151
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Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes. Pathogens 2019; 9:pathogens9010022. [PMID: 31881744 PMCID: PMC7168690 DOI: 10.3390/pathogens9010022] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/10/2019] [Accepted: 12/20/2019] [Indexed: 12/30/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)-leading to the cis-mobilization of an IME carrying tet(O)-was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.
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152
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Pachathundikandi SK, Tegtmeyer N, Arnold IC, Lind J, Neddermann M, Falkeis-Veits C, Chattopadhyay S, Brönstrup M, Tegge W, Hong M, Sticht H, Vieth M, Müller A, Backert S. T4SS-dependent TLR5 activation by Helicobacter pylori infection. Nat Commun 2019; 10:5717. [PMID: 31844047 PMCID: PMC6915727 DOI: 10.1038/s41467-019-13506-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023] Open
Abstract
Toll-like receptor TLR5 recognizes a conserved domain, termed D1, that is present in flagellins of several pathogenic bacteria but not in Helicobacter pylori. Highly virulent H. pylori strains possess a type IV secretion system (T4SS) for delivery of virulence factors into gastric epithelial cells. Here, we show that one of the H. pylori T4SS components, protein CagL, can act as a flagellin-independent TLR5 activator. CagL contains a D1-like motif that mediates adherence to TLR5+ epithelial cells, TLR5 activation, and downstream signaling in vitro. TLR5 expression is associated with H. pylori infection and gastric lesions in human biopsies. Using Tlr5-knockout and wild-type mice, we show that TLR5 is important for efficient control of H. pylori infection. Our results indicate that CagL, by activating TLR5, may modulate immune responses to H. pylori. Toll-like receptor TLR5 recognizes a domain, D1, that is present in flagellins of several pathogenic bacteria but not in Helicobacter pylori. Here, the authors show that TLR5 can be activated independently of flagellin by a component of the H. pylori type IV secretion system that contains a D1-like motif.
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Affiliation(s)
| | - Nicole Tegtmeyer
- Department of Biology, Division of Microbiology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Judith Lind
- Department of Biology, Division of Microbiology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias Neddermann
- Department of Biology, Division of Microbiology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Sujay Chattopadhyay
- JIS Institute of Advanced Studies and Research, JIS University, Kolkata, 700091, India
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Werner Tegge
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Heinrich Sticht
- Institute of Biochemistry, Division of Bioinformatics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Michael Vieth
- Institute for Pathology, Klinikum Bayreuth, Bayreuth, Germany
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Steffen Backert
- Department of Biology, Division of Microbiology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany.
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153
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Molecular anatomy and pathogenic actions of Helicobacter pylori CagA that underpin gastric carcinogenesis. Cell Mol Immunol 2019; 17:50-63. [PMID: 31804619 PMCID: PMC6952403 DOI: 10.1038/s41423-019-0339-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
Chronic infection with Helicobacter pylori cagA-positive strains is the strongest risk factor for gastric cancer. The cagA gene product, CagA, is delivered into gastric epithelial cells via the bacterial type IV secretion system. Delivered CagA then undergoes tyrosine phosphorylation at the Glu-Pro-Ile-Tyr-Ala (EPIYA) motifs in its C-terminal region and acts as an oncogenic scaffold protein that physically interacts with multiple host signaling proteins in both tyrosine phosphorylation-dependent and -independent manners. Analysis of CagA using in vitro cultured gastric epithelial cells has indicated that the nonphysiological scaffolding actions of CagA cell-autonomously promote the malignant transformation of the cells by endowing the cells with multiple phenotypic cancer hallmarks: sustained proliferation, evasion of growth suppressors, invasiveness, resistance to cell death, and genomic instability. Transgenic expression of CagA in mice leads to in vivo oncogenic action of CagA without any overt inflammation. The in vivo oncogenic activity of CagA is further potentiated in the presence of chronic inflammation. Since Helicobacter pylori infection triggers a proinflammatory response in host cells, a feedforward stimulation loop that augments the oncogenic actions of CagA and inflammation is created in CagA-injected gastric mucosa. Given that Helicobacter pylori is no longer colonized in established gastric cancer lesions, the multistep nature of gastric cancer development should include a “hit-and-run” process of CagA action. Thus, acquisition of genetic and epigenetic alterations that compensate for CagA-directed cancer hallmarks may be required for completion of the “hit-and-run” process of gastric carcinogenesis.
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154
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Interspecies and Intraspecies Signals Synergistically Regulate Lysobacter enzymogenes Twitching Motility. Appl Environ Microbiol 2019; 85:AEM.01742-19. [PMID: 31540995 DOI: 10.1128/aem.01742-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
The twitching motility of bacteria is closely related to environmental adaptability and pathogenic behaviors. Lysobacter is a good genus in which to study twitching motility because of the complex social activities and distinct movement patterns of its members. Regardless, the mechanism that induces twitching motility is largely unknown. In this study, we found that the interspecies signal indole caused Lysobacter to have irregular, random twitching motility with significantly enhanced speed. Deletion of qseC or qseB from the two-component system for indole signaling perception resulted in the disappearance of rapid, random movements and significantly decreased twitching activity. Indole-induced, rapid, random twitching was achieved through upregulation of expression of gene cluster pilE1-pilY11-pilX1-pilW1-pilV1-fimT1 In addition, under conditions of extremely low bacterial density, individual Lysobacter cells grew and divided in a stable manner in situ without any movement. The intraspecies quorum-sensing signaling factor 13-methyltetradecanoic acid, designated L. enzymogenes diffusible signaling factor (LeDSF), was essential for Lysobacter to produce twitching motility through indirect regulation of gene clusters pilM-pilN-pilO-pilP-pilQ and pilS1-pilR-pilA-pilB-pilC These results demonstrate that the motility of Lysobacter is induced and regulated by indole and LeDSF, which reveals a novel theory for future studies of the mechanisms of bacterial twitching activities.IMPORTANCE The mechanism underlying bacterial twitching motility is an important research area because it is closely related to social and pathogenic behaviors. The mechanism mediating cell-to-cell perception of twitching motility is largely unknown. Using Lysobacter as a model, we found in this study that the interspecies signal indole caused Lysobacter to exhibit irregular, random twitching motility via activation of gene cluster pilE1-pilY11-pilX1-pilW1-pilV1-fimT1 In addition, population-dependent behavior induced by 13-methyltetradecanoic acid, a quorum-sensing signaling molecule designated LeDSF, was involved in twitching motility by indirectly regulating gene clusters pilM-pilN-pilO-pilP-pilQ and pilS1-pilR-pilA-pilB-pilC The results demonstrate that the twitching motility of Lysobacter is regulated by these two signaling molecules, offering novel clues for exploring the mechanisms of twitching motility and population-dependent behaviors of bacteria.
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155
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Peñil-Celis A, Garcillán-Barcia MP. Crosstalk Between Type VI Secretion System and Mobile Genetic Elements. Front Mol Biosci 2019; 6:126. [PMID: 31799257 PMCID: PMC6863884 DOI: 10.3389/fmolb.2019.00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Many bacterial processes require cell-cell contacts. Such are the cases of bacterial conjugation, one of the main horizontal gene transfer mechanisms that physically spreads DNA, and the type VI secretion systems (T6SSs), which deploy antibacterial activity. Bacteria depend on conjugation to adapt to changing environments, while T6SS killing activity could pose a threat to mating partners. Here we review the experimental evidences of overlapping and interaction between the T6SSs, bacterial conjugation, and conjugative genetic elements.
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Affiliation(s)
- Arancha Peñil-Celis
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Spain
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156
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Hong J, Luo Y, Mou M, Fu J, Zhang Y, Xue W, Xie T, Tao L, Lou Y, Zhu F. Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. Brief Bioinform 2019; 21:1825-1836. [PMID: 31860715 DOI: 10.1093/bib/bbz120] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
The type IV bacterial secretion system (SS) is reported to be one of the most ubiquitous SSs in nature and can induce serious conditions by secreting type IV SS effectors (T4SEs) into the host cells. Recent studies mainly focus on annotating new T4SE from the huge amount of sequencing data, and various computational tools are therefore developed to accelerate T4SE annotation. However, these tools are reported as heavily dependent on the selected methods and their annotation performance need to be further enhanced. Herein, a convolution neural network (CNN) technique was used to annotate T4SEs by integrating multiple protein encoding strategies. First, the annotation accuracies of nine encoding strategies integrated with CNN were assessed and compared with that of the popular T4SE annotation tools based on independent benchmark. Second, false discovery rates of various models were systematically evaluated by (1) scanning the genome of Legionella pneumophila subsp. ATCC 33152 and (2) predicting the real-world non-T4SEs validated using published experiments. Based on the above analyses, the encoding strategies, (a) position-specific scoring matrix (PSSM), (b) protein secondary structure & solvent accessibility (PSSSA) and (c) one-hot encoding scheme (Onehot), were identified as well-performing when integrated with CNN. Finally, a novel strategy that collectively considers the three well-performing models (CNN-PSSM, CNN-PSSSA and CNN-Onehot) was proposed, and a new tool (CNN-T4SE, https://idrblab.org/cnnt4se/) was constructed to facilitate T4SE annotation. All in all, this study conducted a comprehensive analysis on the performance of a collection of encoding strategies when integrated with CNN, which could facilitate the suppression of T4SS in infection and limit the spread of antimicrobial resistance.
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Affiliation(s)
- Jiajun Hong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Tian Xie
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, Zhejiang, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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157
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Activity and Functional Importance of Helicobacter pylori Virulence Factors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1149:35-56. [PMID: 31016624 DOI: 10.1007/5584_2019_358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Helicobacter pylori is a very successful Gram-negative pathogen colonizing the stomach of humans worldwide. Infections with this bacterium can generate pathologies ranging from chronic gastritis and peptic ulceration to gastric cancer. The best characterized H. pylori virulence factors that cause direct cell damage include an effector protein encoded by the cytotoxin-associated gene A (CagA), a type IV secretion system (T4SS) encoded in the cag-pathogenicity island (cag PAI), vacuolating cytotoxin A (VacA), γ-glutamyl transpeptidase (GGT), high temperature requirement A (HtrA, a serine protease) and cholesterol glycosyl-transferase (CGT). Since these H. pylori factors are either surface-exposed, secreted or translocated, they can directly interact with host cell molecules and are able to hijack cellular functions. Studies on these bacterial factors have progressed substantially in recent years. Here, we review the current status in the characterization of signaling cascades by these factors in vivo and in vitro, which comprise the disruption of cell-to-cell junctions, induction of membrane rearrangements, cytoskeletal dynamics, proliferative, pro-inflammatory, as well as, pro-apoptotic and anti-apoptotic responses or immune evasion. The impact of these signal transduction modules in the pathogenesis of H. pylori infections is discussed.
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158
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Meygret A, Peuchant O, Dordet-Frisoni E, Sirand-Pugnet P, Citti C, Bébéar C, Béven L, Pereyre S. High Prevalence of Integrative and Conjugative Elements Encoding Transcription Activator-Like Effector Repeats in Mycoplasma hominis. Front Microbiol 2019; 10:2385. [PMID: 31681239 PMCID: PMC6813540 DOI: 10.3389/fmicb.2019.02385] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/01/2019] [Indexed: 12/02/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are modular mobile genetic elements that can disseminate through excision, circularization, and transfer. Mycoplasma ICEs have recently been found distributed among some mycoplasma species and there is accumulating evidence that they play a pivotal role in horizontal gene transfers. The occurrence of ICEs has not been documented in Mycoplasma hominis, a human urogenital pathogen responsible for urogenital infections, neonatal infections and extragenital infections. In this study, we searched for, characterized, and compared ICEs by genome analyses of 12 strains of M. hominis. ICEs of 27–30 kb were found in one or two copies in seven of the 12 M. hominis strains sequenced. Only five of these ICEs seemed to be functional, as assessed by detection of circular forms of extrachromosomal ICE. Moreover, the prevalence of ICEs in M. hominis was estimated to be 45% in a collection of 120 clinical isolates of M. hominis, including 27 tetracycline-resistant tet(M)-positive isolates. The proportion of ICEs was not higher in isolates carrying the tet(M) gene, suggesting that ICEs are not involved in tetracycline resistance. Notably, all M. hominis ICEs had a very similar structure, consisting of a 4.0–5.1 kb unusual module composed of five to six juxtaposed CDSs. All the genes forming this module were specific to M. hominis ICEs as they had no homologs in other mycoplasma ICEs. In each M. hominis ICE, one to three CDSs encode proteins that share common structural features with transcription activator-like (TAL) effectors involved in polynucleotide recognition and signal transduction in symbiotic plant pathogen bacteria. The conserved and specific structure of M. hominis ICEs and the high prevalence in clinical strains suggest that these ICEs may confer a selective advantage for the physiology or pathogenicity of this human pathogenic bacterium. These data open the way for further studies aiming at unraveling horizontal gene transfers and virulence factors in M. hominis.
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Affiliation(s)
- Alexandra Meygret
- USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,INRA, USC-EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,Department of Bacteriology, French National Reference Center for Bacterial STI, CHU Bordeaux, Bordeaux, France
| | - Olivia Peuchant
- USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,INRA, USC-EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,Department of Bacteriology, French National Reference Center for Bacterial STI, CHU Bordeaux, Bordeaux, France
| | - Emilie Dordet-Frisoni
- IHAP, INRA, Ecole Nationale Vétérinaire de Toulouse, Université de Toulouse, Toulouse, France
| | - Pascal Sirand-Pugnet
- UMR 1332, BFP, University of Bordeaux, Bordeaux, France.,INRA, UMR 1332, BFP, Bordeaux, France
| | - Christine Citti
- IHAP, INRA, Ecole Nationale Vétérinaire de Toulouse, Université de Toulouse, Toulouse, France
| | - Cécile Bébéar
- USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,INRA, USC-EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,Department of Bacteriology, French National Reference Center for Bacterial STI, CHU Bordeaux, Bordeaux, France
| | - Laure Béven
- UMR 1332, BFP, University of Bordeaux, Bordeaux, France.,INRA, UMR 1332, BFP, Bordeaux, France
| | - Sabine Pereyre
- USC EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,INRA, USC-EA 3671 Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,Department of Bacteriology, French National Reference Center for Bacterial STI, CHU Bordeaux, Bordeaux, France
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159
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Avello M, Davis KP, Grossman AD. Identification, characterization and benefits of an exclusion system in an integrative and conjugative element of Bacillus subtilis. Mol Microbiol 2019; 112:1066-1082. [PMID: 31361051 PMCID: PMC6827876 DOI: 10.1111/mmi.14359] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2019] [Indexed: 01/09/2023]
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer from cell to cell by conjugation (like plasmids) and integrate into the chromosomes of bacterial hosts (like lysogenic phages or transposons). ICEs are prevalent in bacterial chromosomes and play a major role in bacterial evolution by promoting horizontal gene transfer. Exclusion prevents the redundant transfer of conjugative elements into host cells that already contain a copy of the element. Exclusion has been characterized mostly for conjugative elements of Gram-negative bacteria. Here, we report the identification and characterization of an exclusion mechanism in ICEBs1 from the Gram-positive bacterium Bacillus subtilis. We found that cells containing ICEBs1 inhibit the activity of the ICEBs1-encoded conjugation machinery in other cells. This inhibition (exclusion) was specific to the cognate conjugation machinery and the ICEBs1 gene yddJ was both necessary and sufficient to mediate exclusion by recipient cells. Through a mutagenesis and enrichment screen, we identified exclusion-resistant mutations in the ICEBs1 gene conG. Using genes from a heterologous but related ICE, we found that the exclusion specificity was determined by ConG and YddJ. Finally, we found that under conditions that support conjugation, exclusion provides a selective advantage to the element and its host cells.
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Affiliation(s)
| | | | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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160
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Kaur A, Bansal K, Kumar S, Sonti RV, Patil PB. Complete genome dynamics of a dominant-lineage strain of Xanthomonas oryzae pv. oryzae harbouring a novel plasmid encoding a type IV secretion system. Access Microbiol 2019; 1:e000063. [PMID: 32974563 PMCID: PMC7472545 DOI: 10.1099/acmi.0.000063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/27/2019] [Indexed: 11/29/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a serious pathogen causing bacterial blight disease in rice. Population genomic studies have revealed that rampant inter-strain rather than inter-lineage differences are contributing to the evolutionary success of this pathogen. Here, we report the complete genome sequence of BXO1, a strain of Xoo belonging to a dominant lineage from India. A complete genome-based investigation revealed the presence of two plasmids, pBXO1-1 (66.7 kb) and pBXO1-2 (25.6 kb). The pBXO1-1 plasmid encodes 71 genes, 38 of which encode hypothetical proteins of unknown function. However, these hypothetical genes possess atypical GC content, pointing towards their acquisition and movement through horizontal gene transfer. Interestingly, pBXO1-2 encodes a type IV secretion system (T4SS), which is known to play an important role in the conjugative transfer of genetic material, and also provides fitness to pathogenic bacteria for their enhanced survival. Neither plasmid has been reported previously in any other complete Xoo genome published to date. Our analysis also revealed that the pBXO1-2 plasmid is present in Xanthomonas albilineans str. GPE PC73, which is known to cause leaf scald, a lethal disease in sugarcane. Our complete genome sequence analysis of BXO1 has provided us with detailed insights into the two novel strain-specific plasmids, in addition to decoding their functional capabilities, which were not assessable when using the draft genome sequence of the strain. Overall, our study has revealed the mobility of a novel T4SS in two pathogenic species of Xanthomonas that infect the vascular tissues of two economically important monocot plants, i.e. rice and sugarcane.
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Affiliation(s)
- Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Kanika Bansal
- 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.,Present address: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ramesh V Sonti
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.,DBT- National Institute of Plant Genome Research, New Delhi, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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161
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Lorenzo-Diaz F, Moreno-Córdoba I, Espinosa M. Complete labelling of pneumococcal DNA-binding proteins with seleno-L-methionine. J Microbiol Methods 2019; 166:105720. [PMID: 31518592 DOI: 10.1016/j.mimet.2019.105720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 10/26/2022]
Abstract
Streptococcus pneumoniae is a pathogenic and opportunistic Gram-positive bacterium that is the leading cause of community-acquired respiratory diseases, varying from mild- to deathly- infections. The appearance of antibiotic-resistant isolates has prompted the search for novel strategies and targets to tackle the bacterial resistances. One of the most promising approaches is the structure-based knowledge of possible targets in conjunction with rational design and docking of inhibitors of the chosen targets. A useful technique that helps to solve protein structures is to label them with an amino acid derivative like seleno-methionine that facilitates tracing of some of the amino acid residues. We have chosen two pneumococcal DNA-binding proteins, namely the relaxase domain of MobM protein from plasmid pMV158, and the RelB-RelE antitoxin-toxin protein complex. Through several changes that improve substantially a previous protocol (Budisa et al., 1995), we have used seleno-L-methionine to incorporate selenium into the amino acid sequence of the selected proteins. We have achieved 100% labelling of the proteins and could demonstrate that the labelled proteins retained full activity as judged from the relaxation of supercoiled plasmid DNA and from gel-retardation assays.
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Affiliation(s)
- Fabián Lorenzo-Diaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Inmaculada Moreno-Córdoba
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
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162
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Anné J, Karamanou S, Economou A. Editorial: Thematic issue on bacterial protein export: from fundamentals to applications. FEMS Microbiol Lett 2019; 365:5092704. [PMID: 30202899 DOI: 10.1093/femsle/fny206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jozef Anné
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, Leuven 3000, BelgiumE-mail:
| | - Spyridoula Karamanou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, Leuven 3000, Belgium
| | - Anastassios Economou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, Leuven 3000, Belgium
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163
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Bayer-Santos E, Cenens W, Matsuyama BY, Oka GU, Di Sessa G, Mininel IDV, Alves TL, Farah CS. The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing. PLoS Pathog 2019; 15:e1007651. [PMID: 31513674 PMCID: PMC6759196 DOI: 10.1371/journal.ppat.1007651] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 09/24/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial type IV secretion systems (T4SS) are a highly diversified but evolutionarily related family of macromolecule transporters that can secrete proteins and DNA into the extracellular medium or into target cells. It was recently shown that a subtype of T4SS harboured by the plant pathogen Xanthomonas citri transfers toxins into target cells. Here, we show that a similar T4SS from the multi-drug-resistant opportunistic pathogen Stenotrophomonas maltophilia is proficient in killing competitor bacterial species. T4SS-dependent duelling between S. maltophilia and X. citri was observed by time-lapse fluorescence microscopy. A bioinformatic search of the S. maltophilia K279a genome for proteins containing a C-terminal domain conserved in X. citri T4SS effectors (XVIPCD) identified twelve putative effectors and their cognate immunity proteins. We selected a putative S. maltophilia effector with unknown function (Smlt3024) for further characterization and confirmed that it is indeed secreted in a T4SS-dependent manner. Expression of Smlt3024 in the periplasm of E. coli or its contact-dependent delivery via T4SS into E. coli by X. citri resulted in reduced growth rates, which could be counteracted by expression of its cognate inhibitor Smlt3025 in the target cell. Furthermore, expression of the VirD4 coupling protein of X. citri can restore the function of S. maltophilia ΔvirD4, demonstrating that effectors from one species can be recognized for transfer by T4SSs from another species. Interestingly, Smlt3024 is homologous to the N-terminal domain of large Ca2+-binding RTX proteins and the crystal structure of Smlt3025 revealed a topology similar to the iron-regulated protein FrpD from Neisseria meningitidis which has been shown to interact with the RTX protein FrpC. This work expands our current knowledge about the function of bacteria-killing T4SSs and increases the panel of effectors known to be involved in T4SS-mediated interbacterial competition, which possibly contribute to the establishment of S. maltophilia in clinical and environmental settings.
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Affiliation(s)
- Ethel Bayer-Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Bruno Yasui Matsuyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Gabriel Umaji Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Giancarlo Di Sessa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Izabel Del Valle Mininel
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Tiago Lubiana Alves
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Chuck Shaker Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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164
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Translocation of effector proteins into host cells by Toxoplasma gondii. Curr Opin Microbiol 2019; 52:130-138. [PMID: 31446366 DOI: 10.1016/j.mib.2019.07.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022]
Abstract
The Apicomplexan parasite, Toxoplasma gondii, is an obligate intracellular organism that must co-opt its host cell to survive. To this end, Toxoplasma parasites introduce a suite of effector proteins from two secretory compartments called rhoptries and dense granules into the host cells. Once inside, these effectors extensively modify the host cell to facilitate parasite penetration, replication and persistence. In this review, we summarize the most recent advances in current understanding of effector translocation from Toxoplasma's rhoptry and dense granule organelles into the host cell, with comparisons to Plasmodium spp. for broader context.
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165
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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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166
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Go D, Lee J, Choi JA, Cho SN, Kim SH, Son SH, Song CH. Reactive oxygen species-mediated endoplasmic reticulum stress response induces apoptosis of Mycobacterium avium-infected macrophages by activating regulated IRE1-dependent decay pathway. Cell Microbiol 2019; 21:e13094. [PMID: 31386788 PMCID: PMC6899680 DOI: 10.1111/cmi.13094] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/15/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
Mycobacterium avium, a slow‐growing nontuberculous mycobacterium, causes fever, diarrhoea, loss of appetite, and weight loss in immunocompromised people. We have proposed that endoplasmic reticulum (ER) stress‐mediated apoptosis plays a critical role in removing intracellular mycobacteria. In the present study, we investigated the role of the regulated IRE1‐dependent decay (RIDD) pathway in macrophages during M. avium infection based on its role in the regulation of gene expression. The inositol‐requiring enzyme 1 (IRE1)/apoptosis signal‐regulating kinase 1 (ASK1)/c‐Jun N‐terminal kinase (JNK) signalling pathway was activated in macrophages after infection with M. avium. The expression of RIDD‐associated genes, such as Bloc1s1 and St3gal5, was decreased in M. avium‐infected macrophages. Interestingly, M. avium‐induced apoptosis was significantly suppressed by pretreatment with irestatin (inhibitor of IRE1α) and 4μ8c (RIDD blocker). Macrophages pretreated with N‐acetyl cysteine (NAC) showed decreased levels of reactive oxygen species (ROS), IRE1α, and apoptosis after M. avium infection. The expression of Bloc1s1 and St3gal5 was increased in NAC‐pretreated macrophages following infection with M. avium. Growth of M. avium was significantly increased in irestatin‐, 4μ8c‐, and NAC‐treated macrophages compared with the control. The data indicate that the ROS‐mediated ER stress response induces apoptosis of M. avium‐infected macrophages by activating IRE1α‐RIDD. Thus, activation of IRE1α suppresses the intracellular survival of M. avium in macrophages.
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Affiliation(s)
- Dam Go
- Department of Medical Science, Chungnam National University, Daejeon, South Korea.,Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Junghwan Lee
- Department of Medical Science, Chungnam National University, Daejeon, South Korea.,Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Ji-Ae Choi
- Department of Medical Science, Chungnam National University, Daejeon, South Korea.,Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Soo-Na Cho
- Department of Medical Science, Chungnam National University, Daejeon, South Korea.,Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Seon-Hwa Kim
- Department of Medical Science, Chungnam National University, Daejeon, South Korea.,Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Sang-Hun Son
- Department of Medical Science, Chungnam National University, Daejeon, South Korea.,Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Chang-Hwa Song
- Department of Medical Science, Chungnam National University, Daejeon, South Korea.,Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, South Korea.,Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, South Korea
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167
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Beinart RA, Luo C, Konstantinidis KT, Stewart FJ, Girguis PR. The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content. Front Microbiol 2019; 10:1818. [PMID: 31474946 PMCID: PMC6702916 DOI: 10.3389/fmicb.2019.01818] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/23/2019] [Indexed: 12/29/2022] Open
Abstract
Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic bacterial lineages. At the broadest level, these symbioses share primary function: the bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals to power the fixation of inorganic carbon and/or other nutrients, providing the bulk of host nutrition. However, it is unclear to what extent the ecological niche of the host species is influenced by differences in symbiont traits, particularly those involved in chemoautotrophic function and interaction with the geochemical environment. Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine whether differences in chemoautotrophic capacity exist among these symbionts that could explain the observed distribution of these snail species into distinct geochemical habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four distinct lineages in the classes γ-proteobacteria or Campylobacteria. The genomes differed with respect to genes related to motility, adhesion, secretion, and amino acid uptake or excretion, though were quite similar in chemoautotrophic function, with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, and oxygen and nitrate respiration. This indicates that differences in the presence or absence of symbiont chemoautotrophic functions does not likely explain the observed geochemical habitat partitioning. Rather, differences in gene expression and regulation, biochemical differences among these chemoautotrophic pathways, and/or differences in host physiology could all influence the observed patterns of habitat partitioning.
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Affiliation(s)
- Roxanne A. Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States
| | - Chengwei Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
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168
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Pachathundikandi SK, Gutiérrez-Escobar AJ, Tegtmeyer N. Tailor-Made Detection of Individual Phosphorylated and Non-Phosphorylated EPIYA-Motifs of Helicobacter pylori Oncoprotein CagA. Cancers (Basel) 2019; 11:cancers11081163. [PMID: 31412675 PMCID: PMC6721621 DOI: 10.3390/cancers11081163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/25/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
The gastric pathogen and carcinogen Helicobacter pylori(H. pylori) encodes a type IV secretion system for translocation of the effector protein CagA into host cells. Injected CagA becomes tyrosine-phosphorylated at the five amino acid residue Glutamate-Proline- Isoleucine-Tyrosine-Alanine (EPIYA)-sequence motifs. These phosphorylated EPIYA-sites represent recognition motifs for binding of multiple host factors, which then manipulate signaling pathways to trigger gastric disease. Thus, efficient detection of single phosphorylated EPIYA-motifs in CagA is required. Detection of phospho-CagA is primarily performed using commercial pan-phosphotyrosine antibodies. However, those antibodies were originally generated to recognize many phosphotyrosines in various mammalian proteins and are not optimized for use in bacteria. To address this important limitation, we synthesized 11-mer phospho- and non-phospho-peptides from EPIYA-motifs A, B, and C, and produced three phospho-specific and three non-phospho-specific rabbit polyclonal CagA antibodies. These antibodies specifically recognized the corresponding phosphorylated and non-phosphorylated EPIYA-motifs, while the EPIYA-C antibodies also recognized the related East-Asian EPIYA-D motif. Otherwise, no cross-reactivity of the antibodies among EPIYAs was observed. Western blotting demonstrated that each EPIYA-motif can be predominantly phosphorylated during H. pylori infection. This represents the first complete set of phospho-specific antibodies for an effector protein in bacteria, providing useful tools to gather information for the categorization of CagA phosphorylation, cancer signaling, and gastric disease progression.
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Affiliation(s)
- Suneesh Kumar Pachathundikandi
- Department of Biology, Division of Microbiology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstraße 5, D-91058 Erlangen, Germany
| | - Andrés Julián Gutiérrez-Escobar
- Department of Biology, Division of Microbiology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstraße 5, D-91058 Erlangen, Germany
| | - Nicole Tegtmeyer
- Department of Biology, Division of Microbiology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstraße 5, D-91058 Erlangen, Germany.
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169
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Li X, Xie Y, Liu M, Tai C, Sun J, Deng Z, Ou HY. oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. Nucleic Acids Res 2019; 46:W229-W234. [PMID: 29733379 PMCID: PMC6030822 DOI: 10.1093/nar/gky352] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
oriTfinder is a web server that facilitates the rapid identification of the origin of transfer site (oriT) of a conjugative plasmid or chromosome-borne integrative and conjugative element. The utilized back-end database oriTDB was built upon more than one thousand known oriT regions of bacterial mobile genetic elements (MGEs) as well as the known MGE-encoding relaxases and type IV coupling proteins (T4CP). With a combination of similarity searches for the oriTDB-archived oriT nucleotide sequences and the co-localization of the flanking relaxase homologous genes, the oriTfinder can predict the oriT region with high accuracy in the DNA sequence of a bacterial plasmid or chromosome in minutes. The server also detects the other transfer-related modules, including the potential relaxase gene, T4CP gene and the type IV secretion system gene cluster, and the putative genes coding for virulence factors and acquired antibiotic resistance determinants. oriTfinder may contribute to meeting the increasing demands of re-annotations for bacterial conjugative, mobilizable or non-transferable elements and aid in the rapid risk accession of disease-relevant trait dissemination in pathogenic bacteria of interest. oriTfinder is freely available to all users without any login requirement at http://bioinfo-mml.sjtu.edu.cn/oriTfinder.
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Affiliation(s)
- Xiaobin Li
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yingzhou Xie
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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170
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Structural bases for F plasmid conjugation and F pilus biogenesis in Escherichia coli. Proc Natl Acad Sci U S A 2019; 116:14222-14227. [PMID: 31239340 DOI: 10.1073/pnas.1904428116] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial conjugation systems are members of the large type IV secretion system (T4SS) superfamily. Conjugative transfer of F plasmids residing in the Enterobacteriaceae was first reported in the 1940s, yet the architecture of F plasmid-encoded transfer channel and its physical relationship with the F pilus remain unknown. We visualized F-encoded structures in the native bacterial cell envelope by in situ cryoelectron tomography (CryoET). Remarkably, F plasmids encode four distinct structures, not just the translocation channel or channel-pilus complex predicted by prevailing models. The F1 structure is composed of distinct outer and inner membrane complexes and a connecting cylinder that together house the envelope-spanning translocation channel. The F2 structure is essentially the F1 complex with the F pilus attached at the outer membrane (OM). Remarkably, the F3 structure consists of the F pilus attached to a thin, cell envelope-spanning stalk, whereas the F4 structure consists of the pilus docked to the OM without an associated periplasmic density. The traffic ATPase TraC is configured as a hexamer of dimers at the cytoplasmic faces of the F1 and F2 structures, where it respectively regulates substrate transfer and F pilus biogenesis. Together, our findings present architectural renderings of the DNA conjugation or "mating" channel, the channel-pilus connection, and unprecedented pilus basal structures. These structural snapshots support a model for biogenesis of the F transfer system and allow for detailed comparisons with other structurally characterized T4SSs.
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171
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Kohler V, Goessweiner-Mohr N, Aufschnaiter A, Fercher C, Probst I, Pavkov-Keller T, Hunger K, Wolinski H, Büttner S, Grohmann E, Keller W. TraN: A novel repressor of an Enterococcus conjugative type IV secretion system. Nucleic Acids Res 2019; 46:9201-9219. [PMID: 30060171 PMCID: PMC6158623 DOI: 10.1093/nar/gky671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/18/2018] [Indexed: 11/19/2022] Open
Abstract
The dissemination of multi-resistant bacteria represents an enormous burden on modern healthcare. Plasmid-borne conjugative transfer is the most prevalent mechanism, requiring a type IV secretion system that enables bacteria to spread beneficial traits, such as resistance to last-line antibiotics, among different genera. Inc18 plasmids, like the Gram-positive broad host-range plasmid pIP501, are substantially involved in propagation of vancomycin resistance from Enterococci to methicillin-resistant strains of Staphylococcus aureus. Here, we identified the small cytosolic protein TraN as a repressor of the pIP501-encoded conjugative transfer system, since deletion of traN resulted in upregulation of transfer factors, leading to highly enhanced conjugative transfer. Furthermore, we report the complex structure of TraN with DNA and define the exact sequence of its binding motif. Targeting this protein–DNA interaction might represent a novel therapeutic approach against the spreading of antibiotic resistances.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Nikolaus Goessweiner-Mohr
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria.,Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria
| | | | - Christian Fercher
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Ines Probst
- Division of Infectious Diseases, University Medical Center Freiburg, Freiburg 79106, Germany
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Kristin Hunger
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Sabrina Büttner
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 10691, Sweden
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Freiburg 79106, Germany.,Life Sciences and Technology, Beuth University of Applied Sciences, Berlin 13353, Germany
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria.,BioTechMed-Graz, Austria
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172
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Chung JM, Sheedlo MJ, Campbell AM, Sawhney N, Frick-Cheng AE, Lacy DB, Cover TL, Ohi MD. Structure of the Helicobacter pylori Cag type IV secretion system. eLife 2019; 8:e47644. [PMID: 31210639 PMCID: PMC6620104 DOI: 10.7554/elife.47644] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/17/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial type IV secretion systems (T4SSs) are molecular machines that can mediate interbacterial DNA transfer through conjugation and delivery of effector molecules into host cells. The Helicobacter pylori Cag T4SS translocates CagA, a bacterial oncoprotein, into gastric cells, contributing to gastric cancer pathogenesis. We report the structure of a membrane-spanning Cag T4SS assembly, which we describe as three sub-assemblies: a 14-fold symmetric outer membrane core complex (OMCC), 17-fold symmetric periplasmic ring complex (PRC), and central stalk. Features that differ markedly from those of prototypical T4SSs include an expanded OMCC and unexpected symmetry mismatch between the OMCC and PRC. This structure is one of the largest bacterial secretion system assemblies ever reported and illustrates the remarkable structural diversity that exists among bacterial T4SSs.
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Affiliation(s)
- Jeong Min Chung
- Life Sciences InstituteUniversity of MichiganAnn ArborUnited States
| | - Michael J Sheedlo
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University School of MedicineNashvilleUnited States
| | - Anne M Campbell
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
| | - Neha Sawhney
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
| | - Arwen E Frick-Cheng
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University School of MedicineNashvilleUnited States
- Department of Immunology and MicrobiologyUniversity of Michigan School of MedicineAnn ArborUnited States
| | - Dana Borden Lacy
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University School of MedicineNashvilleUnited States
- Veterans Affairs Tennessee Valley Healthcare SystemNashvilleUnited States
| | - Timothy L Cover
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University School of MedicineNashvilleUnited States
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
- Veterans Affairs Tennessee Valley Healthcare SystemNashvilleUnited States
| | - Melanie D Ohi
- Life Sciences InstituteUniversity of MichiganAnn ArborUnited States
- Department of Cell and Developmental BiologyUniversity of Michigan School of MedicineAnn ArborUnited States
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173
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Sinha A, Li Z, Sun L, Carlow CKS. Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus. Genome Biol Evol 2019; 11:706-720. [PMID: 30715337 PMCID: PMC6414309 DOI: 10.1093/gbe/evz025] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2019] [Indexed: 12/21/2022] Open
Abstract
Wolbachia, an alpha-proteobacterium closely related to Rickettsia, is a maternally transmitted, intracellular symbiont of arthropods and nematodes. Aedes albopictus mosquitoes are naturally infected with Wolbachia strains wAlbA and wAlbB. Cell line Aa23 established from Ae. albopictus embryos retains only wAlbB and is a key model to study host–endosymbiont interactions. We have assembled the complete circular genome of wAlbB from the Aa23 cell line using long-read PacBio sequencing at 500× median coverage. The assembled circular chromosome is 1.48 megabases in size, an increase of more than 300 kb over the published draft wAlbB genome. The annotation of the genome identified 1,205 protein coding genes, 34 tRNA, 3 rRNA, 1 tmRNA, and 3 other ncRNA loci. The long reads enabled sequencing over complex repeat regions which are difficult to resolve with short-read sequencing. Thirteen percent of the genome comprised insertion sequence elements distributed throughout the genome, some of which cause pseudogenization. Prophage WO genes encoding some essential components of phage particle assembly are missing, while the remainder are found in five prophage regions/WO-like islands or scattered around the genome. Orthology analysis identified a core proteome of 535 orthogroups across all completed Wolbachia genomes. The majority of proteins could be annotated using Pfam and eggNOG analyses, including ankyrins and components of the Type IV secretion system. KEGG analysis revealed the absence of five genes in wAlbB which are present in other Wolbachia. The availability of a complete circular chromosome from wAlbB will enable further biochemical, molecular, and genetic analyses on this strain and related Wolbachia.
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Affiliation(s)
- Amit Sinha
- New England Biolabs, Ipswich, Massachusetts
| | - Zhiru Li
- New England Biolabs, Ipswich, Massachusetts
| | - Luo Sun
- New England Biolabs, Ipswich, Massachusetts
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174
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Pena RT, Blasco L, Ambroa A, González-Pedrajo B, Fernández-García L, López M, Bleriot I, Bou G, García-Contreras R, Wood TK, Tomás M. Relationship Between Quorum Sensing and Secretion Systems. Front Microbiol 2019; 10:1100. [PMID: 31231316 PMCID: PMC6567927 DOI: 10.3389/fmicb.2019.01100] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/30/2019] [Indexed: 01/15/2023] Open
Abstract
Quorum sensing (QS) is a communication mechanism between bacteria that allows specific processes to be controlled, such as biofilm formation, virulence factor expression, production of secondary metabolites and stress adaptation mechanisms such as bacterial competition systems including secretion systems (SS). These SS have an important role in bacterial communication. SS are ubiquitous; they are present in both Gram-negative and Gram-positive bacteria and in Mycobacterium sp. To date, 8 types of SS have been described (T1SS, T2SS, T3SS, T4SS, T5SS, T6SS, T7SS, and T9SS). They have global functions such as the transport of proteases, lipases, adhesins, heme-binding proteins, and amidases, and specific functions such as the synthesis of proteins in host cells, adaptation to the environment, the secretion of effectors to establish an infectious niche, transfer, absorption and release of DNA, translocation of effector proteins or DNA and autotransporter secretion. All of these functions can contribute to virulence and pathogenesis. In this review, we describe the known types of SS and discuss the ones that have been shown to be regulated by QS. Due to the large amount of information about this topic in some pathogens, we focus mainly on Pseudomonas aeruginosa and Vibrio spp.
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Affiliation(s)
- Rocio Trastoy Pena
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Lucia Blasco
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Antón Ambroa
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Bertha González-Pedrajo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Fernández-García
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Maria López
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Ines Bleriot
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - German Bou
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Thomas Keith Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
| | - Maria Tomás
- Deapartamento de Microbiología y Parasitología, Complejo Hospitalario Universitario A Coruña (CHUAC), Instituto de Investigación Biomédica (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
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175
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Classical chaperone-usher (CU) adhesive fimbriome: uropathogenic Escherichia coli (UPEC) and urinary tract infections (UTIs). Folia Microbiol (Praha) 2019; 65:45-65. [DOI: 10.1007/s12223-019-00719-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022]
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176
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Kohler V, Keller W, Grohmann E. Regulation of Gram-Positive Conjugation. Front Microbiol 2019; 10:1134. [PMID: 31191478 PMCID: PMC6540685 DOI: 10.3389/fmicb.2019.01134] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022] Open
Abstract
Type IV Secretion Systems (T4SSs) are membrane-spanning multiprotein complexes dedicated to protein secretion or conjugative DNA transport (conjugation systems) in bacteria. The prototype and best-characterized T4SS is that of the Gram-negative soil bacterium Agrobacterium tumefaciens. For Gram-positive bacteria, only conjugative T4SSs have been characterized in some biochemical, structural, and mechanistic details. These conjugation systems are predominantly encoded by self-transmissible plasmids but are also increasingly detected on integrative and conjugative elements (ICEs) and transposons. Here, we report regulatory details of conjugation systems from Enterococcus model plasmids pIP501 and pCF10, Bacillus plasmid pLS1, Clostridium plasmid pCW3, and staphylococcal plasmid pSK41. In addition, regulation of conjugative processes of ICEs (ICEBs1, ICESt1, ICESt3) by master regulators belonging to diverse repressor families will be discussed. A special focus of this review lies on the comparison of regulatory mechanisms executed by proteins belonging to the RRNPP family. These regulators share a common fold and govern several essential bacterial processes, including conjugative transfer.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, Berlin, Germany
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177
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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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178
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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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179
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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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180
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Rehman S, Li YG, Schmitt A, Lassinantti L, Christie PJ, Berntsson RPA. Enterococcal PcfF Is a Ribbon-Helix-Helix Protein That Recruits the Relaxase PcfG Through Binding and Bending of the oriT Sequence. Front Microbiol 2019; 10:958. [PMID: 31134011 PMCID: PMC6514445 DOI: 10.3389/fmicb.2019.00958] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/16/2019] [Indexed: 11/13/2022] Open
Abstract
The conjugative plasmid pCF10 from Enterococcus faecalis encodes a Type 4 Secretion System required for plasmid transfer. The accessory factor PcfF and relaxase PcfG initiate pCF10 transfer by forming the catalytically active relaxosome at the plasmid’s origin-of-transfer (oriT) sequence. Here, we report the crystal structure of the homo-dimeric PcfF, composed of an N-terminal DNA binding Ribbon-Helix-Helix (RHH) domain and a C-terminal stalk domain. We identified key residues in the RHH domain that are responsible for binding pCF10’s oriT sequence in vitro, and further showed that PcfF bends the DNA upon oriT binding. By mutational analysis and pull-down experiments, we identified residues in the stalk domain that contribute to interaction with PcfG. PcfF variant proteins defective in oriT or PcfG binding attenuated plasmid transfer in vivo, but also suggested that intrinsic or extrinsic factors might modulate relaxosome assembly. We propose that PcfF initiates relaxosome assembly by binding oriT and inducing DNA bending, which serves to recruit PcfG as well as extrinsic factors necessary for optimal plasmid processing and engagement with the pCF10 transfer machine.
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Affiliation(s)
- Saima Rehman
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, United States
| | - Andreas Schmitt
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Lena Lassinantti
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, United States
| | - 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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181
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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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182
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Christie PJ, Gomez Valero L, Buchrieser C. Biological Diversity and Evolution of Type IV Secretion Systems. Curr Top Microbiol Immunol 2019; 413:1-30. [PMID: 29536353 PMCID: PMC5912172 DOI: 10.1007/978-3-319-75241-9_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bacterial type IV secretion systems (T4SSs) are a highly functionally and structurally diverse superfamily of secretion systems found in many species of Gram-negative and -positive bacteria. Collectively, the T4SSs can translocate DNA and monomeric and multimeric protein substrates to a variety of bacterial and eukaryotic cell types. Detailed phylogenomics analyses have established that the T4SSs evolved from ancient conjugation machines whose original functions were to disseminate mobile DNA elements within and between bacterial species. How members of the T4SS superfamily evolved to recognize and translocate specific substrate repertoires to prokaryotic or eukaryotic target cells is a fascinating question from evolutionary, biological, and structural perspectives. In this chapter, we will summarize recent findings that have shaped our current view of the biological diversity of the T4SSs. We focus mainly on two subtypes, designated as the types IVA (T4ASS) and IVB (T4BSS) systems that respectively are represented by the paradigmatic Agrobacterium tumefaciens VirB/VirD4 and Legionella pneumophila Dot/Icm T4SSs. We present current information about the composition and architectures of these representative systems. We also describe how these and a few related T4ASS and T4BSS members evolved as specialized nanomachines through acquisition of novel domains or subunits, a process that ultimately generated extensive genetic and structural mosaicism among this secretion superfamily. Finally, we present new phylogenomics information establishing that the T4BSSs are much more broadly distributed than initially envisioned.
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Affiliation(s)
- Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA.
| | - Laura Gomez Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, 75724, Paris, France
- CNRS, UMR 3525, 75724, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, 75724, Paris, France
- CNRS, UMR 3525, 75724, Paris, France
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183
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Role and Function of the Type IV Secretion System in Anaplasma and Ehrlichia Species. Curr Top Microbiol Immunol 2019; 413:297-321. [PMID: 29536364 DOI: 10.1007/978-3-319-75241-9_12] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The obligatory intracellular pathogens Anaplasma phagocytophilum and Ehrlichia chaffeensis proliferate within membrane-bound vacuoles of human leukocytes and cause potentially fatal emerging infectious diseases. Despite the reductive genome evolution in this group of bacteria, genes encoding the type IV secretion system (T4SS), which is homologous to the VirB/VirD4 system of the plant pathogen Agrobacterium tumefaciens, have been expanded and are highly expressed in A. phagocytophilum and E. chaffeensis in human cells. Of six T4SS effector proteins identified in them, roles and functions have been described so far only for ankyrin repeat domain-containing protein A (AnkA), Anaplasma translocated substrate 1 (Ats-1), and Ehrlichia translocated factor 1 (Etf-1, ECH0825). These effectors are abundantly produced and secreted into the host cytoplasm during infection, but not toxic to host cells. They contain eukaryotic protein motifs or organelle localization signals and have distinct subcellular localization, target to specific host cell molecules to promote infection. Ats-1 and Etf-1 are orthologous proteins, subvert two important innate immune mechanisms against intracellular infection, cellular apoptosis and autophagy, and manipulate autophagy to gain nutrients from host cells. Although Ats-1 and Etf-1 have similar functions and roles in obligatory intracellular infection, they are specifically adapted to the distinct membrane-bound intracellular niche of A. phagocytophilum and E. chaffeensis, respectively. Ectopic expression of these effectors enhances respective bacterial infection, whereas intracellular delivery of antibodies against these effectors or targeted knockdown of the effector with antisense peptide nucleic acid significantly impairs bacterial infection. Thus, both T4SSs have evolved as important survival and nutritional virulence mechanism in these obligatory intracellular bacteria. Future studies on the functions of Anaplasma and Ehrlichia T4SS effector molecules and signaling pathways will undoubtedly advance our understanding of the complex interplay between obligatory intracellular pathogens and their hosts. Such data can be applied toward the treatment and control of anaplasmosis and ehrlichiosis.
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184
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Callaghan MM, Heilers JH, van der Does C, Dillard JP. Secretion of Chromosomal DNA by the Neisseria gonorrhoeae Type IV Secretion System. Curr Top Microbiol Immunol 2019; 413:323-345. [PMID: 29536365 PMCID: PMC5935271 DOI: 10.1007/978-3-319-75241-9_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Approximately 80% of Neisseria gonorrhoeae and 17.5% of Neisseria meningitidis clinical isolates carry a ~59 kb genomic island known as the gonococcal genetic island (GGI). About half of the GGI consists of genes encoding a type IV secretion system (T4SS), and most of these genes are clustered in a ~28 kb region at one end of the GGI. Two additional genes (parA and parB) are found at the other end of the island. The remainder of the GGI consists mostly of hypothetical proteins, with several being identified as DNA-binding or DNA-processing proteins. The T4SS genes show similarity to those of the F-plasmid family of conjugation systems, with similarity in gene order and a low but significant level of sequence identity for the encoded proteins. However, several GGI-encoded proteins are unique from the F-plasmid system, such as AtlA, Yag, and TraA. Interestingly, the gonococcal T4SS does not act as a conjugation system. Instead, this T4SS secretes ssDNA into the extracellular milieu, where it can serve to transform highly competent Neisseria species, thereby increasing the transfer of genetic information. Although many of the T4SS proteins are expressed at low levels, this system has been implicated in several cellular processes. The secreted ssDNA is involved in the initial stages of biofilm formation, and the presence of the T4SS enables TonB-independent intracellular survival of N. gonorrhoeae strains during infection of cervical cells. Other GGI-like T4SSs have been identified in several other α-, β-, and γ-proteobacteria, but the function of these GGI-like T4SSs is unknown. Remarkably, the presence of the GGI is related to resistance to several antibiotics. Here, we describe our current knowledge about the GGI and its unique ssDNA-secreting T4SS.
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Affiliation(s)
- Melanie M Callaghan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
| | - Jan-Hendrik Heilers
- Institut für Biologie II-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Chris van der Does
- Institut für Biologie II-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA.
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185
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Hilbi H, Nagai H, Kubori T, Roy CR. Subversion of Host Membrane Dynamics by the Legionella Dot/Icm Type IV Secretion System. Curr Top Microbiol Immunol 2019. [PMID: 29536361 DOI: 10.1007/978-3-319-75241-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Legionella species are Gram-negative ubiquitous environmental bacteria, which thrive in biofilms and parasitize protozoa. Employing an evolutionarily conserved mechanism, the opportunistic pathogens also replicate intracellularly in mammalian macrophages. This feature is a prerequisite for the pathogenicity of Legionella pneumophila, which causes the vast majority of clinical cases of a severe pneumonia, termed "Legionnaires' disease." In macrophages as well as in amoeba, L. pneumophila grows in a distinct membrane-bound compartment, the Legionella-containing vacuole (LCV). Formation of this replication-permissive pathogen compartment requires the bacterial Dot/Icm type IV secretion system (T4SS). Through the T4SS as many as 300 different "effector" proteins are injected into host cells, where they presumably subvert pivotal processes. Less than 40 Dot/Icm substrates have been characterized in detail to date, a number of which show unprecedented biological activities. Some of these effector proteins target host cell small GTPases, phosphoinositide lipids, the chelator phytate, the ubiquitination machinery, the retromer complex, the actin cytoskeleton, or the autophagy pathway. A recently discovered class of L. pneumophila effectors modulates the activity of other effectors and is termed "metaeffectors." Here, we summarize recent insight into the cellular functions and biochemical activities of L. pneumophila effectors and metaeffectors targeting the host's endocytic, retrograde, or autophagic pathways.
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Affiliation(s)
- Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zurich, Switzerland.
| | - Hiroki Nagai
- School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1194, Japan.
| | - Tomoko Kubori
- School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1194, Japan.
| | - Craig R Roy
- Department of Microbial Pathogenesis, Yale University, 295 Congress Avenue, BCMM 354B, New Haven, CT, 06536-0812, USA.
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186
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Boudaher E, Shaffer CL. Inhibiting bacterial secretion systems in the fight against antibiotic resistance. MEDCHEMCOMM 2019; 10:682-692. [PMID: 31741728 PMCID: PMC6677025 DOI: 10.1039/c9md00076c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/22/2019] [Indexed: 12/11/2022]
Abstract
Antimicrobial resistance is a mounting global health crisis that threatens a resurgence of life-threatening bacterial infections. Despite intensive drug discovery efforts, the rate of antimicrobial resistance outpaces the discovery of new antibiotic agents. One of the major mechanisms driving the rapid propagation of antibiotic resistance is bacterial conjugation mediated by the versatile type IV secretion system (T4SS). The search for therapeutic compounds that prevent the spread of antibiotic resistance via T4SS-dependent mechanisms has identified several promising molecular scaffolds that disrupt resistance determinant dissemination. In this brief review, we highlight the progress and potential of conjugation inhibitors and anti-virulence compounds that target diverse T4SS machineries. These studies provide a solid foundation for the future development of potent, dual-purpose molecular scaffolds that can be used as biochemical tools to probe type IV secretion mechanisms and target bacterial conjugation in clinical settings to prevent the dissemination of antibiotic resistance throughout microbial populations.
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Affiliation(s)
- Elizabeth Boudaher
- University of Kentucky , Department of Veterinary Science , Gluck Equine Research Center , 1400 Nicholasville Road , Lexington , KY , USA . ; Tel: +1 (859) 218 1168
| | - Carrie L Shaffer
- University of Kentucky , Department of Veterinary Science , Gluck Equine Research Center , 1400 Nicholasville Road , Lexington , KY , USA . ; Tel: +1 (859) 218 1168
- University of Kentucky , Department of Microbiology, Immunology, and Molecular Genetics , 800 Rose Street , Lexington , KY , USA
- University of Kentucky , Department of Pharmaceutical Sciences , 789 South Limestone Street , Lexington , KY , USA
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187
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Dehio C, Tsolis RM. Type IV Effector Secretion and Subversion of Host Functions by Bartonella and Brucella Species. Curr Top Microbiol Immunol 2019. [PMID: 29536363 DOI: 10.1007/978-3-319-75241-9_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
Abstract
Bartonella and Brucella species comprise closely related genera of the order Rhizobiales within the class α-proteobacteria. Both groups of bacteria are mammalian pathogens with a facultative intracellular lifestyle and are capable of causing chronic infections, but members of each genus have evolved broadly different infection and transmission strategies. While Brucella spp. transmit in general via the reproductive tract in their natural hosts, the Bartonella spp. have evolved to transmit via arthropod vectors. However, a shared feature of both groups of pathogens is their reliance on type IV secretion systems (T4SSs) to interact with cells in their mammalian hosts. The genomes of Bartonella spp. encode three types of T4SS, Trw, Vbh/TraG, and VirB/VirD4, whereas those of Brucella spp. uniformly contain a single T4SS of the VirB type. The VirB systems of Bartonella and Brucella are associated with distinct groups of effector proteins that collectively mediate interactions with host cells. This chapter discusses recent findings on the role of T4SS in the biology of Bartonella spp. and Brucella spp. with emphasis on effector repertoires, on recent advances in our understanding of their evolution, how individual effectors function at the molecular level, and on the consequences of these interactions for cellular and immune responses in the host.
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Affiliation(s)
| | - Renée M Tsolis
- Medical Microbiology and Immunology, University of California at Davis, Davis, CA, 95616, USA.
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188
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Stingl K, Koraimann G. Prokaryotic Information Games: How and When to Take up and Secrete DNA. Curr Top Microbiol Immunol 2019. [PMID: 29536355 DOI: 10.1007/978-3-319-75241-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Besides transduction via bacteriophages natural transformation and bacterial conjugation are the most important mechanisms driving bacterial evolution and horizontal gene spread. Conjugation systems have evolved in eubacteria and archaea. In Gram-positive and Gram-negative bacteria, cell-to-cell DNA transport is typically facilitated by a type IV secretion system (T4SS). T4SSs also mediate uptake of free DNA in Helicobacter pylori, while most transformable bacteria use a type II secretion/type IV pilus system. In this chapter, we focus on how and when bacteria "decide" that such a DNA transport apparatus is to be expressed and assembled in a cell that becomes competent. Development of DNA uptake competence and DNA transfer competence is driven by a variety of stimuli and often involves intricate regulatory networks leading to dramatic changes in gene expression patterns and bacterial physiology. In both cases, genetically homogeneous populations generate a distinct subpopulation that is competent for DNA uptake or DNA transfer or might uniformly switch into competent state. Phenotypic conversion from one state to the other can rely on bistable genetic networks that are activated stochastically with the integration of external signaling molecules. In addition, we discuss principles of DNA uptake processes in naturally transformable bacteria and intend to understand the exceptional use of a T4SS for DNA import in the gastric pathogen H. pylori. Realizing the events that trigger developmental transformation into competence within a bacterial population will eventually help to create novel and effective therapies against the transmission of antibiotic resistances among pathogens.
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Affiliation(s)
- Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany.
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
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189
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Abstract
Type IV secretion systems (T4SSs) are nanomachines that Gram-negative, Gram-positive bacteria, and some archaea use to transport macromolecules across their membranes into bacterial or eukaryotic host targets or into the extracellular milieu. They are the most versatile secretion systems, being able to deliver both proteins and nucleoprotein complexes into targeted cells. By mediating conjugation and/or competence, T4SSs play important roles in determining bacterial genome plasticity and diversity; they also play a pivotal role in the spread of antibiotic resistance within bacterial populations. T4SSs are also used by human pathogens such as Legionella pneumophila, Bordetella pertussis, Brucella sp., or Helicobacter pylori to sustain infection. Since they are essential virulence factors for these important pathogens, T4SSs might represent attractive targets for vaccines and therapeutics. The best-characterized conjugative T4SSs of Gram-negative bacteria are composed of twelve components that are conserved across many T4SSs. In this chapter, we will review our current structural knowledge on the T4SSs by describing the structures of the individual components and how they assemble into large macromolecular assemblies. With the combined efforts of X-ray crystallography, nuclear magnetic resonance (NMR), and more recently electron microscopy, structural biology of the T4SS has made spectacular progress during the past fifteen years and has unraveled the properties of unique proteins and complexes that assemble dynamically in a highly sophisticated manner.
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190
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Arya T, Oudouhou F, Casu B, Bessette B, Sygusch J, Baron C. Fragment-based screening identifies inhibitors of ATPase activity and of hexamer formation of Cagα from the Helicobacter pylori type IV secretion system. Sci Rep 2019; 9:6474. [PMID: 31019200 PMCID: PMC6482174 DOI: 10.1038/s41598-019-42876-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/05/2019] [Indexed: 01/16/2023] Open
Abstract
Type IV secretion systems are multiprotein complexes that mediate the translocation of macromolecules across the bacterial cell envelope. In Helicobacter pylori a type IV secretion system encoded by the cag pathogenicity island encodes 27 proteins and most are essential for virulence. We here present the identification and characterization of inhibitors of Cagα, a hexameric ATPase and member of the family of VirB11-like proteins that is essential for translocation of the CagA cytotoxin into mammalian cells. We conducted fragment-based screening using a differential scanning fluorimetry assay and identified 16 molecules that stabilize the protein suggesting that they bind Cagα. Several molecules affect binding of ADP and four of them inhibit the ATPase activity. Analysis of enzyme kinetics suggests that their mode of action is non-competitive, suggesting that they do not bind to the active site. Cross-linking suggests that the active molecules change protein conformation and gel filtration and transmission electron microscopy show that molecule 1G2 dissociates the Cagα hexamer. Addition of the molecule 1G2 inhibits the induction of interleukin-8 production in gastric cancer cells after co-incubation with H. pylori suggesting that it inhibits Cagα in vivo. Our results reveal a novel mechanism for the inhibition of the ATPase activity of VirB11-like proteins.
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Affiliation(s)
- Tarun Arya
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Flore Oudouhou
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Bastien Casu
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Benoit Bessette
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Jurgen Sygusch
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Christian Baron
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec, Canada.
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191
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Zhang Z, Huang Q, Tao X, Song G, Zheng P, Li H, Sun H, Xia W. The unique trimeric assembly of the virulence factor HtrA from Helicobacter pylori occurs via N-terminal domain swapping. J Biol Chem 2019; 294:7990-8000. [PMID: 30936204 DOI: 10.1074/jbc.ra119.007387] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the molecular mechanisms of specific bacterial virulence factors can significantly contribute to antibacterial drug discovery. Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects almost half of the world's population, leading to gastric disorders and even gastric cancer. H. pylori expresses a series of virulence factors in the host, among which high-temperature requirement A (HpHtrA) is a newly identified serine protease secreted by H. pylori. HpHtrA cleaves the extracellular domain of the epithelial cell surface adhesion protein E-cadherin and disrupts gastric epithelial cell junctions, allowing H. pylori to access the intercellular space. Here we report the first crystal structure of HpHtrA at 3.0 Å resolution. The structure revealed a new type of HtrA protease trimer stabilized by unique N-terminal domain swapping distinct from other known HtrA homologs. We further observed that truncation of the N terminus completely abrogates HpHtrA trimer formation as well as protease activity. In the presence of unfolded substrate, HpHtrA assembled into cage-like 12-mers or 24-mers. Combining crystallographic, biochemical, and mutagenic data, we propose a mechanistic model of how HpHtrA recognizes and cleaves the well-folded E-cadherin substrate. Our study provides a fundamental basis for the development of anti-H. pylori agents by using a previously uncharacterized HtrA protease as a target.
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Affiliation(s)
- Zhemin Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qi Huang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xuan Tao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guobing Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hongyan Li
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Hongzhe Sun
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China.
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192
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Zhu J, He M, Xu W, Li Y, Huang R, Wu S, Niu H. Development of TEM-1 β-lactamase based protein translocation assay for identification of Anaplasma phagocytophilum type IV secretion system effector proteins. Sci Rep 2019; 9:4235. [PMID: 30862835 PMCID: PMC6414681 DOI: 10.1038/s41598-019-40682-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 02/20/2019] [Indexed: 11/24/2022] Open
Abstract
Anaplasma phagocytophilum, the aetiologic agent of human granulocytic anaplasmosis (HGA) is an obligate intracellular Gram-negative bacterium with the genome size of 1.47 megabases. The intracellular life style and small size of genome suggest that A. phagocytophilum has to modulate a multitude of host cell physiological processes to facilitate its replication. One strategy employed by A. phagocytophilum is through its type IV secretion system (T4SS), which translocates bacterial effectors into target cells to disrupt normal cellular activities. In this study we developed a TEM-1 β-lactamase based protein translocation assay and applied this assay for identification of A. phagocytophilum T4SS effectors. An A. phagocytophilum hypothetical protein, APH0215 is identified as a T4SS effector protein and found interacting with trans-Golgi network in transfected cells. Hereby, this protein translocation assay developed in this study will facilitate the identification of A. phagocytophilum T4SS effectors and elucidation of HGA pathogenesis.
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Affiliation(s)
- Jiafeng Zhu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Meiling He
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Wenting Xu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Yuanyuan Li
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Rui Huang
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Shuyan Wu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Hua Niu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China.
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193
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Wagner A, Dehio C. Role of distinct type-IV-secretion systems and secreted effector sets in host adaptation by pathogenic Bartonella species. Cell Microbiol 2019; 21:e13004. [PMID: 30644157 PMCID: PMC6519360 DOI: 10.1111/cmi.13004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/17/2018] [Accepted: 01/06/2019] [Indexed: 12/12/2022]
Abstract
The α‐proteobacterial genus Bartonella comprises a large number of facultative intracellular pathogens that share a common lifestyle hallmarked by hemotrophic infection and arthropod transmission. Speciation in the four deep‐branching lineages (L1–L4) occurred by host adaptation facilitating the establishment of long lasting bacteraemia in specific mammalian reservoir host(s). Two distinct type‐IV‐secretion systems (T4SSs) acquired horizontally by different Bartonella lineages mediate essential host interactions during infection and represent key innovations for host adaptation. The Trw‐T4SS confined to the species‐rich L4 mediates host‐specific erythrocyte infection and likely has functionally replaced flagella as ancestral virulence factors implicated in erythrocyte colonisation by bartonellae of the other lineages. The VirB/VirD4‐T4SS translocates Bartonella effector proteins (Bep) into various host cell types to modulate diverse cellular and innate immune functions involved in systemic spreading of bacteria following intradermal inoculation. Independent acquisition of the virB/virD4/bep locus by L1, L3, and L4 was likely driven by arthropod vectors associated with intradermal inoculation of bacteria rather than facilitating direct access to blood. Subsequently, adaptation to colonise specific niches in the new host has shaped the evolution of complex species‐specific Bep repertoires. This diversification of the virulence factor repertoire of Bartonella spp. represents a remarkable example for parallel evolution of host adaptation.
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Affiliation(s)
- Alexander Wagner
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
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194
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Abstract
Many bacteria have evolved specialized nanomachines with the remarkable ability to inject multiple bacterially encoded effector proteins into eukaryotic or prokaryotic cells. Known as type III, type IV, and type VI secretion systems, these machines play a central role in the pathogenic or symbiotic interactions between multiple bacteria and their eukaryotic hosts, or in the establishment of bacterial communities in a diversity of environments. Here we focus on recent progress elucidating the structure and assembly pathways of these machines. As many of the interactions shaped by these machines are of medical importance, they provide an opportunity to develop novel therapeutic approaches to combat important human diseases.
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Affiliation(s)
- Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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195
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Hayek I, Berens C, Lührmann A. Modulation of host cell metabolism by T4SS-encoding intracellular pathogens. Curr Opin Microbiol 2019; 47:59-65. [PMID: 30640035 DOI: 10.1016/j.mib.2018.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022]
Abstract
Intracellular bacterial pathogens intimately interact with the infected host cell to prevent elimination and to ensure survival. One group of intracellular pathogens, including Coxiella burnetii, Legionella pneumophila, Brucella spp., Anaplasma phagocytophilum, and Ehrlichia chaffeensis, utilizes a type IV secretion system (T4SS) that injects effectors to modulate host cell signalling, vesicular trafficking, autophagy, cell death and transcription to ensure survival [1]. So far, little emphasis has been directed towards understanding how these bacteria manipulate host cell metabolism. This manipulation is not only important for gaining access to nutrients, but also for regulating specific virulence programs [2,3]. Here, we will summarize recent progress made in characterizing the manipulation of host cell metabolism by C. burnetii and other intracellular pathogens utilizing a T4SS.
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Affiliation(s)
- Inaya Hayek
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Wasserturmstraße 3/5, D-91054 Erlangen, Germany
| | - Christian Berens
- Institut für molekulare Pathogenese, Friedrich-Loeffler-Institut, Naumburger Str. 96a, D-07743 Jena, Germany
| | - Anja Lührmann
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Wasserturmstraße 3/5, D-91054 Erlangen, Germany.
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196
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Waksman G. From conjugation to T4S systems in Gram-negative bacteria: a mechanistic biology perspective. EMBO Rep 2019; 20:embr.201847012. [PMID: 30602585 PMCID: PMC6362355 DOI: 10.15252/embr.201847012] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 12/19/2022] Open
Abstract
Conjugation is the process by which bacteria exchange genetic materials in a unidirectional manner from a donor cell to a recipient cell. The discovery of conjugation signalled the dawn of genetics and molecular biology. In Gram-negative bacteria, the process of conjugation is mediated by a large membrane-embedded machinery termed "conjugative type IV secretion (T4S) system", a large injection nanomachine, which together with a DNA-processing machinery termed "the relaxosome" and a large extracellular tube termed "pilus" orchestrates directional DNA transfer. Here, the focus is on past and latest research in the field of conjugation and T4S systems in Gram-negative bacteria, with an emphasis on the various questions and debates that permeate the field from a mechanistic perspective.
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Affiliation(s)
- Gabriel Waksman
- Institute of Structural and Molecular Biology, UCL and Birkbeck, London, UK
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197
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Abstract
To interact with the external environments, bacteria often display long proteinaceous appendages on their cell surface, called pili or fimbriae. These non-flagellar thread-like structures are polymers composed of covalently or non-covalently interacting repeated pilin subunits. Distinct pilus classes can be identified on basis of their assembly pathways, including chaperone-usher pili, type V pili, type IV pili, curli and fap fibers, conjugative and type IV secretion pili, as well as sortase-mediated pili. Pili play versatile roles in bacterial physiology, and can be involved in adhesion and host cell invasion, DNA and protein secretion and uptake, biofilm formation, cell motility and more. Recent advances in structure determination of components involved in the various pilus systems has enabled a better molecular understanding of their mechanisms of assembly and function. In this chapter we describe the diversity in structure, biogenesis and function of the different pilus systems found in Gram-positive and Gram-negative bacteria, and review their potential as anti-microbial targets.
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Affiliation(s)
- Magdalena Lukaszczyk
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Brajabandhu Pradhan
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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198
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Javed S, Skoog EC, Solnick JV. Impact of Helicobacter pylori Virulence Factors on the Host Immune Response and Gastric Pathology. Curr Top Microbiol Immunol 2019; 421:21-52. [PMID: 31123884 DOI: 10.1007/978-3-030-15138-6_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Helicobacter pylori chronically infects nearly half the world's population, yet most of those infected remain asymptomatic throughout their lifetime. The outcome of infection-peptic ulcer disease or gastric cancer versus asymptomatic colonization-is a product of host genetics, environmental influences, and differences in bacterial virulence factors. Here, we review the current understanding of the cag pathogenicity island (cagPAI), the vacuolating cytotoxin (VacA), and a large family of outer membrane proteins (OMPs), which are among the best understood H. pylori virulence determinants that contribute to disease. Each of these virulence factors is characterized by allelic and phenotypic diversity that is apparent within and across individuals, as well as over time, and modulates inflammation. From the bacterial perspective, inflammation is probably a necessary evil because it promotes nutrient acquisition, but at the cost of reduction in bacterial load and therefore decreases the chance of transmission to a new host. The general picture that emerges is one of a chronic bacterial infection that is dependent on both inducing and carefully regulating the host inflammatory response. A better understanding of these regulatory mechanisms may have implications for the control of chronic inflammatory diseases that are increasingly common causes of human morbidity and mortality.
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Affiliation(s)
- Sundus Javed
- Department of Medicine, Department of Microbiology & Immunology, Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616, USA.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Emma C Skoog
- Department of Medicine, Department of Microbiology & Immunology, Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616, USA
| | - Jay V Solnick
- Department of Medicine, Department of Microbiology & Immunology, Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616, USA. .,Center for Comparative Medicine, University of California, Davis, Davis, CA, 95616, USA.
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199
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Bravo A, Ruiz-Cruz S, Alkorta I, Espinosa M. When Humans Met Superbugs: Strategies to Tackle Bacterial Resistances to Antibiotics. Biomol Concepts 2018; 9:216-226. [PMID: 30811343 DOI: 10.1515/bmc-2018-0021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/17/2018] [Indexed: 12/25/2022] Open
Abstract
Bacterial resistance to antibiotics poses enormous health and economic burdens to our society, and it is of the essence to explore old and new ways to deal with these problems. Here we review the current status of multi-resistance genes and how they spread among bacteria. We discuss strategies to deal with resistant bacteria, namely the search for new targets and the use of inhibitors of protein-protein interactions, fragment-based methods, or modified antisense RNAs. Finally, we discuss integrated approaches that consider bacterial populations and their niches, as well as the role of global regulators that activate and/or repress the expression of multiple genes in fluctuating environments and, therefore, enable resistant bacteria to colonize new niches. Understanding how the global regulatory circuits work is, probably, the best way to tackle bacterial resistance.
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Affiliation(s)
- Alicia Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Sofia Ruiz-Cruz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Itziar Alkorta
- Instituto BIOFISIKA (CSIC, UPV/EHU), Departamento de Bioquímica y Biología Molecular, Universidad del Pais Vasco, P.O. Box 644, 48080 Bilbao, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
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200
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Mu DS, Liang QY, Wang XM, Lu DC, Shi MJ, Chen GJ, Du ZJ. Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. MICROBIOME 2018; 6:230. [PMID: 30587241 PMCID: PMC6307301 DOI: 10.1186/s40168-018-0613-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/04/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be "culturable" may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state. RESULTS We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the "uncultured" not only through enriching the abundance of "uncultured," but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures. CONCLUSIONS Considering that cultivation techniques must evolve further-from axenic to mixed cultures-for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Qi-Yun Liang
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Xiao-Man Wang
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - De-Chen Lu
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Ming-Jing Shi
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China.
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