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Hu Y, Wang Y, Hu X, Chao H, Li S, Ni Q, Zhu Y, Hu Y, Zhao Z, Chen M. T4SEpp: A pipeline integrating protein language models to predict bacterial type IV secreted effectors. Comput Struct Biotechnol J 2024; 23:801-812. [PMID: 38328004 PMCID: PMC10847861 DOI: 10.1016/j.csbj.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/20/2024] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Many pathogenic bacteria use type IV secretion systems (T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs and compared their performance. We integrated three modules into a model called T4SEpp. The first module searched for full-length homologs of known T4SEs, signal sequences, and effector domains; the second module fine-tuned a machine learning model using data for a signal sequence feature; and the third module used the three best-performing pre-trained protein language models. T4SEpp outperformed other state-of-the-art (SOTA) software tools, achieving ∼0.98 accuracy at a high specificity of ∼0.99, based on the assessment of an independent validation dataset. T4SEpp predicted 13 T4SEs from Helicobacter pylori, including the well-known CagA and 12 other potential ones, among which eleven could potentially interact with human proteins. This suggests that these potential T4SEs may be associated with the pathogenicity of H. pylori. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible at https://bis.zju.edu.cn/T4SEpp.
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Affiliation(s)
- Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
- Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qinyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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Mikhailovich V, Heydarov R, Zimenkov D, Chebotar I. Stenotrophomonas maltophilia virulence: a current view. Front Microbiol 2024; 15:1385631. [PMID: 38741741 PMCID: PMC11089167 DOI: 10.3389/fmicb.2024.1385631] [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: 02/14/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen intrinsically resistant to multiple and broad-spectrum antibiotics. Although the bacterium is considered a low-virulence pathogen, it can cause various severe diseases and contributes significantly to the pathogenesis of multibacterial infections. During the COVID-19 pandemic, S. maltophilia has been recognized as one of the most common causative agents of respiratory co-infections and bacteremia in critically ill COVID-19 patients. The high ability to adapt to unfavorable environments and new habitat niches, as well as the sophisticated switching of metabolic pathways, are unique mechanisms that attract the attention of clinical researchers and experts studying the fundamental basis of virulence. In this review, we have summarized the current knowledge on the molecular aspects of S. maltophilia virulence and putative virulence factors, partially touched on interspecific bacterial interactions and iron uptake systems in the context of virulence, and have not addressed antibiotic resistance.
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Affiliation(s)
- Vladimir Mikhailovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Rustam Heydarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Danila Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Igor Chebotar
- Pirogov Russian National Research Medical University, Moscow, Russia
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3
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Carhuaricra-Huaman D, Gonzalez IHL, Ramos PL, da Silva AM, Setubal JC. Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths ( Bradypus variegatus), the first from a non-human host. PeerJ 2024; 12:e17206. [PMID: 38584940 PMCID: PMC10999152 DOI: 10.7717/peerj.17206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.
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Affiliation(s)
| | - Irys H L Gonzalez
- Coordenadoria de Fauna Silvestre, Secretaria do Meio Ambiente, São Paulo, SP, Brazil
| | - Patricia L Ramos
- Coordenadoria de Fauna Silvestre, Secretaria do Meio Ambiente, São Paulo, SP, Brazil
| | - Aline M da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Joao C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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Stevens MJA, Stephan R, Horlbog JA, Cernela N, Nüesch-Inderbinen M. Whole genome sequence-based characterization of Campylobacter isolated from broiler carcasses over a three-year period in a big poultry slaughterhouse reveals high genetic diversity and a recurring genomic lineage of Campylobacter jejuni. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 119:105578. [PMID: 38417639 DOI: 10.1016/j.meegid.2024.105578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Campylobacter is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 Campylobacter isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from broilers from three different types of farming systems (particularly animal-friendly stabling (PAFS), free-range farms, and organic farms). Campylobacter jejuni (n = 127) and Campylobacter coli (n = 28) were analysed using a whole genome sequencing (WGS) approach (MiniSeq; Illumina). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into complex types (CTs) using the cgMLST SeqSphere+ scheme. Antimicrobial resistance genes were identified using the Resistance Gene Identifier (RGI), and virulence genes were identified using the virulence factor database (VFDB). A high degree of genetic diversity was observed. Many sequence types (C. jejuni ST19, ST21, ST48, ST50, ST122, ST262 and C. coli ST827) occurred more than once and were distributed throughout the study period, irrespective of the year of isolation and of the broiler farming type. Antimicrobial resistance determinants included blaOXA and tet(O) genes, as well as the T86I substitution within GyrA. Virulence genes known to play a role in human Campylobacter infection were identified such as the wlaN, cstIII, neuA1, neuB1, and neuC1. Subtyping of the Campylobacter isolates identified the occurrence of a highly clonal population of C. jejuni ST21 that was isolated throughout the three-year study period from carcasses from farms with geographically different locations and different farming systems. The high rate of genetic diversity observed among broiler carcass isolates is consistent with previous studies. The identification of a persisting highly clonal C. jejuni ST21 subtype suggests that the slaughterhouse may represent an environment in which C. jejuni ST21 may survive, however, the ecological reservoir potentially maintaining this clone remains unknown.
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Affiliation(s)
- Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Jule Anna Horlbog
- National Reference Centre for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Magdalena Nüesch-Inderbinen
- National Reference Centre for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Costa TRD, Patkowski JB, Macé K, Christie PJ, Waksman G. Structural and functional diversity of type IV secretion systems. Nat Rev Microbiol 2024; 22:170-185. [PMID: 37814112 DOI: 10.1038/s41579-023-00974-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances have substantially improved our understanding of the mechanisms underlying the recruitment and delivery of DNA and protein substrates to the extracellular environment or target cells. In this Review, we aim to summarize these exciting structural and molecular biology findings and to discuss their functional implications for substrate recognition, recruitment and translocation, as well as the biogenesis of extracellular pili. We also describe adaptations necessary for deploying a breadth of processes, such as bacterial survival, host-pathogen interactions and biotic and abiotic adhesion. We highlight the functional and structural diversity that allows this extremely versatile secretion superfamily to function under different environmental conditions and in different bacterial species. Additionally, we emphasize the importance of further understanding the mechanism of type IV secretion, which will support us in combating antimicrobial resistance and treating type IV secretion system-related infections.
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Affiliation(s)
- Tiago R D Costa
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK.
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK
- Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes and CNRS, Rennes, France
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA.
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK.
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Wang B, Xu F, Zhang Z, Shen D, Wang L, Wu H, Yan Q, Cui C, Wang P, Wei Q, Shao X, Wang M, Qian G. Type IV secretion system effector sabotages multiple defense systems in a competing bacterium. THE ISME JOURNAL 2024; 18:wrae121. [PMID: 38959853 DOI: 10.1093/ismejo/wrae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/22/2024] [Accepted: 07/02/2024] [Indexed: 07/05/2024]
Abstract
Effector proteins secreted by bacteria that infect mammalian and plant cells often subdue eukaryotic host cell defenses by simultaneously affecting multiple targets. However, instances when a bacterial effector injected in the competing bacteria sabotage more than a single target have not been reported. Here, we demonstrate that the effector protein, LtaE, translocated by the type IV secretion system from the soil bacterium Lysobacter enzymogenes into the competing bacterium, Pseudomonas protegens, affects several targets, thus disabling the antibacterial defenses of the competitor. One LtaE target is the transcription factor, LuxR1, that regulates biosynthesis of the antimicrobial compound, orfamide A. Another target is the sigma factor, PvdS, required for biosynthesis of another antimicrobial compound, pyoverdine. Deletion of the genes involved in orfamide A and pyoverdine biosynthesis disabled the antibacterial activity of P. protegens, whereas expression of LtaE in P. protegens resulted in the near-complete loss of the antibacterial activity against L. enzymogenes. Mechanistically, LtaE inhibits the assembly of the RNA polymerase complexes with each of these proteins. The ability of LtaE to bind to LuxR1 and PvdS homologs from several Pseudomonas species suggests that it can sabotage defenses of various competitors present in the soil or on plant matter. Our study thus reveals that the multi-target effectors have evolved to subdue cell defenses not only in eukaryotic hosts but also in bacterial competitors.
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Affiliation(s)
- Bingxin Wang
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Fugui Xu
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Zeyu Zhang
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Danyu Shen
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Limin Wang
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Huijun Wu
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, United States
| | - Chuanbin Cui
- Department of Plant Pathology, Shaanxi Provincial Tobacco Corporation of CNTC, Xi'an 710061, China
| | - Pingping Wang
- Department of Plant Pathology, Shaanxi Provincial Tobacco Corporation of CNTC, Xi'an 710061, China
| | - Qi Wei
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Xiaolong Shao
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou 310058, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guoliang Qian
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
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Zehra M, Heo J, Chung JM, Durie CL. Comparative Analysis of T4SS Molecular Architectures. J Microbiol Biotechnol 2023; 33:1543-1551. [PMID: 37528551 PMCID: PMC10772558 DOI: 10.4014/jmb.2307.07006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/03/2023]
Abstract
The recently published high-resolution R388 T4SS structure provides exciting new details about the complete complex of T4SS, including the components making up the stalk and arches, numerous symmetry mismatches between regions of the complex, and an intriguing interpretation of the closed stalk and radial symmetry of the inner membrane complex, which is related to pilus biogenesis assembly. However, there are a few unidentified densities in the electron microscopy map and portions of the identified component sequences for which the structure is not yet known. It is also unclear how well this minimized DNA-transporting T4SS predicts the structure of other T4SSs, such as expanded systems and those that transport proteins rather than DNA. In this review, we evaluate what can be inferred from the recent high-resolution structure of the R388 T4SS with respect to the Cag and Dot/Icm systems. These systems were selected because, given what is currently known about these systems, we expect them to present most structural differences compared to the R388 T4SS structure. Furthermore, we discuss bacterial physiology and diversity, the T4SS structures and their variations between different bacterial species. These insights may prove beneficial for researchers who elucidate the structure and functions of T4SS in different bacterial species.
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Affiliation(s)
- Mishghan Zehra
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jiwon Heo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Republic of Korea
| | - Jeong Min Chung
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Gyeonggi, Republic of Korea
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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Breidenstein A, Ter Beek J, Berntsson RPA. Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing. Life Sci Alliance 2023; 6:e202201775. [PMID: 36669792 PMCID: PMC9868005 DOI: 10.26508/lsa.202201775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.
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Affiliation(s)
- Annika Breidenstein
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
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9
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Kang YS, Kirby JE. A Versatile Nanoluciferase Reporter Reveals Structural Properties Associated with a Highly Efficient, N-Terminal Legionella pneumophila Type IV Secretion Translocation Signal. Microbiol Spectr 2023; 11:e0233822. [PMID: 36815834 PMCID: PMC10100965 DOI: 10.1128/spectrum.02338-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
Many Gram-negative pathogens rely on type IV secretion systems (T4SS) for infection. One limitation has been the lack of ideal reporters to identify T4SS translocated effectors and study T4SS function. Most reporter systems make use of fusions to reporter proteins, in particular, β-lactamase (TEM) and calmodulin-dependent adenylate cyclase (CYA), that allow detection of translocated enzymatic activity inside host cells. However, both systems require costly reagents and use complex, multistep procedures for loading host cells with substrate (TEM) or for analysis (CYA). Therefore, we have developed and characterized a novel reporter system using nanoluciferase (NLuc) fusions to address these limitations. Serendipitously, we discovered that Nluc itself is efficiently translocated by Legionella pneumophila T4SS in an IcmSW chaperone-dependent manner via an N-terminal translocation signal. Extensive mutagenesis in the NLuc N terminus suggested the importance of an α-helical domain spanning D5 to V9, as mutations predicted to disrupt this structure, with one exception, were translocation defective. Notably, NLuc was capable of translocating several proteins examined when fused to the N or C terminus, while maintaining robust luciferase activity. In particular, it delivered the split GFP11 fragment into J774 macrophages transfected with GFPopt, thereby resulting in in vivo assembly of superfolder green fluorescent protein (GFP). This provided a bifunctional assay in which translocation could be assayed by fluorescence microplate, confocal microscopy, and/or luciferase assays. We further identified an optimal NLuc substrate which allowed a robust, inexpensive, one-step, high-throughput screening assay to identify T4SS translocation substrates and inhibitors. Taken together, these results indicate that NLuc provides both new insight into and also tools for studying T4SS biology. IMPORTANCE Type IV secretion systems (T4SS) are used by Gram-negative pathogens to coopt host cell function. However, the translocation signals recognized by T4SS are not fully explained by primary amino acid sequence, suggesting yet-to-be-defined contributions of secondary and tertiary structure. Here, we unexpectedly identified nanoluciferase (NLuc) as an efficient IcmSW-dependent translocated T4SS substrate, and we provide extensive mutagenesis data suggesting that the first N-terminal, alpha-helix domain is a critical translocation recognition motif. Notably, most existing reporter systems for studying translocated proteins make use of fusions to reporters to permit detection of translocated enzymatic activity inside the host cell. However, existing systems require extremely costly substrates, complex technical procedures to isolate eukaryotic cytoplasm for analysis, and/or are insensitive. Importantly, we found that NLuc provides a powerful, cost-effective new tool to address these limitations and facilitate high-throughput exploration of secretion system biology.
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Affiliation(s)
- Yoon-Suk Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - James E. Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Li J, Qi L, Diao Z, Zhang M, Li B, Zhai Y, Hao M, Zhou D, Liu W, Jin Y, Wang A. Brucella BtpB Manipulates Apoptosis and Autophagic Flux in RAW264.7 Cells. Int J Mol Sci 2022; 23:ijms232214439. [PMID: 36430916 PMCID: PMC9693124 DOI: 10.3390/ijms232214439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/02/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Brucella transfers effectors into host cells, manipulating cellular processes to its advantage; however, the mechanism by which effectors regulate cellular processes during infection is poorly understood. A growing number of studies have shown that apoptosis and autophagy are critical mechanisms for target cells to cope with pathogens and maintain cellular homeostasis. BtpB is a Brucella type IV secretion system effector with a complex mechanism for manipulating host infection. Here, we show that the ectopic expression of BtpB promoted DNA fragmentation. In contrast, an isogenic mutant strain, ΔbtpB, inhibited apoptosis compared to the wild-type strain B. suis S2 in RAW264.7 cells. In addition, BtpB inhibited autophagy, as determined by LC3-II protein levels, the number of LC3 puncta, and p62 degradation. We also found that BtpB reduced autophagolysosome formation and blocked the complete autophagic flux. Moreover, our results revealed that the autophagy inhibitor, chloroquine, reduces Brucella's intracellular survival. Overall, our data unveil new mechanisms of virulence implicating the effector BtpB in regulating host intracellular infection.
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Affiliation(s)
- Junmei Li
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Lin Qi
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Ziyang Diao
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Mengyu Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Bin Li
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yunyi Zhai
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Mingyue Hao
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Dong Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Wei Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
- Correspondence: or
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11
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Developmental Transitions Coordinate Assembly of the Coxiella burnetii Dot/Icm Type IV Secretion System. Infect Immun 2022; 90:e0041022. [PMID: 36190257 PMCID: PMC9584302 DOI: 10.1128/iai.00410-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Coxiella burnetii is an obligate intracellular bacterial pathogen that has evolved a unique biphasic developmental cycle. The infectious form of C. burnetii is the dormant small cell variant (SCV), which transitions to a metabolically active large cell variant (LCV) that replicates inside the lysosome-derived host vacuole. A Dot/Icm type IV secretion system (T4SS), which can deliver over 100 effector proteins to host cells, is essential for the biogenesis of the vacuole and intracellular replication. How the distinct C. burnetii life cycle impacts the assembly and function of the Dot/Icm T4SS has remained unknown. Here, we combine advanced cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) imaging to visualize all developmental transitions and the assembly of the Dot/Icm T4SS in situ. Importantly, assembled Dot/Icm machines were not present in the infectious SCV. The appearance of the assembled Dot/Icm machine correlated with the transition of the SCV to the LCV intracellularly. Furthermore, temporal characterization of C. burnetii morphological changes revealed regions of the inner membrane that invaginate to form tightly packed stacks during the LCV-to-SCV transition at late stages of infection, which may enable the SCV-to-LCV transition that occurs upon infection of a new host cell. Overall, these data establish how C. burnetii developmental transitions control critical bacterial processes to promote intracellular replication and transmission.
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12
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Astafyeva Y, Gurschke M, Qi M, Bergmann L, Indenbirken D, de Grahl I, Katzowitsch E, Reumann S, Hanelt D, Alawi M, Streit WR, Krohn I. Microalgae and Bacteria Interaction-Evidence for Division of Diligence in the Alga Microbiota. Microbiol Spectr 2022; 10:e0063322. [PMID: 35913168 PMCID: PMC9430724 DOI: 10.1128/spectrum.00633-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/07/2022] [Indexed: 11/20/2022] Open
Abstract
Microalgae are one of the most dominant forms of life on earth that is tightly associated with a distinct and specialized microbiota. We have previously shown that the microbiota of Scenedesmus quadricauda harbors less than 10 distinct microbial species. Here, we provide evidence that dominant species are affiliated with the genera of Variovorax, Porphyrobacter, and Dyadobacter. Experimental and transcriptome-based evidence implies that within this multispecies interaction, Dyadobacter is a key to alga growth and fitness and is highly adapted to live in the phycosphere. While presumably under light conditions the alga provides the energy source to the bacteria, Dyadobacter produces and releases mainly a large variety of polysaccharides modifying enzymes. This is coherent with high-level expression of the T9SS in alga cocultures. The transcriptome data further imply that quorum-quenching proteins (QQ) and biosynthesis of vitamins B1, B2, B5, B6, and B9 are expressed by Dyadobacter at high levels in comparison to Variovorax and Porphyrobacter. Notably, Dyadobacter produces a significant number of leucine-rich repeat (LRR) proteins and enzymes involved in bacterial reactive oxygen species (ROS) tolerance. Complementary to this, Variovorax expresses the genes of the biosynthesis of vitamins B2, B5, B6, B7, B9, and B12, and Porphyrobacter is specialized in the production of vitamins B2 and B6. Thus, the shared currency between partners are vitamins, microalgae growth-promoting substances, and dissolved carbon. This work significantly enlarges our knowledge on alga-bacteria interaction and demonstrates physiological investigations of microalgae and associated bacteria, using microscopy observations, photosynthetic activity measurements, and flow cytometry. IMPORTANCE The current study gives a detailed insight into mutualistic collaboration of microalgae and bacteria, including the involvement of competitive interplay between bacteria. We provide experimental evidence that Gram-negative bacteria belonging to the Dyadobacter, Porphyrobacter, and Variovorax are the key players in a Scenedesmus quadricauda alga-bacteria interaction. We impart strong evidence that Dyadobacter produces and releases polysaccharides degradation enzymes and leucine-rich repeat proteins; Variovorax supplies the consortium with auxins and vitamin B12, while Porphyrobacter produces a broad spectrum of B vitamins. We show not only that the microalgae collaborate with the bacteria and vice versa but also that the bacteria interact with each other via quorum-sensing and secretion system mechanisms. The shared currency between partners appears to be vitamins, microalgae growth-promoting substances, and dissolved carbon.
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Affiliation(s)
- Yekaterina Astafyeva
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Marno Gurschke
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Minyue Qi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Core, Hamburg, Germany
| | - Lutgardis Bergmann
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Imke de Grahl
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Plant Biochemistry and Infection Biology, Hamburg, Germany
| | - Elena Katzowitsch
- University of Würzburg, Core Unit Systems Medicine, Würzburg, Germany
| | - Sigrun Reumann
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Plant Biochemistry and Infection Biology, Hamburg, Germany
| | - Dieter Hanelt
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Malik Alawi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Core, Hamburg, Germany
| | - Wolfgang R. Streit
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Ines Krohn
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
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13
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Abstract
Bacterial type IV secretion systems (T4SSs) are a versatile group of nanomachines that can horizontally transfer DNA through conjugation and deliver effector proteins into a wide range of target cells. The components of T4SSs in gram-negative bacteria are organized into several large subassemblies: an inner membrane complex, an outer membrane core complex, and, in some species, an extracellular pilus. Cryo-electron tomography has been used to define the structures of T4SSs in intact bacteria, and high-resolution structural models are now available for isolated core complexes from conjugation systems, the Xanthomonas citri T4SS, the Helicobacter pylori Cag T4SS, and the Legionella pneumophila Dot/Icm T4SS. In this review, we compare the molecular architectures of these T4SSs, focusing especially on the structures of core complexes. We discuss structural features that are shared by multiple T4SSs as well as evolutionary strategies used for T4SS diversification. Finally, we discuss how structural variations among T4SSs may confer specialized functional properties.
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Affiliation(s)
- Michael J. Sheedlo
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Melanie D. Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - D. Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
| | - Timothy L. Cover
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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14
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Wu Y, Xiang L, Wang H, Ma L, Qiu X, Liu D, Feng L, Lu X. Transcriptome analysis of an arsenite-/antimonite-oxidizer, Bosea sp. AS-1 reveals the importance of the type 4 secretion system in antimony resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154168. [PMID: 35231521 DOI: 10.1016/j.scitotenv.2022.154168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Bosea sp. AS-1 is an arsenite [As(III)] and antimonite [Sb(III)] oxidizer previously isolated by our group from the Xikuangshan Antimony (Sb) Mine area. Our previous study showed that Bosea sp. AS-1 had a preference for oxidizing As(III) or Sb(III) with different carbon sources, which suggested that different metabolic mechanisms may be utilized by the bacteria to survive in As(III)- or Sb(III)-contaminated environments. Here, we conducted whole-genome and transcriptome sequencing to reveal the molecular mechanisms utilized by Bosea sp. AS-1 to resist As(III) or Sb(III). We discovered that AS-1 acquired various As- and Sb-resistant genes in its genome and might resist As(III) or Sb(III) through the regulation of multiple pathways, such as As and Sb metabolism, the bacterial secretion system, oxidative phosphorylation, the TCA cycle and bacterial flagellar motility. Interestingly, we discovered that genes of the type IV secretion system (T4SS) were activated in response to Sb(III), and inhibiting T4SS activity in AS-1 dramatically reduced its oxidation efficiency and tolerance to Sb(III). To our knowledge, this is the first study showing the activation of T4SS genes by Sb and a direct involvement of T4SS in bacterial Sb resistance. Our findings establish the T4SS as an important Sb resistance factor in bacteria and may help us understand the spread of Sb resistance genes in the environment.
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Affiliation(s)
- Yanmei Wu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Li Xiang
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China; State Key Laboratory of Biogeology and Environmental Geology, China University of China (Wuhan), Wuhan 430074, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Xuan Qiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of China (Wuhan), Wuhan 430074, China
| | - Deng Liu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Liang Feng
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China.
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15
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Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol 2022; 20:146. [PMID: 35710371 PMCID: PMC9205054 DOI: 10.1186/s12915-022-01347-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. RESULTS Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. CONCLUSIONS This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.
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Affiliation(s)
- Erwin Tantoso
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Miles Kirsch
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: Northeastern University, Boston, USA
| | - Vladimir Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Zhiya Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: The University of Cambridge, Cambridge, UK
| | - Frank Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore, Republic of Singapore.
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16
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Neupane S, Bonilla SI, Manalo AM, Pelz-Stelinski KS. Complete de novo assembly of Wolbachia endosymbiont of Diaphorina citri Kuwayama (Hemiptera: Liviidae) using long-read genome sequencing. Sci Rep 2022; 12:125. [PMID: 34996906 PMCID: PMC8741817 DOI: 10.1038/s41598-021-03184-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/26/2021] [Indexed: 01/23/2023] Open
Abstract
Wolbachia, a gram-negative \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm{\alpha }$$\end{document}α-proteobacterium, is an endosymbiont found in some arthropods and nematodes. Diaphorina citri Kuwayama, the vector of ‘Candidatus Liberibacter asiaticus’ (CLas), are naturally infected with a strain of Wolbachia (wDi), which has been shown to colocalize with the bacteria pathogens CLas, the pathogen associated with huanglongbing (HLB) disease of citrus. The relationship between wDi and CLas is poorly understood in part because the complete genome of wDi has not been available. Using high-quality long-read PacBio circular consensus sequences, we present the largest complete circular wDi genome among supergroup-B members. The assembled circular chromosome is 1.52 megabases with 95.7% genome completeness with contamination of 1.45%, as assessed by checkM. We identified Insertion Sequences (ISs) and prophage genes scattered throughout the genomes. The proteins were annotated using Pfam, eggNOG, and COG that assigned unique domains and functions. The wDi genome was compared with previously sequenced Wolbachia genomes using pangenome and phylogenetic analyses. The availability of a complete circular chromosome of wDi will facilitate understanding of its role within the insect vector, which may assist in developing tools for disease management. This information also provides a baseline for understanding phylogenetic relationships among Wolbachia of other insect vectors.
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Affiliation(s)
- Surendra Neupane
- Entomology and Nematology Department, Citrus Research and Education Center/IFAS, University of Florida, Lake Alfred, Florida, 33850, USA
| | - Sylvia I Bonilla
- Entomology and Nematology Department, Citrus Research and Education Center/IFAS, University of Florida, Lake Alfred, Florida, 33850, USA
| | - Andrew M Manalo
- Entomology and Nematology Department, Citrus Research and Education Center/IFAS, University of Florida, Lake Alfred, Florida, 33850, USA
| | - Kirsten S Pelz-Stelinski
- Entomology and Nematology Department, Citrus Research and Education Center/IFAS, University of Florida, Lake Alfred, Florida, 33850, USA.
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17
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Cheok YY, Lee CYQ, Cheong HC, Vadivelu J, Looi CY, Abdullah S, Wong WF. An Overview of Helicobacter pylori Survival Tactics in the Hostile Human Stomach Environment. Microorganisms 2021; 9:microorganisms9122502. [PMID: 34946105 PMCID: PMC8705132 DOI: 10.3390/microorganisms9122502] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 12/17/2022] Open
Abstract
Helicobacter pylori is well established as a causative agent for gastritis, peptic ulcer, and gastric cancer. Armed with various inimitable virulence factors, this Gram-negative bacterium is one of few microorganisms that is capable of circumventing the harsh environment of the stomach. The unique spiral structure, flagella, and outer membrane proteins accelerate H. pylori movement within the viscous gastric mucosal layers while facilitating its attachment to the epithelial cells. Furthermore, secretion of urease from H. pylori eases the acidic pH within the stomach, thus creating a niche for bacteria survival and replication. Upon gaining a foothold in the gastric epithelial lining, bacterial protein CagA is injected into host cells through a type IV secretion system (T4SS), which together with VacA, damage the gastric epithelial cells. H. pylori does not only establishes colonization in the stomach, but also manipulates the host immune system to permit long-term persistence. Prolonged H. pylori infection causes chronic inflammation that precedes gastric cancer. The current review provides a brief outlook on H. pylori survival tactics, bacterial-host interaction and their importance in therapeutic intervention as well as vaccine development.
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Affiliation(s)
- Yi Ying Cheok
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (Y.Y.C.); (C.Y.Q.L.); (H.C.C.); (J.V.)
| | - Chalystha Yie Qin Lee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (Y.Y.C.); (C.Y.Q.L.); (H.C.C.); (J.V.)
| | - Heng Choon Cheong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (Y.Y.C.); (C.Y.Q.L.); (H.C.C.); (J.V.)
| | - Jamuna Vadivelu
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (Y.Y.C.); (C.Y.Q.L.); (H.C.C.); (J.V.)
| | - Chung Yeng Looi
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor’s University, Subang Jaya 47500, Malaysia;
| | - Suhailah Abdullah
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (Y.Y.C.); (C.Y.Q.L.); (H.C.C.); (J.V.)
- Correspondence:
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18
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Hu M, Li C, Xue Y, Hu A, Chen S, Chen Y, Lu G, Zhou X, Zhou J. Isolation, Characterization, and Genomic Investigation of a Phytopathogenic Strain of Stenotrophomonas maltophilia. PHYTOPATHOLOGY 2021; 111:2088-2099. [PMID: 33759550 DOI: 10.1094/phyto-11-20-0501-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Stenotrophomonas maltophilia is ubiquitous in diverse environmental habitats. It merits significant concern because of its increasing incidence of nosocomial and community-acquired infection in immunocompromised patients and multiple drug resistance. It is rarely reported as a phytopathogen except in causing white stripe disease of rice in India and postharvest fruit rot of Lanzhou lily. For this study, Dickeya zeae and S. maltophilia strains were simultaneously isolated from soft rot leaves of Clivia miniata in Guangzhou, China, and were both demonstrated to be pathogenic to the host. Compared with the D. zeae strains, S. maltophilia strains propagated faster for greater growth in lysogeny broth medium and produced no cellulases or polygalacturonases, but did produce more proteases and fewer extracellular polysaccharides. Furthermore, S. maltophilia strains swam and swarmed dramatically less on semisolid media, but formed a great many more biofilms. Both D. zeae and S. maltophilia strains isolated from clivia caused rot symptoms on other monocot hosts, but not on dicots. Similar to previously reported S. maltophilia strains isolated from other sources, the strain JZL8 survived under many antibiotic stresses. The complete genome sequence of S. maltophilia strain JZL8 consists of a chromosome of 4,635,432 bp without a plasmid. Pan-genome analysis of JZL8 and 180 other S. maltophilia strains identified 50 genes that are unique to JZL8, seven of which implicate JZL8 as the potential pathogen contributor in plants. JZL8 also contains three copies of Type I Secretion System machinery; this is likely responsible for its greater production of proteases. Findings from this study extend our knowledge on the host range of S. maltophilia and provide insight into the phenotypic and genetic features underlying the plant pathogenicity of JZL8.
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Affiliation(s)
- Ming Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Chuhao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yang Xue
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Anqun Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shanshan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yufan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Guangtao Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
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19
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Undercover Agents of Infection: The Stealth Strategies of T4SS-Equipped Bacterial Pathogens. Toxins (Basel) 2021; 13:toxins13100713. [PMID: 34679006 PMCID: PMC8539587 DOI: 10.3390/toxins13100713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Intracellular bacterial pathogens establish their replicative niches within membrane-encompassed compartments, called vacuoles. A subset of these bacteria uses a nanochannel called the type 4 secretion system (T4SS) to inject effector proteins that subvert the host cell machinery and drive the biogenesis of these compartments. These bacteria have also developed sophisticated ways of altering the innate immune sensing and response of their host cells, which allow them to cause long-lasting infections and chronic diseases. This review covers the mechanisms employed by intravacuolar pathogens to escape innate immune sensing and how Type 4-secreted bacterial effectors manipulate host cell mechanisms to allow the persistence of bacteria.
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20
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Patil PP, Kumar S, Kaur A, Midha S, Bansal K, Patil PB. Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature. Microb Genom 2021; 7. [PMID: 34252021 PMCID: PMC8477401 DOI: 10.1099/mgen.0.000600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Stenotrophomonas maltophilia is a typical example of an environmental originated opportunistic human pathogen, which can thrive at different habitats including the human body and can cause a wide range of infections. It must cope with heat stress during transition from the environment to the human body as the physiological temperature of the human body (37 °C) is higher than environmental niches (22–30 °C). Interestingly, S. rhizophila a phylogenetic neighbour of S. maltophilia within genus Stenotrophomonas is unable to grow at 37 °C. Thus, it is crucial to understand how S. maltophilia is adapted to human body temperature, which could suggest its evolution as an opportunistic human pathogen. In this study, we have performed comparative transcriptome analysis of S. maltophilia grown at 28 and 37 °C as temperature representative for environmental niches and the human body, respectively. RNA-Seq analysis revealed several interesting findings showing alterations in gene-expression levels at 28 and 37 °C, which can play an important role during infection. We have observed downregulation of genes involved in cellular motility, energy production and metabolism, replication and repair whereas upregulation of VirB/D4 type IV secretion system, aerotaxis, cation diffusion facilitator family transporter and LacI family transcriptional regulators at 37 °C. Microscopy and plate assays corroborated altered expression of genes involved in motility. The results obtained enhance our understanding of the strategies employed by S. maltophilia during adaptation towards the human body.
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Affiliation(s)
- Prashant P Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,Present address: Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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21
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Effectors of the Stenotrophomonas maltophilia Type IV Secretion System Mediate Killing of Clinical Isolates of Pseudomonas aeruginosa. mBio 2021; 12:e0150221. [PMID: 34182776 PMCID: PMC8262851 DOI: 10.1128/mbio.01502-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Previously, we documented that Stenotrophomonas maltophilia encodes a type IV secretion system (T4SS) that allows the organism to kill, in contact-dependent fashion, heterologous bacteria, including wild-type Pseudomonas aeruginosa. Bioinformatic screens based largely on the presence of both a C-terminal consensus sequence and an adjacent gene encoding a cognate immunity protein identified 13 potential antibacterial effectors, most of which were highly conserved among sequenced strains of S. maltophilia. The immunity proteins of two of these proved especially capable of protecting P. aeruginosa and Escherichia coli against attack from the Stenotrophomonas T4SS. In turn, S. maltophilia mutants lacking the putative effectors RS14245 and RS14255 were impaired for killing not only laboratory E. coli but clinical isolates of P. aeruginosa, including ones isolated from the lungs of cystic fibrosis patients. That complemented mutants behaved as wild type did confirmed that RS14245 and RS14255 are required for the bactericidal activity of the S. maltophilia T4SS. Moreover, a mutant lacking both of these proteins was as impaired as a mutant lacking the T4SS apparatus, indicating that RS14245 and RS14255 account for (nearly) all of the bactericidal effects seen. Utilizing an interbacterial protein translocation assay, we determined that RS14245 and RS14255 are bona fide substrates of the T4SS, a result confirmed by examination of mutants lacking both the T4SS and the individual effectors. Delivery of the cloned 14245 protein (alone) into the periplasm resulted in the killing of target bacteria, indicating that this effector, a putative lipase, is both necessary and sufficient for bactericidal activity.
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22
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McLean JS, Bor B, Kerns KA, Liu Q, To TT, Solden L, Hendrickson EL, Wrighton K, Shi W, He X. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Rep 2021; 32:107939. [PMID: 32698001 PMCID: PMC7427843 DOI: 10.1016/j.celrep.2020.107939] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200-300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.
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Affiliation(s)
- Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Kristopher A Kerns
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Quanhui Liu
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Thao T To
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Erik L Hendrickson
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Kelly Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
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23
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Sheedlo MJ, Durie CL, Chung JM, Chang L, Roberts J, Swanson M, Lacy DB, Ohi MD. Cryo-EM reveals new species-specific proteins and symmetry elements in the Legionella pneumophila Dot/Icm T4SS. eLife 2021; 10:70427. [PMID: 34519271 PMCID: PMC8486379 DOI: 10.7554/elife.70427] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/14/2021] [Indexed: 01/21/2023] Open
Abstract
Legionella pneumophila is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly, the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure.
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Affiliation(s)
- Michael J Sheedlo
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
| | - Clarissa L Durie
- Life Sciences Institute, University of MichiganAnn ArborUnited States
| | - Jeong Min Chung
- Life Sciences Institute, University of MichiganAnn ArborUnited States,Department of Biotechnology, The Catholic University of KoreaGyeonggiRepublic of Korea
| | - Louise Chang
- Life Sciences Institute, University of MichiganAnn ArborUnited States
| | - Jacquelyn Roberts
- Life Sciences Institute, University of MichiganAnn ArborUnited States
| | - Michele Swanson
- Department of Microbiology and Immunology, University Of MichiganAnn ArborUnited States
| | - Dana Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical CenterNashvilleUnited States,The Veterans Affairs Tennessee Valley Healthcare SystemNasvhilleUnited States
| | - Melanie D Ohi
- Life Sciences Institute, University of MichiganAnn ArborUnited States,Department of Cell and Developmental Biology, University of MichiganAnn ArborUnited States
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24
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Disruption of VirB6 Paralogs in Anaplasma phagocytophilum Attenuates Its Growth. J Bacteriol 2020; 202:JB.00301-20. [PMID: 32928930 PMCID: PMC7648143 DOI: 10.1128/jb.00301-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/08/2020] [Indexed: 01/25/2023] Open
Abstract
Knowledge of the T4SS is derived from model systems, such as Agrobacterium tumefaciens. The structure of the T4SS in Rickettsiales differs from the classical arrangement. These differences include missing and duplicated components with structural alterations. Particularly, two sequenced virB6-4 genes encode unusual C-terminal structural extensions resulting in proteins of 4,322 (GenBank accession number AGR79286.1) and 9,935 (GenBank accession number ANC34101.1) amino acids. To understand how the T4SS is used in A. phagocytophilum, we describe the expression of the virB6 paralogs and explore their role as the bacteria replicate within its host cell. Conclusions about the importance of these paralogs for colonization of human and tick cells are supported by the deficient phenotype of an A. phagocytophilum mutant isolated from a sequence-defined transposon insertion library. Many pathogenic bacteria translocate virulence factors into their eukaryotic hosts by means of type IV secretion systems (T4SS) spanning the inner and outer membranes. Genes encoding components of these systems have been identified within the order Rickettsiales based upon their sequence similarities to other prototypical systems. Anaplasma phagocytophilum strains are obligate intracellular, tick-borne bacteria that are members of this order. The organization of these components at the genomic level was determined in several Anaplasma phagocytophilum strains, showing overall conservation, with the exceptions of the virB2 and virB6 genes. The virB6 loci are characterized by the presence of four virB6 copies (virB6-1 through virB6-4) arranged in tandem within a gene cluster known as the sodB-virB operon. Interestingly, the virB6-4 gene varies significantly in length among different strains due to extensive tandem repeats at the 3′ end. To gain an understanding of how these enigmatic virB6 genes function in A. phagocytophilum, we investigated their expression in infected human and tick cells. Our results show that these genes are expressed by A. phagocytophilum replicating in both cell types and that VirB6-3 and VirB6-4 proteins are surface exposed. Analysis of an A. phagocytophilum mutant carrying the Himar1 transposon within the virB6-4 gene demonstrated that the insertion not only disrupted its expression but also exerted a polar effect on the sodB-virB operon. Moreover, the altered expression of genes within this operon was associated with the attenuated in vitro growth of A. phagocytophilum in human and tick cells, indicating the importance of these genes in the physiology of this obligate intracellular bacterium in such different environments. IMPORTANCE Knowledge of the T4SS is derived from model systems, such as Agrobacterium tumefaciens. The structure of the T4SS in Rickettsiales differs from the classical arrangement. These differences include missing and duplicated components with structural alterations. Particularly, two sequenced virB6-4 genes encode unusual C-terminal structural extensions resulting in proteins of 4,322 (GenBank accession number AGR79286.1) and 9,935 (GenBank accession number ANC34101.1) amino acids. To understand how the T4SS is used in A. phagocytophilum, we describe the expression of the virB6 paralogs and explore their role as the bacteria replicate within its host cell. Conclusions about the importance of these paralogs for colonization of human and tick cells are supported by the deficient phenotype of an A. phagocytophilum mutant isolated from a sequence-defined transposon insertion library.
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25
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Lee YW, Wang J, Newton HJ, Lithgow T. Mapping bacterial effector arsenals: in vivo and in silico approaches to defining the protein features dictating effector secretion by bacteria. Curr Opin Microbiol 2020; 57:13-21. [PMID: 32505919 DOI: 10.1016/j.mib.2020.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 12/25/2022]
Abstract
Many bacterial pathogens rely on dedicated secretion systems to translocate virulence proteins termed 'effectors' into host cells. These effectors engage and manipulate host cellular functions to support bacterial colonization and propagation. The secretion systems are molecular machines that recognize targeting 'features' in these effector proteins in vivo to selectively and efficiently secrete them. The joint analysis of whole genome sequencing data and computational predictions of amino acid characteristics of effector proteins has made available extensive lists of candidate effectors for many bacterial pathogens, among which Dot/Icm type IVB secretion system in Legionella pneumophila reigns with the largest number of effectors identified to-date. This system is also used by the causative agent of Q fever, Coxiella burnetii, to secrete a large pool of distinct effectors. By comparing these two pathogens, we provide an understanding of the rationale behind effector repertoire expansion. We will also discuss recent bioinformatic advances facilitating high-throughput discovery of secreted effectors through in silico 'feature' recognition, and the current challenge to substantiate the biological relevance and bona fide nature of effectors identified in silico.
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Affiliation(s)
- Yi Wei Lee
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000 Victoria, Australia
| | - Jiawei Wang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800 Victoria, Australia
| | - Hayley J Newton
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000 Victoria, Australia.
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800 Victoria, Australia.
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26
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Abstract
The translocation of proteins across membranes is a fundamental cellular function. Bacteria have evolved a striking array of pathways for delivering proteins into or across cytoplasmic membranes and, when present, outer membranes. Translocated proteins can form part of the membrane landscape, reside in the periplasmic space situated between the inner and outer membranes of Gram-negative bacteria, deposit on the cell surface, or be released to the extracellular milieu or injected directly into target cells. One protein translocation system, the general secretory pathway, is conserved in all domains of life. A second, the twin-arginine translocation pathway, is also phylogenetically distributed among most bacteria and plant chloroplasts. While all cell types have evolved additional systems dedicated to the translocation of protein cargoes, the number of such systems in bacteria is now known to exceed nine. These dedicated protein translocation systems, which include the types 1 through 9 secretion systems (T1SSs-T9SSs), the chaperone-usher pathway, and type IV pilus system, are the subject of this review. Most of these systems were originally identified and have been extensively characterized in Gram-negative or diderm (two-membrane) species. It is now known that several of these systems also have been adapted to function in Gram-positive or monoderm (single-membrane) species, and at least one pathway is found only in monoderms. This review briefly summarizes the distinctive mechanistic and structural features of each dedicated pathway, as well as the shared properties, that together account for the broad biological diversity of protein translocation in bacteria.
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Affiliation(s)
- Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St., Houston, TX, USA.
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27
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The Helicobacter pylori Cag Type IV Secretion System. Trends Microbiol 2020; 28:682-695. [PMID: 32451226 DOI: 10.1016/j.tim.2020.02.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/30/2020] [Accepted: 02/25/2020] [Indexed: 12/24/2022]
Abstract
Colonization of the human stomach with Helicobacter pylori strains containing the cag pathogenicity island is a risk factor for development of gastric cancer. The cag pathogenicity island contains genes encoding a secreted effector protein (CagA) and components of a type IV secretion system (Cag T4SS). The molecular architecture of the H. pylori Cag T4SS is substantially more complex than that of prototype T4SSs in other bacterial species. In this review, we discuss recent discoveries pertaining to the structure and function of the Cag T4SS and its role in gastric cancer pathogenesis.
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28
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Park D, Chetrit D, Hu B, Roy CR, Liu J. Analysis of Dot/Icm Type IVB Secretion System Subassemblies by Cryoelectron Tomography Reveals Conformational Changes Induced by DotB Binding. mBio 2020; 11:e03328-19. [PMID: 32071271 PMCID: PMC7029142 DOI: 10.1128/mbio.03328-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Type IV secretion systems (T4SSs) are sophisticated nanomachines used by many bacterial pathogens to translocate protein and DNA substrates across a host cell membrane. Although T4SSs have important roles in promoting bacterial infections, little is known about the biogenesis of the apparatus and the mechanism of substrate transfer. Here, high-throughput cryoelectron tomography (cryo-ET) was used to visualize Legionella pneumophila T4SSs (also known as Dot/Icm secretion machines) in both the whole-cell context and at the cell pole. These data revealed the distribution patterns of individual Dot/Icm machines in the bacterial cell and identified five distinct subassembled intermediates. High-resolution in situ structures of the Dot/Icm machine derived from subtomogram averaging revealed that docking of the cytoplasmic DotB (VirB11-related) ATPase complex onto the DotO (VirB4-related) ATPase complex promotes a conformational change in the secretion system that results in the opening of a channel in the bacterial inner membrane. A model is presented for how the Dot/Icm apparatus is assembled and for how this machine may initiate the transport of cytoplasmic substrates across the inner membrane.IMPORTANCE Many bacteria use type IV secretion systems (T4SSs) to translocate proteins and nucleic acids into target cells, which promotes DNA transfer and host infection. The Dot/Icm T4SS in Legionella pneumophila is a multiprotein nanomachine that is known to translocate over 300 different protein effectors into eukaryotic host cells. Here, advanced cryoelectron tomography and subtomogram analysis were used to visualize the Dot/Icm machine assembly and distribution in a single L. pneumophila cell. Extensive classification and averaging revealed five distinct intermediates of the Dot/Icm machine at high resolution. Comparative analysis of the Dot/Icm machine and subassemblies derived from wild-type cells and several mutants provided a structural basis for understanding mechanisms that underlie the assembly and activation of the Dot/Icm machine.
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Affiliation(s)
- Donghyun Park
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
| | - David Chetrit
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Craig R Roy
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
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29
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Stenotrophomonas maltophilia Encodes a VirB/VirD4 Type IV Secretion System That Modulates Apoptosis in Human Cells and Promotes Competition against Heterologous Bacteria, Including Pseudomonas aeruginosa. Infect Immun 2019; 87:IAI.00457-19. [PMID: 31235638 DOI: 10.1128/iai.00457-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 06/17/2019] [Indexed: 12/11/2022] Open
Abstract
Stenotrophomonas maltophilia is an emerging opportunistic and nosocomial pathogen. S. maltophilia is also a risk factor for lung exacerbations in cystic fibrosis patients. S. maltophilia attaches to various mammalian cells, and we recently documented that the bacterium encodes a type II secretion system which triggers detachment-induced apoptosis in lung epithelial cells. We have now confirmed that S. maltophilia also encodes a type IVA secretion system (VirB/VirD4 [VirB/D4] T4SS) that is highly conserved among S. maltophilia strains and, looking beyond the Stenotrophomonas genus, is most similar to the T4SS of Xanthomonas To define the role(s) of this T4SS, we constructed a mutant of strain K279a that is devoid of secretion activity due to loss of the VirB10 component. The mutant induced a higher level of apoptosis upon infection of human lung epithelial cells, indicating that a T4SS effector(s) has antiapoptotic activity. However, when we infected human macrophages, the mutant triggered a lower level of apoptosis, implying that the T4SS also elaborates a proapoptotic factor(s). Moreover, when we cocultured K279a with strains of Pseudomonas aeruginosa, the T4SS promoted the growth of S. maltophilia and reduced the numbers of heterologous bacteria, signaling that another effector(s) has antibacterial activity. In all cases, the effect of the T4SS required S. maltophilia contact with its target. Thus, S. maltophilia VirB/D4 T4SS appears to secrete multiple effectors capable of modulating death pathways. That a T4SS can have anti- and prokilling effects on different targets, including both human and bacterial cells, has, to our knowledge, not been seen before.
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30
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Sgro GG, Oka GU, Souza DP, Cenens W, Bayer-Santos E, Matsuyama BY, Bueno NF, dos Santos TR, Alvarez-Martinez CE, Salinas RK, Farah CS. Bacteria-Killing Type IV Secretion Systems. Front Microbiol 2019; 10:1078. [PMID: 31164878 PMCID: PMC6536674 DOI: 10.3389/fmicb.2019.01078] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteria have been constantly competing for nutrients and space for billions of years. During this time, they have evolved many different molecular mechanisms by which to secrete proteinaceous effectors in order to manipulate and often kill rival bacterial and eukaryotic cells. These processes often employ large multimeric transmembrane nanomachines that have been classified as types I-IX secretion systems. One of the most evolutionarily versatile are the Type IV secretion systems (T4SSs), which have been shown to be able to secrete macromolecules directly into both eukaryotic and prokaryotic cells. Until recently, examples of T4SS-mediated macromolecule transfer from one bacterium to another was restricted to protein-DNA complexes during bacterial conjugation. This view changed when it was shown by our group that many Xanthomonas species carry a T4SS that is specialized to transfer toxic bacterial effectors into rival bacterial cells, resulting in cell death. This review will focus on this special subtype of T4SS by describing its distinguishing features, similar systems in other proteobacterial genomes, and the nature of the effectors secreted by these systems and their cognate inhibitors.
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Affiliation(s)
- Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel U. Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Diorge P. Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Y. Matsuyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Natalia F. Bueno
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Cristina E. Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, University of Campinas (UNICAMP), Campinas, Brazil
| | - Roberto K. Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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31
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Abstract
Helicobacter pylori colonizes about half of humans worldwide, and its presence in the gastric mucosa is associated with an increased risk of gastric adenocarcinoma, gastric lymphoma, and peptic ulcer disease. H. pylori strains carrying the cag pathogenicity island (cagPAI) are associated with increased risk of disease progression. The cagPAI encodes the Cag type IV secretion system (CagT4SS), which delivers the CagA oncoprotein and other effector molecules into human gastric epithelial cells. We visualized structures of native and mutant CagT4SS machines on the H. pylori cell envelope by cryoelectron tomography. Individual H. pylori cells contain multiple CagT4SS nanomachines, each composed of a wheel-shaped outer membrane complex (OMC) with 14-fold symmetry and an inner membrane complex (IMC) with 6-fold symmetry. CagX, CagY, and CagM are required for assembly of the OMC, whereas strains lacking Cag3 and CagT produce outer membrane complexes lacking peripheral components. The IMC, which has never been visualized in detail, is configured as six tiers in cross-section view and three concentric rings surrounding a central channel in end-on view. The IMC contains three T4SS ATPases: (i) VirB4-like CagE, arranged as a hexamer of dimers at the channel entrance; (ii) a hexamer of VirB11-like Cagα, docked at the base of the CagE hexamer; and (iii) VirD4-like Cagβ and other unspecified Cag subunits, associated with the stacked CagE/Cagα complex and forming the outermost rings. The CagT4SS and recently solved Legionella pneumophila Dot/Icm system comprise new structural prototypes for the T4SS superfamily.IMPORTANCE Bacterial type IV secretion systems (T4SSs) have been phylogenetically grouped into two subfamilies. The T4ASSs, represented by the Agrobacterium tumefaciens VirB/VirD4T4SS, include "minimized" machines assembled from 12 VirB- and VirD4-like subunits and compositionally larger systems such as the Helicobacter pylori CagT4SS T4BSSs encompass systems closely related in subunit composition to the Legionella pneumophila Dot/IcmT4SS Here, we present structures of native and mutant H. pylori Cag machines determined by in situ cryoelectron tomography. We identify distinct outer and inner membrane complexes and, for the first time, visualize structural contributions of all three "signature" ATPases of T4SSs at the cytoplasmic entrance of the translocation channel. Despite their evolutionary divergence, the CagT4SS aligns structurally much more closely to the Dot/IcmT4SS than an available VirB/VirD4 subcomplex. Our findings highlight the diversity of T4SSs and suggest a structural classification scheme in which T4SSs are grouped as minimized VirB/VirD4-like or larger Cag-like and Dot/Icm-like systems.
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32
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Abstract
The bacterial type IV secretion systems (T4SSs) are a functionally diverse superfamily of secretion systems found in many species of bacteria. Collectively, the T4SSs translocate DNA and monomeric and multimeric protein substrates to bacterial and eukaryotic cell types. T4SSs are composed of two large subfamilies, the conjugation machines and the effector translocators that transmit their cargoes through establishment of direct donor-target cell contacts, and a third small subfamily capable of importing or exporting substrates from or to the milieu. This review summarizes recent mechanistic and structural findings that are shedding new light on how T4SSs have evolved such functional diversity. Translocation signals are now known to be located C terminally or embedded internally in structural folds; these signals in combination with substrate-associated adaptor proteins mediate the docking of specific substrate repertoires to cognate VirD4-like receptors. For the Legionella pneumophila Dot/Icm system, recent work has elucidated the structural basis for adaptor-dependent substrate loading onto the VirD4-like DotL receptor. Advances in definition of T4SS machine structures now allow for detailed comparisons of nanomachines closely related to the Agrobacterium tumefaciens VirB/VirD4 T4SS with those more distantly related, e.g., the Dot/Icm and Helicobacter pylori Cag T4SSs. Finally, it is increasingly evident that T4SSs have evolved a variety of mechanisms dependent on elaboration of conjugative pili, membrane tubes, or surface adhesins to establish productive contacts with target cells. T4SSs thus have evolved extreme functional diversity through a plethora of adaptations impacting substrate selection, machine architecture, and target cell binding.
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33
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Francis MS, Auerbuch V. Editorial: The Pathogenic Yersiniae-Advances in the Understanding of Physiology and Virulence, Second Edition. Front Cell Infect Microbiol 2019; 9:119. [PMID: 31058103 PMCID: PMC6482262 DOI: 10.3389/fcimb.2019.00119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/03/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Matthew S Francis
- Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Victoria Auerbuch
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
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34
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Lasek R, Szuplewska M, Mitura M, Decewicz P, Chmielowska C, Pawłot A, Sentkowska D, Czarnecki J, Bartosik D. Genome Structure of the Opportunistic Pathogen Paracoccus yeei ( Alphaproteobacteria) and Identification of Putative Virulence Factors. Front Microbiol 2018; 9:2553. [PMID: 30410477 PMCID: PMC6209633 DOI: 10.3389/fmicb.2018.02553] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/05/2018] [Indexed: 12/17/2022] Open
Abstract
Bacteria of the genus Paracoccus are common components of the microbiomes of many naturally- and anthropogenically shaped environments. One species, Paracoccus yeei, is unique within the genus because it is associated with opportunistic human infections. Therefore, strains of P. yeei may serve as an interesting model to study the transition from a saprophytic to a pathogenic lifestyle in environmental bacteria. Unfortunately, knowledge concerning the biology, genetics and genomic content of P. yeei is fragmentary; also the mechanisms of pathogenicity of this bacterium remain unclear. In this study we provide the first insight into the genome composition and metabolic potential of a clinical isolate, P. yeei CCUG 32053. This strain has a multipartite genome (4,632,079 bp) composed of a circular chromosome plus eight extrachromosomal replicons pYEE1–8: 3 chromids and 5 plasmids, with a total size of 1,247,173 bp. The genome has been significantly shaped by the acquisition of genomic islands, prophages (Myoviridae and Siphoviridae phage families) and numerous insertion sequences (ISs) representing seven IS families. Detailed comparative analysis with other complete genomic sequences of Paracoccus spp. (including P. yeei FDAARGOS_252 and TT13, as well as non-pathogenic strains of other species in this genus) enabled us to identify P. yeei species-specific genes and to predict putative determinants of virulence. This is the first attempt to identify pathoadaptive genetic information of P. yeei and to estimate the role of the mobilome in the evolution of pathogenicity in this species.
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Affiliation(s)
- Robert Lasek
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Szuplewska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Monika Mitura
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Przemysław Decewicz
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Cora Chmielowska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Pawłot
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dorota Sentkowska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Czarnecki
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
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González-Rivera C, Khara P, Awad D, Patel R, Li YG, Bogisch M, Christie PJ. Two pKM101-encoded proteins, the pilus-tip protein TraC and Pep, assemble on the Escherichia coli cell surface as adhesins required for efficient conjugative DNA transfer. Mol Microbiol 2018; 111:96-117. [PMID: 30264928 DOI: 10.1111/mmi.14141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 01/10/2023]
Abstract
Mobile genetic elements (MGEs) encode type IV secretion systems (T4SSs) known as conjugation machines for their transmission between bacterial cells. Conjugation machines are composed of an envelope-spanning translocation channel, and those functioning in Gram-negative species additionally elaborate an extracellular pilus to initiate donor-recipient cell contacts. We report that pKM101, a self-transmissible MGE functioning in the Enterobacteriaceae, has evolved a second target cell attachment mechanism. Two pKM101-encoded proteins, the pilus-tip adhesin TraC and a protein termed Pep, are exported to the cell surface where they interact and also form higher order complexes appearing as distinct foci or patches around the cell envelope. Surface-displayed TraC and Pep are required for an efficient conjugative transfer, 'extracellular complementation' potentially involving intercellular protein transfer, and activation of a Pseudomonas aeruginosa type VI secretion system. Both proteins are also required for bacteriophage PRD1 infection. TraC and Pep are exported across the outer membrane by a mechanism potentially involving the β-barrel assembly machinery. The pKM101 T4SS, thus, deploys alternative routing pathways for the delivery of TraC to the pilus tip or both TraC and Pep to the cell surface. We propose that T4SS-encoded, pilus-independent attachment mechanisms maximize the probability of MGE propagation and might be widespread among this translocation superfamily.
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Affiliation(s)
- Christian González-Rivera
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Dominik Awad
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Roosheel Patel
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | | | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
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Tegtmeyer N, Wessler S, Necchi V, Rohde M, Harrer A, Rau TT, Asche CI, Boehm M, Loessner H, Figueiredo C, Naumann M, Palmisano R, Solcia E, Ricci V, Backert S. Helicobacter pylori Employs a Unique Basolateral Type IV Secretion Mechanism for CagA Delivery. Cell Host Microbe 2018; 22:552-560.e5. [PMID: 29024645 DOI: 10.1016/j.chom.2017.09.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/26/2017] [Accepted: 09/08/2017] [Indexed: 01/16/2023]
Abstract
The Helicobacter pylori (Hp) type IV secretion system (T4SS) forms needle-like pili, whose binding to the integrin-β1 receptor results in injection of the CagA oncoprotein. However, the apical surface of epithelial cells is exposed to Hp, whereas integrins are basolateral receptors. Hence, the mechanism of CagA delivery into polarized gastric epithelial cells remains enigmatic. Here, we demonstrate that T4SS pilus formation during infection of polarized cells occurs predominantly at basolateral membranes, and not at apical sites. Hp accomplishes this by secreting another bacterial protein, the serine protease HtrA, which opens cell-to-cell junctions through cleaving epithelial junctional proteins including occludin, claudin-8, and E-cadherin. Using a genetic system expressing a peptide inhibitor, we demonstrate that HtrA activity is necessary for paracellular transmigration of Hp across polarized cell monolayers to reach basolateral membranes and inject CagA. The contribution of this unique signaling cascade to Hp pathogenesis is discussed.
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Affiliation(s)
- Nicole Tegtmeyer
- Department of Biology, Division of Microbiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Silja Wessler
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Vittorio Necchi
- Pathologic Anatomy and Human Physiology Units and Centro Grandi Strumenti, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Microscopy Unit, Braunschweig, Germany
| | - Aileen Harrer
- Department of Biology, Division of Microbiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Tilman T Rau
- Institute of Pathology, University of Erlangen-Nuremberg, Erlangen, Germany; Institute of Pathology, University of Bern, Bern, Switzerland
| | - Carmen Isabell Asche
- Department of Biology, Division of Microbiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Manja Boehm
- Department of Biology, Division of Microbiology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Holger Loessner
- Paul Ehrlich Institute, Department of Microbiology, Langen, Germany
| | - Ceu Figueiredo
- University of Porto, i3S, IPATIMUP, Faculty of Medicine, Porto, Portugal
| | - Michael Naumann
- Otto von Guericke University, Institute of Experimental Internal Medicine, Magdeburg, Germany
| | - Ralf Palmisano
- Optical Imaging Centre, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Enrico Solcia
- Pathologic Anatomy and Human Physiology Units and Centro Grandi Strumenti, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Vittorio Ricci
- Pathologic Anatomy and Human Physiology Units and Centro Grandi Strumenti, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Steffen Backert
- Department of Biology, Division of Microbiology, University of Erlangen-Nuremberg, Erlangen, Germany.
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Molina‐Santiago C. Insights in a novel gram‐positive type IV secretion system. Environ Microbiol 2018; 20:2334-2336. [DOI: 10.1111/1462-2920.14296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Molina‐Santiago
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos) Málaga Spain
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38
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Genomic analysis of a Raoultella ornithinolytica strain causing prosthetic joint infection in an immunocompetent patient. Sci Rep 2018; 8:9462. [PMID: 29930334 PMCID: PMC6013458 DOI: 10.1038/s41598-018-27833-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 05/25/2018] [Indexed: 11/08/2022] Open
Abstract
We sequenced the genome of Raoultella ornithinolytica strain Marseille-P1025 that caused a rare case of prosthetic joint infection in a 67-year-old immunocompetent male. The 6.7-Mb genome exhibited a genomic island (RoGI) that was unique among R. ornithinolytica strains. RoGI was likely acquired by lateral gene transfer from a member of the Pectobacterium genus and coded for a type IVa secretion system found in other pathogenic bacteria and that may have conferred strain Marseille-P1025 an increased virulence. Strain Marseille-P1025 was also able to infect, multiply within, and kill Acanthamoaeba castellanii amoebae.
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39
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Yuan XY, Wang Y, Wang MY. The type IV secretion system in Helicobacter pylori. Future Microbiol 2018; 13:1041-1054. [PMID: 29927340 DOI: 10.2217/fmb-2018-0038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori (H. pylori) has an essential role in the pathogenesis of gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue lymphoma and gastric cancer. The severity of the host inflammatory responses against the bacteria have been straightly associated with a special bacterial virulence factor, the cag pathogenicity island, which is a type IV secretion system (T4SS) to deliver CagA into the host cells. Besides cag-T4SS, the chromosomes of H. pylori can encode another three T4SSs, including comB, tfs3 and tfs4. In this review, we systematically reviewed the four T4SSs of H. pylori and explored their roles in the pathogenesis of gastroduodenal diseases. The information summarized in this review might provide valuable insights into the pathogenic mechanism for H. pylori.
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Affiliation(s)
- Xiao-Yan Yuan
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
| | - Ying Wang
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
| | - Ming-Yi Wang
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
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40
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A unique cytoplasmic ATPase complex defines the Legionella pneumophila type IV secretion channel. Nat Microbiol 2018; 3:678-686. [PMID: 29784975 PMCID: PMC5970066 DOI: 10.1038/s41564-018-0165-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/18/2018] [Indexed: 01/07/2023]
Abstract
Type IV secretion systems (T4SSs) are complex machines used by bacteria to deliver protein and DNA complexes into target host cells 1–5. Conserved ATPases are essential for T4SS function, but how they coordinate their activities to promote substrate transfer remains poorly understood. Here, we show that the DotB ATPase associates with the Dot/Icm T4SS at the Legionella cell pole through interactions with the DotO ATPase. The structure of the Dot/Icm apparatus was solved in situ by cryo-electron tomography at 3.5 nanometer resolution and the cytoplasmic complex was solved at 3.0 nanometer resolution. These structures revealed a cell-envelope-spanning channel that connects to the cytoplasmic complex. Further analysis revealed a hexameric assembly of DotO dimers associated with the inner membrane complex, and a DotB hexamer associated with the base of this cytoplasmic complex. The assembly of a DotB/DotO energy complex creates a cytoplasmic channel and directs the translocation of substrates through the T4SS. These data define distinct stages in Dot/Icm machine biogenesis, advance our understanding of channel activation, and identify an envelope-spanning T4SS channel.
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41
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Shiu J, Thai M, Elsensohn AN, Nguyen NQ, Lin KY, Cassarino DS. A case series of primary cutaneous coccidioidomycosis after a record-breaking rainy season. JAAD Case Rep 2018; 4:412-414. [PMID: 29984266 PMCID: PMC6031486 DOI: 10.1016/j.jdcr.2017.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Jessica Shiu
- Department of Dermatology, University of California, Irvine, Irvine, California
| | - Megan Thai
- University of California, Irvine, Irvine, California
| | - Ashley N Elsensohn
- Department of Dermatology, University of California, Irvine, Irvine, California
| | - Nathalie Q Nguyen
- Department of Dermatology, Kaiser Permanente Orange County, Irvine, California
| | - Kelly Y Lin
- Department of Dermatology, Kaiser Permanente Orange County, Irvine, California
| | - David S Cassarino
- Department of Pathology, Kaiser Permanente Los Angeles, Los Angeles, California
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42
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Scott NE, Hartland EL. Post-translational Mechanisms of Host Subversion by Bacterial Effectors. Trends Mol Med 2017; 23:1088-1102. [PMID: 29150361 DOI: 10.1016/j.molmed.2017.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 12/19/2022]
Abstract
Bacterial effector proteins are a specialized class of secreted proteins that are translocated directly into the host cytoplasm by bacterial pathogens. Effector proteins have diverse activities and targets, and many mediate post-translational modifications of host proteins. Effector proteins offer potential in novel biotechnological and medical applications as enzymes that may modify human proteins. Here, we discuss the mechanisms used by effectors to subvert the human host through blocking, blunting, or subverting immune mechanisms. This capacity allows bacteria to control host cell function to support pathogen survival, replication and dissemination to other hosts. In addition, we highlight that knowledge of effector protein activity may be used to develop chemical inhibitors as a new approach to treat bacterial infections.
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Affiliation(s)
- Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Elizabeth L Hartland
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton 3168, Australia; Department of Molecular and Translational Science, Monash University, Clayton 3168, Australia.
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43
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Harms A, Segers FHID, Quebatte M, Mistl C, Manfredi P, Körner J, Chomel BB, Kosoy M, Maruyama S, Engel P, Dehio C. Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella. Genome Biol Evol 2017; 9:761-776. [PMID: 28338931 PMCID: PMC5381568 DOI: 10.1093/gbe/evx042] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2017] [Indexed: 12/23/2022] Open
Abstract
The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution. Here, we report the discovery of a third repertoire of Beps associated with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any signs of host adaptability and is only distantly related to the two species-rich lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella isolates from under-sampled lineages enabled combined in silico analyses and wet lab experiments that suggest several parallel layers of functional diversification during evolution of the three Bep repertoires from a single ancestral effector. Our analyses show that the Beps of B. ancashensis share many features with the two other repertoires, but may represent a more ancestral state that has not yet unleashed the adaptive potential of such an effector set. We anticipate that the effectors of B. ancashensis will enable future studies to dissect the evolutionary history of Bartonella effectors and help unraveling the evolutionary forces underlying bacterial host adaptation.
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Affiliation(s)
- Alexander Harms
- Focal Area Infection Biology, Biozentrum, University of Basel, Switzerland
| | | | - Maxime Quebatte
- Focal Area Infection Biology, Biozentrum, University of Basel, Switzerland
| | - Claudia Mistl
- Focal Area Infection Biology, Biozentrum, University of Basel, Switzerland
| | - Pablo Manfredi
- Focal Area Infection Biology, Biozentrum, University of Basel, Switzerland
| | - Jonas Körner
- Focal Area Infection Biology, Biozentrum, University of Basel, Switzerland
| | - Bruno B Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis
| | - Michael Kosoy
- Bacterial Diseases Branch, Division of Vector-Borne Disease, Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Tokyo, Japan
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Switzerland
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Substrate translocation involves specific lysine residues of the central channel of the conjugative coupling protein TrwB. Mol Genet Genomics 2017; 292:1037-1049. [PMID: 28597316 DOI: 10.1007/s00438-017-1331-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
Conjugative transfer of plasmid R388 requires the coupling protein TrwB for protein and DNA transport, but their molecular role in transport has not been deciphered. We investigated the role of residues protruding into the central channel of the TrwB hexamer by a mutational analysis. Mutations affecting lysine residues K275, K398, and K421, and residue S441, all facing the internal channel, affected transport of both DNA and the relaxase protein in vivo. The ATPase activity of the purified soluble variants was affected significantly in the presence of accessory protein TrwA or DNA, correlating with their behaviour in vivo. Alteration of residues located at the cytoplasmic or the inner membrane interface resulted in lower activity in vivo and in vitro, while variants affecting residues in the central region of the channel showed increased DNA and protein transfer efficiency and higher ATPase activity, especially in the absence of TrwA. In fact, these variants could catalyze DNA transfer in the absence of TrwA under conditions in which the wild-type system was transfer deficient. Our results suggest that protein and DNA molecules have the same molecular requirements for translocation by Type IV secretion systems, with residues at both ends of the TrwB channel controlling the opening-closing mechanism, while residues embedded in the channel would set the pace for substrate translocation (both protein and DNA) in concert with TrwA.
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Abstract
Type IV coupling proteins (T4CPs) are essential constituents of most type IV secretion systems (T4SSs), and probably the most intriguing component in terms of their evolutionary origin and functional role. Coupling proteins have coevolved with their cognate secretion system and translocated substrates. They are present in all conjugative systems, leading to the suggestion that they play a specific role in DNA transfer. However, they are also part of many T4SSs involved in bacterial virulence, where they are required for protein translocation, with no apparent involvement in DNA secretion. Their name reflects genetic and biochemical evidence of a connecting role between the substrate and the T4SS, thus probably playing a major role in substrate recruitment. Increasing evidence supports also a role in signal transmission leading to activation of secretion. Most studies have addressed conjugative coupling proteins of the VirD4-like protein family. Their conserved features include a nucleotide-binding domain, essential for substrate translocation, a C-terminal domain involved in substrate interactions, and a transmembrane domain anchoring them to the inner membrane, which is an important regulator of protein function. Purified soluble deletion mutants display ATP hydrolysis activity and unspecific DNA binding. Elucidation of the 3D structure of the soluble deletion mutant of the conjugative coupling protein TrwB, TrwBΔN70, provided the basis for further mutagenesis studies rendering interesting insights into the structure-function of these proteins. Their key role as couplers between substrate and transporter provides biotechnological potential as targets for anti-virulence strategies, as well as for customization of substrate delivery through heterologous secretion systems.
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Affiliation(s)
- Matxalen Llosa
- Departamento de Biología Molecular, Universidad de Cantabria (UC), and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-SODERCAN, C/Albert Einstein 22, 39011, Santander, Spain.
| | - Itziar Alkorta
- Departamento de Bioquímica y Biología Molecular (UPV/EHU), Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena S/N, 48940, Leioa, Spain
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46
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Grohmann E, Keller W, Muth G. Mechanisms of Conjugative Transfer and Type IV Secretion-Mediated Effector Transport in Gram-Positive Bacteria. Curr Top Microbiol Immunol 2017. [PMID: 29536357 DOI: 10.1007/978-3-319-75241-9_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Conjugative DNA transfer is the most important means to transfer antibiotic resistance genes and virulence determinants encoded by plasmids, integrative conjugative elements (ICE), and pathogenicity islands among bacteria. In gram-positive bacteria, there exist two types of conjugative systems, (i) type IV secretion system (T4SS)-dependent ones, like those encoded by the Enterococcus, Streptococcus, Staphylococcus, Bacillus, and Clostridia mobile genetic elements and (ii) T4SS-independent ones, as those found on Streptomyces plasmids. Interestingly, very recently, on the Streptococcus suis genome, the first gram-positive T4SS not only involved in conjugative DNA transfer but also in effector translocation to the host was detected. Although no T4SS core complex structure from gram-positive bacteria is available, several structures from T4SS protein key factors from Enterococcus and Clostridia plasmids have been solved. In this chapter, we summarize the current knowledge on the molecular mechanisms and structure-function relationships of the diverse conjugation machineries and emerging research needs focused on combatting infections and spread of multiple resistant gram-positive pathogens.
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Affiliation(s)
- Elisabeth Grohmann
- Beuth University of Applied Sciences Berlin, Life Sciences and Technology, 13347, Berlin, Germany.
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed, University of Graz, 8010, Graz, Austria
| | - Günther Muth
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University Tübingen, 72076, Tübingen, Germany
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