Antony E, Dickenson NE. Spa47 is an oligomerization-activated type three secretion system (T3SS) ATPase from Shigella flexneri. Protein Sci 2016; 25:1037-48. [PMID: 26947936 DOI: 10.1002/pro.2917] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/23/2016] [Accepted: 03/02/2016] [Indexed: 02/06/2023]
Abstract
Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa47 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 with the largest greater than 8 fold more active for ATP hydrolysis than the monomer. An ATPase inactive Spa47 point mutant was then engineered by targeting a conserved Lysine within the predicted Walker A motif of Spa47. Interestingly, the mutant maintained a similar oligomerization pattern as active Spa47, but was unable to restore invasion phenotype when used to complement a spa47 null S. flexneri strain. Together, these results identify Spa47 as a Shigella T3SS ATPase and suggest that its activity is linked to oligomerization, perhaps as a regulatory mechanism as seen in some related pathogens. Additionally, Spa47 catalyzed ATP hydrolysis appears to be essential for host cell invasion, providing a strong platform for additional studies dissecting its role in virulence and providing an attractive target for anti-infective agents.
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Affiliation(s)
- Jamie L Burgess
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322
| | - Heather B Jones
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322
| | - Prashant Kumar
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - Ronald T Toth
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, 53201
| | - Nicholas E Dickenson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322
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Bergeron JR. Structural modeling of the flagellum MS ring protein FliF reveals similarities to the type III secretion system and sporulation complex. PeerJ 2016; 4:e1718. [PMID: 26925337 PMCID: PMC4768692 DOI: 10.7717/peerj.1718] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/31/2016] [Indexed: 11/29/2022] Open
Abstract
The flagellum is a large proteinaceous organelle found at the surface of many bacteria, whose primary role is to allow motility through the rotation of a long extracellular filament. It is an essential virulence factor in many pathogenic species, and is also a priming component in the formation of antibiotic-resistant biofilms. The flagellum consists of the export apparatus on the cytosolic side; the basal body and rotor, spanning the bacterial membrane(s) and periplasm; and the hook-filament, that protrudes away from the bacterial surface. Formation of the basal body MS ring region, constituted of multiple copies of the protein FliF, is one of the initial steps of flagellum assembly. However, the precise architecture of FliF is poorly understood. Here, I report a bioinformatics analysis of the FliF sequence from various bacterial species, suggesting that its periplasmic region is composed of three globular domains. The first two are homologous to that of the type III secretion system injectisome proteins SctJ, and the third possesses a similar fold to that of the sporulation complex component SpoIIIAG. I also describe that Chlamydia possesses an unusual FliF protein, lacking part of the SctJ homology domain and the SpoIIIAG-like domain, and fused to the rotor component FliG at its C-terminus. Finally, I have combined the sequence analysis of FliF with the EM map of the MS ring, to propose the first atomic model for the FliF oligomer, suggesting that FliF is structurally akin to a fusion of the two injectisome components SctJ and SctD. These results further define the relationship between the flagellum, injectisome and sporulation complex, and will facilitate future structural characterization of the flagellum basal body.
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Affiliation(s)
- Julien R Bergeron
- Department of Biochemistry, University of Washington , Seattle, WA , USA
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10
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Ferrell JC, Fields KA. A working model for the type III secretion mechanism in Chlamydia. Microbes Infect 2015; 18:84-92. [PMID: 26515030 DOI: 10.1016/j.micinf.2015.10.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 01/09/2023]
Abstract
It has been appreciated for almost 20 years that members of the Chlamydiales possess a virulence-associated type III secretion mechanism. Given the obligate intracellular nature of these bacteria, defining exactly how type III secretion functions to promote pathogenesis has been challenging. We present a working model herein that is based on current evidence.
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Affiliation(s)
- Joshua C Ferrell
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Kenneth A Fields
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY 40536, USA.
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11
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Park J, Zhang Y, Chen C, Dudley EG, Harvill ET. Diversity of secretion systems associated with virulence characteristics of the classical bordetellae. MICROBIOLOGY-SGM 2015; 161:2328-40. [PMID: 26459829 DOI: 10.1099/mic.0.000197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Secretion systems are key virulence factors, modulating interactions between pathogens and the host's immune response. Six potential secretion systems (types 1-6; T1SS-T6SS) have been discussed in classical bordetellae, respiratory commensals/pathogens of mammals. The prototypical Bordetella bronchiseptica strain RB50 genome seems to contain all six systems, whilst two human-restricted subspecies, Bordetella parapertussis and Bordetella pertussis, have lost different subsets of these. This implicates secretion systems in the divergent evolutionary histories that have led to their success in different niches. Based on our previous work demonstrating that changes in secretion systems are associated with virulence characteristics, we hypothesized there would be substantial divergence of the loci encoding each amongst sequenced strains. Here, we describe extensive differences in secretion system loci; 10 of the 11 sequenced strains had lost subsets of genes or one entire secretion system locus. These loci contained genes homologous to those present in the respective loci in distantly related organisms, as well as genes unique to bordetellae, suggesting novel and/or auxiliary functions. The high degree of conservation of the T3SS locus, a complex machine with interdependent parts that must be conserved, stands in dramatic contrast to repeated loss of T5aSS 'autotransporters', which function as an autonomous unit. This comparative analysis provided insights into critical aspects of each pathogen's adaptation to its different niche, and the relative contributions of recombination, mutation and horizontal gene transfer. In addition, the relative conservation of various secretion systems is an important consideration in the ongoing search for more highly conserved protective antigens for the next generation of pertussis vaccines.
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Affiliation(s)
- Jihye Park
- 1 Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 2 Graduate Program in Bioinformatics and Genomics, Pennsylvania State University, University Park, PA, USA
| | - Ying Zhang
- 1 Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chun Chen
- 3 Department of Food Science, Pennsylvania State University, University Park, PA, USA
| | - Edward G Dudley
- 3 Department of Food Science, Pennsylvania State University, University Park, PA, USA
| | - Eric T Harvill
- 1 Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 4 Singapore Centre on Environmental Life Sciences Engineering, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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12
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Barta ML, Battaile KP, Lovell S, Hefty PS. Hypothetical protein CT398 (CdsZ) interacts with σ(54) (RpoN)-holoenzyme and the type III secretion export apparatus in Chlamydia trachomatis. Protein Sci 2015; 24:1617-32. [PMID: 26173998 DOI: 10.1002/pro.2746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022]
Abstract
A significant challenge to bacteriology is the relatively large proportion of proteins that lack sufficient sequence similarity to support functional annotation (i.e. hypothetical proteins). The aim of this study was to apply protein structural homology to gain insights into a candidate protein of unknown function (CT398) within the medically important, obligate intracellular bacterium Chlamydia trachomatis. C. trachomatis is a major human pathogen responsible for numerous infections throughout the world that can lead to blindness and infertility. A 2.12 Å crystal structure of hypothetical protein CT398 was determined that was comprised of N-terminal coiled-coil and C-terminal Zn-ribbon domains. The structure of CT398 displayed a high degree of structural similarity to FlgZ (Flagellar-associated zinc-ribbon domain protein) from Helicobacter pylori. This observation directed analyses of candidate protein partners of CT398, revealing interactions with two paralogous type III secretion system (T3SS) ATPase-regulators (CdsL and FliH) and the alternative sigma factor RpoN (σ(54) ). Furthermore, genetic introduction of a conditional expression, affinity-tagged construct into C. trachomatis enabled the purification of a CT398-RpoN-holoenzyme complex, suggesting a potential role for CT398 in modulating transcriptional activity during infection. The interactions reported here, in tandem with previous FlgZ studies in H. pylori, indicate that CT398 functions as a regulator of several key areas of chlamydial biology throughout the developmental cycle. Accordingly, we propose that CT398 be named CdsZ (Contact-dependent secretion-associated zinc-ribbon domain protein).
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Affiliation(s)
- Michael L Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045
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13
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Identification of in vivo-induced bacterial protein antigens during calf infection with Chlamydia psittaci. Int J Med Microbiol 2015; 305:310-21. [DOI: 10.1016/j.ijmm.2014.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/19/2014] [Accepted: 12/20/2014] [Indexed: 01/21/2023] Open
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14
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Hung NB, Ramkumar G, Lee YH. An effector gene hopA1 influences on virulence, host specificity, and lifestyles of Pseudomonas cichorii JBC1. Res Microbiol 2014; 165:620-9. [PMID: 25127676 DOI: 10.1016/j.resmic.2014.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/05/2014] [Accepted: 08/05/2014] [Indexed: 11/30/2022]
Abstract
Pseudomonas cichorii is a devastating pathogen which infects a wide range of ornamental as well as agricultural crops worldwide. Characterization of virulence genes helps to understand pathogens' infection processes, which may lead to development of resistant crops. For functional validation of novel genes, we re-constructed pUCP18 vector with λ phage red operon and sacB gene (pUCP18_RedS), which simplified conventional marker exchange system. The effector gene hopA1 of P. cichorii JBC1 was marker exchanged with PCR product of kanamycin gene flanked by hopA1 flanking region using pUCP18_RedS. The virulence and internal growth of hopA1 defective mutant (ΔhopA1) in tomato seedlings was significantly reduced compared to wild type (WT) and hopA1 complemented strain (ΔhopA1::phopA1). The analysis on role of hopA1 in host range revealed that P. cichorii was hopA1-dependent to infect cabbage, tomato, soybean, hot pepper, and cucumber, but not melon and eggplant. Despite the similarity in growth pattern, the biofilm formation and swarming motility of ΔhopA1 were significantly reduced compared to WT and ΔhopA1::phopA1. The results of this study indicate that hopA1 plays a significant role not only in virulence and host specificity, but also motility and biofilm formation of P. cichorii which may influence the infection processes.
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Affiliation(s)
- Nguyen Bao Hung
- Division of Biotechnology, Chonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 570-752, Republic of Korea
| | - Gandhimani Ramkumar
- Division of Biotechnology, Chonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 570-752, Republic of Korea
| | - Yong Hoon Lee
- Division of Biotechnology, Chonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 570-752, Republic of Korea; Advanced Institute of Environment and Bioscience, and Plant Medical Research Center, Chonbuk National University, Republic of Korea.
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15
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Diepold A, Wagner S. Assembly of the bacterial type III secretion machinery. FEMS Microbiol Rev 2014; 38:802-22. [PMID: 24484471 DOI: 10.1111/1574-6976.12061] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 01/02/2014] [Accepted: 01/13/2014] [Indexed: 11/29/2022] Open
Abstract
Many bacteria that live in contact with eukaryotic hosts, whether as symbionts or as pathogens, have evolved mechanisms that manipulate host cell behaviour to their benefit. One such mechanism, the type III secretion system, is employed by Gram-negative bacterial species to inject effector proteins into host cells. This function is reflected by the overall shape of the machinery, which resembles a molecular syringe. Despite the simplicity of the concept, the type III secretion system is one of the most complex known bacterial nanomachines, incorporating one to more than hundred copies of up to twenty different proteins into a multi-MDa transmembrane complex. The structural core of the system is the so-called needle complex that spans the bacterial cell envelope as a tripartite ring system and culminates in a needle protruding from the bacterial cell surface. Substrate targeting and translocation are accomplished by an export machinery consisting of various inner membrane embedded and cytoplasmic components. The formation of such a multimembrane-spanning machinery is an intricate task that requires precise orchestration. This review gives an overview of recent findings on the assembly of type III secretion machines, discusses quality control and recycling of the system and proposes an integrated assembly model.
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Affiliation(s)
- Andreas Diepold
- Department of Biochemistry, University of Oxford, Oxford, UK
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Abstract
Members of the order Chlamydiales comprise a group of exquisitely evolved parasites of eukaryotic hosts that extends from single-celled amoeba to mammals. The most notable are human pathogens and include the agent of oculogenital disease Chlamydia trachomatis, the respiratory pathogen C. pneumoniae, and the zoonotic agent C. psittaci. All of these species are obligate intracellular bacteria that develop within parasitophorous vesicles termed inclusions. This demanding lifestyle necessitates orchestrated entry into nonphagocytic cells, creation of a privileged intracellular niche, and subversion of potent host defenses. All chlamydial genomes contain the coding capacity for a nonflagellar type III secretion system, and this mechanism has arisen as an essential contributor to chlamydial virulence. The emergence of tractable approaches to the genetic manipulation of chlamydiae raises the possibility of explosive progress in understanding this important contributor to chlamydial pathogenesis. This minireview considers challenges and recent advances that have revealed how chlamydiae have maintained conserved aspects of T3S while exploiting diversification to yield a system that exerts a fundamental role in the unique biology of Chlamydia species.
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Hartmann N, Büttner D. The inner membrane protein HrcV from Xanthomonas spp. is involved in substrate docking during type III secretion. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1176-1189. [PMID: 23777429 DOI: 10.1094/mpmi-01-13-0019-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pathogenicity of the gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria depends on a membrane-spanning type III secretion (T3S) system, which translocates effector proteins into eukaryotic host cells. In this study, we characterized the T3S system component HrcV, which is a member of the YscV/FlhA family of inner membrane proteins. HrcV consists of eight transmembrane helices and a cytoplasmic region (HrcVC). Mutant and protein-protein interaction studies showed that HrcVC is essential for protein function and binds to T3S substrates, including the early substrate HrpB2, the pilus protein HrpE, and effector proteins. Furthermore, HrcVC interacts with itself and with components and control proteins of the T3S apparatus. The interaction of HrcVC with HrpB2, HrpE, and T3S system components depends on amino acid residues in a conserved motif, designated flagella/hypersensitive response/invasion proteins export pore (FHIPEP), which is located in a cytoplasmic loop between transmembrane helix four and five of HrcV. Mutations in the FHIPEP motif abolish HrcV function but do not affect the interaction of HrcVC with effector proteins.
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The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type-Three Secretion System effectors and identification of other virulence factors. Proteome Sci 2013; 11:42. [PMID: 24073886 PMCID: PMC3852671 DOI: 10.1186/1477-5956-11-42] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/23/2013] [Indexed: 01/24/2023] Open
Abstract
Background Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Several virulence factors have been described, but the type-three secretion system (T3SS) is recognized as having a major effect on virulence by injecting effectors directly into fish cells. In this study we used high-throughput proteomics to display the differences between in vitro secretome of A. salmonicida wild-type (wt, hypervirulent, JF2267) and T3SS-deficient (isogenic ΔascV, extremely low-virulent, JF2747) strains in exponential and stationary phases of growth. Results Results confirmed the secretion of effectors AopH, AexT, AopP and AopO via T3SS, and for the first time demonstrated the impact of T3SS in secretion of Ati2, AopN and ExsE that are known as effectors in other pathogens. Translocators, needle subunits, Ati1, and AscX were also secreted in supernatants (SNs) dependent on T3SS. AopH, Ati2, AexT, AopB and AopD were in the top seven most abundant excreted proteins. EF-G, EF-Tu, DnaK, HtpG, PNPase, PepN and MdeA were moderately secreted in wt SNs and predicted to be putative T3 effectors by bioinformatics. Pta and ASA_P5G088 were increased in wt SNs and T3-associated in other bacteria. Ten conserved cytoplasmic proteins were more abundant in wt SNs than in the ΔascV mutant, but without any clear association to a secretion system. T1-secreted proteins were predominantly found in wt SNs: OmpAI, OmpK40, DegQ, insulinase ASA_0716, hypothetical ASA_0852 and ASA_3619. Presence of T3SS components in pellets was clearly decreased by ascV deletion, while no impact was observed on T1- and T2SS. Our results demonstrated that the ΔascV mutant strain excreted well-described (VapA, AerA, AerB, GCAT, Pla1, PlaC, TagA, Ahe2, GbpA and enolase) and yet uncharacterized potential toxins, adhesins and enzymes as much as or even more than the wt strain. Other putative important virulence factors were not detected. Conclusions We demonstrated the whole in vitro secretome and T3SS repertoire of hypervirulent A. salmonicida. Several toxins, adhesins and enzymes that are not part of the T3SS secretome were secreted to a higher extent in the extremely low-virulent ΔascV mutant. All together, our results show the high importance of an intact T3SS to initiate the furunculosis and offer new information about the pathogenesis.
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Maier CJ, Maier RH, Virok DP, Maass M, Hintner H, Bauer JW, Onder K. Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae. BMC Genomics 2012; 13:632. [PMID: 23157390 PMCID: PMC3534531 DOI: 10.1186/1471-2164-13-632] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/11/2012] [Indexed: 12/02/2022] Open
Abstract
Background The Gram-negative bacterium Chlamydia pneumoniae (Cpn) is the leading intracellular human pathogen responsible for respiratory infections such as pneumonia and bronchitis. Basic and applied research in pathogen biology, especially the elaboration of new mechanism-based anti-pathogen strategies, target discovery and drug development, rely heavily on the availability of the entire set of pathogen open reading frames, the ORFeome. The ORFeome of Cpn will enable genome- and proteome-wide systematic analysis of Cpn, which will improve our understanding of the molecular networks and mechanisms underlying and governing its pathogenesis. Results Here we report the construction of a comprehensive gene collection covering 98.5% of the 1052 predicted and verified ORFs of Cpn (Chlamydia pneumoniae strain CWL029) in Gateway® ‘entry’ vectors. Based on genomic DNA isolated from the vascular chlamydial strain CV-6, we constructed an ORFeome library that contains 869 unique Gateway® entry clones (83% coverage) and an additional 168 PCR-verified ‘pooled’ entry clones, reaching an overall coverage of ~98.5% of the predicted CWL029 ORFs. The high quality of the ORFeome library was verified by PCR-gel electrophoresis and DNA sequencing, and its functionality was demonstrated by expressing panels of recombinant proteins in Escherichia coli and by genome-wide protein interaction analysis for a test set of three Cpn virulence factors in a yeast 2-hybrid system. The ORFeome is available in different configurations of resource stocks, PCR-products, purified plasmid DNA, and living cultures of E. coli harboring the desired entry clone or pooled entry clones. All resources are available in 96-well microtiterplates. Conclusion This first ORFeome library for Cpn provides an essential new tool for this important pathogen. The high coverage of entry clones will enable a systems biology approach for Cpn or host–pathogen analysis. The high yield of recombinant proteins and the promising interactors for Cpn virulence factors described here demonstrate the possibilities for proteome-wide studies.
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Affiliation(s)
- Christina J Maier
- Department of Dermatology, Paracelsus Medical University, Salzburg, Austria
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20
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Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant- and animal-pathogenic bacteria. Microbiol Mol Biol Rev 2012; 76:262-310. [PMID: 22688814 DOI: 10.1128/mmbr.05017-11] [Citation(s) in RCA: 299] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Flagellar and translocation-associated type III secretion (T3S) systems are present in most gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. The architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated T3S systems. The needle/pilus is connected to a bacterial translocon that is inserted into the host plasma membrane and mediates the transkingdom transport of bacterial effector proteins into eukaryotic cells. During the last 3 to 5 years, significant progress has been made in the characterization of membrane-associated core components and extracellular structures of T3S systems. Furthermore, transcriptional and posttranscriptional regulators that control T3S gene expression and substrate specificity have been described. Given the architecture of the T3S system, it is assumed that extracellular components of the secretion apparatus are secreted prior to effector proteins, suggesting that there is a hierarchy in T3S. The aim of this review is to summarize our current knowledge of T3S system components and associated control proteins from both plant- and animal-pathogenic bacteria.
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The chlamydiales pangenome revisited: structural stability and functional coherence. Genes (Basel) 2012; 3:291-319. [PMID: 24704919 PMCID: PMC3899948 DOI: 10.3390/genes3020291] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/02/2012] [Accepted: 05/08/2012] [Indexed: 11/25/2022] Open
Abstract
The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales.
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22
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Suh MJ, Fedorova ND, Cagas SE, Hastings S, Fleischmann RD, Peterson SN, Perlin DS, Nierman WC, Pieper R, Momany M. Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome. Proteome Sci 2012; 10:30. [PMID: 22545825 PMCID: PMC3424117 DOI: 10.1186/1477-5956-10-30] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/30/2012] [Indexed: 11/14/2022] Open
Abstract
Background The pathogenic mold Aspergillus fumigatus is the most frequent infectious cause of death in severely immunocompromised individuals such as leukemia and bone marrow transplant patients. Germination of inhaled conidia (asexual spores) in the host is critical for the initiation of infection, but little is known about the underlying mechanisms of this process. Results To gain insights into early germination events and facilitate the identification of potential stage-specific biomarkers and vaccine candidates, we have used quantitative shotgun proteomics to elucidate patterns of protein abundance changes during early fungal development. Four different stages were examined: dormant conidia, isotropically expanding conidia, hyphae in which germ tube emergence has just begun, and pre-septation hyphae. To enrich for glycan-linked cell wall proteins we used an alkaline cell extraction method. Shotgun proteomic resulted in the identification of 375 unique gene products with high confidence, with no evidence for enrichment of cell wall-immobilized and secreted proteins. The most interesting discovery was the identification of 52 proteins enriched in dormant conidia including 28 proteins that have never been detected in the A. fumigatus conidial proteome such as signaling protein Pil1, chaperones BipA and calnexin, and transcription factor HapB. Additionally we found many small, Aspergillus specific proteins of unknown function including 17 hypothetical proteins. Thus, the most abundant protein, Grg1 (AFUA_5G14210), was also one of the smallest proteins detected in this study (M.W. 7,367). Among previously characterized proteins were melanin pigment and pseurotin A biosynthesis enzymes, histones H3 and H4.1, and other proteins involved in conidiation and response to oxidative or hypoxic stress. In contrast, expanding conidia, hyphae with early germ tubes, and pre-septation hyphae samples were enriched for proteins responsible for housekeeping functions, particularly translation, respiratory metabolism, amino acid and carbohydrate biosynthesis, and the tricarboxylic acid cycle. Conclusions The observed temporal expression patterns suggest that the A. fumigatus conidia are dominated by small, lineage-specific proteins. Some of them may play key roles in host-pathogen interactions, signal transduction during conidial germination, or survival in hostile environments.
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Affiliation(s)
- Moo-Jin Suh
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Natalie D Fedorova
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Steven E Cagas
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Susan Hastings
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | - Scott N Peterson
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - David S Perlin
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - William C Nierman
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Rembert Pieper
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Michelle Momany
- Department of Plant Biology, University of Georgia, Athens, GA, USA
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Collingro A, Tischler P, Weinmaier T, Penz T, Heinz E, Brunham RC, Read TD, Bavoil PM, Sachse K, Kahane S, Friedman MG, Rattei T, Myers GSA, Horn M. Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol 2011; 28:3253-70. [PMID: 21690563 DOI: 10.1093/molbev/msr161] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
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Betts-Hampikian HJ, Fields KA. The Chlamydial Type III Secretion Mechanism: Revealing Cracks in a Tough Nut. Front Microbiol 2010; 1:114. [PMID: 21738522 PMCID: PMC3125583 DOI: 10.3389/fmicb.2010.00114] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 09/22/2010] [Indexed: 12/22/2022] Open
Abstract
Present-day members of the Chlamydiaceae contain parasitic bacteria that have been co-evolving with their eukaryotic hosts over hundreds of millions of years. Likewise, a type III secretion system encoded within all genomes has been refined to complement the unique obligate intracellular niche colonized so successfully by Chlamydia spp. All this adaptation has occurred in the apparent absence of the horizontal gene transfer responsible for creating the wide range of diversity in other Gram-negative, type III-expressing bacteria. The result is a system that is, in many ways, uniquely chlamydial. A critical mass of information has been amassed that sheds significant light on how the chlamydial secretion system functions and contributes to an obligate intracellular lifestyle. Although the overall mechanism is certainly similar to homologous systems, an image has emerged where the chlamydial secretion system is essential for both survival and virulence. Numerous apparent differences, some subtle and some profound, differentiate chlamydial type III secretion from others. Herein, we provide a comprehensive review of the current state of knowledge regarding the Chlamydia type III secretion mechanism. We focus on the aspects that are distinctly chlamydial and comment on how this important system influences chlamydial pathogenesis. Gaining a grasp on this fascinating system has been challenging in the absence of a tractable genetic system. However, the surface of this tough nut has been scored and the future promises to be fruitful and revealing.
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Moore SA, Jia Y. Structure of the cytoplasmic domain of the flagellar secretion apparatus component FlhA from Helicobacter pylori. J Biol Chem 2010; 285:21060-9. [PMID: 20442410 PMCID: PMC2898369 DOI: 10.1074/jbc.m110.119412] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 04/21/2010] [Indexed: 11/06/2022] Open
Abstract
Using x-ray crystallography we have determined the structure of the cytoplasmic fragment (residues 384-732) of the flagellum secretion system protein FlhA from Helicobacter pylori at 2.4-A resolution (r = 0.224; R(free) = 0.263). FlhA proteins and their type III secretion homologues contain an N-terminal integral membrane domain (residues 1-350), a linker segment, and a globular C-terminal cytoplasmic region. The tertiary structure of the cytoplasmic fragment contains a thioredoxin-like domain, an RNA recognition motif-like domain inserted within the thioredoxin-fold, a helical domain, and a C-terminal beta/alpha domain. Inter-domain contacts are extensive and the H. pylori FlhA structure appears to be in a closed conformation where the C-terminal domain closes against the RNA recognition motif-fold domain. Highly conserved surface residues in FlhA proteins are concentrated on a narrow surface strip comprising the thioredoxin-like and helical domains, possibly close to the export channel opening. The conformation of the FlhA N-terminal linker segment suggests a likely orientation for the FlhA cytoplasmic fragment relative to the membrane-embedded export pore. Comparison with the recently published structures of the Salmonella FlhA cytoplasmic fragment and its type III secretion counterpart InvA highlight a conformational change where the C-terminal beta/alpha domain in H. pylori FlhA moves 15 A relative to Salmonella FlhA. The conformational change is complex but primarily involves hinge-like movements of the helical and C-terminal domains. Interpretation of previous mutational screens suggest that the C-terminal domain of FlhA(C) plays a regulatory role in substrate class switching in flagellum export.
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Affiliation(s)
- Stanley A Moore
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
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