51
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Russo DA, Zedler JAZ. Genomic insights into cyanobacterial protein translocation systems. Biol Chem 2020; 402:39-54. [PMID: 33544489 DOI: 10.1515/hsz-2020-0247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
Cyanobacteria are ubiquitous oxygenic photosynthetic bacteria with a versatile metabolism that is highly dependent on effective protein targeting. Protein sorting in diderm bacteria is not trivial and, in cyanobacteria, even less so due to the presence of a complex membrane system: the outer membrane, the plasma membrane and the thylakoid membrane. In cyanobacteria, protein import into the thylakoids is essential for photosynthesis, export to the periplasm fulfills a multifunctional role in maintaining cell homeostasis, and secretion mediates motility, DNA uptake and environmental interactions. Intriguingly, only one set of genes for the general secretory and the twin-arginine translocation pathways seem to be present. However, these systems have to operate in both plasma and thylakoid membranes. This raises the question of how substrates are recognized and targeted to their correct, final destination. Additional complexities arise when a protein has to be secreted across the outer membrane, where very little is known regarding the mechanisms involved. Given their ecological importance and biotechnological interest, a better understanding of protein targeting in cyanobacteria is of great value. This review will provide insights into the known knowns of protein targeting, propose hypotheses based on available genomic sequences and discuss future directions.
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Affiliation(s)
- David A Russo
- Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Julie A Z Zedler
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Dornburgerstr. 159, D-07743 Jena, Germany
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52
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Liu S, Wang J, Zhang J, Wang T, Zhou Y, Lv Q, Hu N, Shen X, Deng X. Tectorigenin reduces type IV pilus-dependent cell adherence in Clostridium perfringens. FEMS Microbiol Lett 2020; 366:5498297. [PMID: 31125043 DOI: 10.1093/femsle/fnz112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridium perfringens is an anaerobic, Gram-positive bacterium that causes a range of diseases in humans and animals around the globe. The type IV pilus (TFP) system plays a key role in the colonization and invasion of host cells, biofilm formation and gliding motility, which is vital for C. perfringens infection. Therefore, targeting TFP function may be a promising strategy for the treatment of C. perfringens infection. Here, we investigated the potential inhibitory effects of tectorigenin (TE), an isoflavone extracted from the rhizome of the Chinese herb Belamcanda chinensis (L.) DC, on gliding motility, biofilm formation, adherence to cells and antibacterial activity of C. perfringens. Tectorigenin significantly inhibited gliding motility, biofilm formation and adherence to Caco-2 cells without observable antibacterial activity against C. perfringens. In addition, we also demonstrated that the inhibitory effect of TE on TFP function appears to be partially achieved by the suppression of TFP-associated genes. These findings demonstrate that TE may have the potential to be developed as a new anti-virulence drug for C. perfringens infection, particularly for the targeting of TFP.
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Affiliation(s)
- Shui Liu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, China
| | - Jianfeng Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, China
| | - Jian Zhang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Tingting Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Yonglin Zhou
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Qianghua Lv
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Naiyu Hu
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Xue Shen
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Xuming Deng
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, China
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53
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Baidya AK, Rosenshine I, Ben-Yehuda S. Donor-delivered cell wall hydrolases facilitate nanotube penetration into recipient bacteria. Nat Commun 2020; 11:1938. [PMID: 32321911 PMCID: PMC7176660 DOI: 10.1038/s41467-020-15605-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 03/16/2020] [Indexed: 11/09/2022] Open
Abstract
Bacteria can produce membranous nanotubes that mediate contact-dependent exchange of molecules among bacterial cells. However, it is unclear how nanotubes cross the cell wall to emerge from the donor or to penetrate into the recipient cell. Here, we report that Bacillus subtilis utilizes cell wall remodeling enzymes, the LytC amidase and its enhancer LytB, for efficient nanotube extrusion and penetration. Nanotube production is reduced in a lytBC mutant, and the few nanotubes formed appear deficient in penetrating into target cells. Donor-derived LytB molecules localize along nanotubes and on the surface of nanotube-connected neighbouring cells, primarily at sites of nanotube penetration. Furthermore, LytB from donor B. subtilis can activate LytC of recipient bacteria from diverse species, facilitating cell wall hydrolysis to establish nanotube connection. Our data provide a mechanistic view of how intercellular connecting devices can be formed among neighbouring bacteria. Bacteria can produce membranous nanotubes that mediate contact-dependent exchange of molecules between bacterial cells. Here, Baidya et al. show that cell-wall remodelling enzymes from Bacillus subtilis are required for efficient nanotube extrusion and penetration, and can be delivered to other bacterial species via nanotubes.
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Affiliation(s)
- Amit K Baidya
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, POB 12272, 91120, Jerusalem, Israel
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, POB 12272, 91120, Jerusalem, Israel
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, POB 12272, 91120, Jerusalem, Israel.
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54
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Caldicellulosiruptor bescii Adheres to Polysaccharides via a Type IV Pilin-Dependent Mechanism. Appl Environ Microbiol 2020; 86:AEM.00200-20. [PMID: 32086304 DOI: 10.1128/aem.00200-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
Biological hydrolysis of cellulose above 70°C involves microorganisms that secrete free enzymes and deploy separate protein systems to adhere to their substrate. Strongly cellulolytic Caldicellulosiruptor bescii is one such extreme thermophile, which deploys modular, multifunctional carbohydrate-acting enzymes to deconstruct plant biomass. Additionally, C. bescii also encodes noncatalytic carbohydrate binding proteins, which likely evolved as a mechanism to compete against other heterotrophs in carbon-limited biotopes that these bacteria inhabit. Analysis of the Caldicellulosiruptor pangenome identified a type IV pilus (T4P) locus encoded upstream of the tāpirins, that is encoded by all Caldicellulosiruptor species. In this study, we sought to determine if the C. bescii T4P plays a role in attachment to plant polysaccharides. The major C. bescii pilin (CbPilA) was identified by the presence of pilin-like protein domains, paired with transcriptomics and proteomics data. Using immuno-dot blots, we determined that the plant polysaccharide xylan induced production of CbPilA 10- to 14-fold higher than glucomannan or xylose. Furthermore, we are able to demonstrate that recombinant CbPilA directly interacts with xylan and cellulose at elevated temperatures. Localization of CbPilA at the cell surface was confirmed by immunofluorescence microscopy. Lastly, a direct role for CbPilA in cell adhesion was demonstrated using recombinant CbPilA or anti-CbPilA antibodies to reduce C. bescii cell adhesion to xylan and crystalline cellulose up to 4.5- and 2-fold, respectively. Based on these observations, we propose that CbPilA and, by extension, the T4P play a role in Caldicellulosiruptor cell attachment to plant biomass.IMPORTANCE Most microorganisms are capable of attaching to surfaces in order to persist in their environment. Type IV (T4) pili produced by certain mesophilic Firmicutes promote adherence; however, a role for T4 pili encoded by thermophilic members of this phylum has yet to be demonstrated. Prior comparative genomics analyses identified a T4 pilus locus possessed by an extremely thermophilic genus within the Firmicutes Here, we demonstrate that attachment to plant biomass-related carbohydrates by strongly cellulolytic Caldicellulosiruptor bescii is mediated by T4 pilins. Surprisingly, xylan but not cellulose induced expression of the major T4 pilin. Regardless, the C. bescii T4 pilin interacts with both polysaccharides at high temperatures and is located to the cell surface, where it is directly involved in C. bescii attachment. Adherence to polysaccharides is likely key to survival in environments where carbon sources are limiting, allowing C. bescii to compete against other plant-degrading microorganisms.
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55
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Floyd KA, Lee CK, Xian W, Nametalla M, Valentine A, Crair B, Zhu S, Hughes HQ, Chlebek JL, Wu DC, Hwan Park J, Farhat AM, Lomba CJ, Ellison CK, Brun YV, Campos-Gomez J, Dalia AB, Liu J, Biais N, Wong GCL, Yildiz FH. c-di-GMP modulates type IV MSHA pilus retraction and surface attachment in Vibrio cholerae. Nat Commun 2020; 11:1549. [PMID: 32214098 PMCID: PMC7096442 DOI: 10.1038/s41467-020-15331-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/02/2020] [Indexed: 11/21/2022] Open
Abstract
Biofilm formation by Vibrio cholerae facilitates environmental persistence, and hyperinfectivity within the host. Biofilm formation is regulated by 3',5'-cyclic diguanylate (c-di-GMP) and requires production of the type IV mannose-sensitive hemagglutinin (MSHA) pilus. Here, we show that the MSHA pilus is a dynamic extendable and retractable system, and its activity is directly controlled by c-di-GMP. The interaction between c-di-GMP and the ATPase MshE promotes pilus extension, whereas low levels of c-di-GMP correlate with enhanced retraction. Loss of retraction facilitated by the ATPase PilT increases near-surface roaming motility, and impairs initial surface attachment. However, prolonged retraction upon surface attachment results in reduced MSHA-mediated surface anchoring and increased levels of detachment. Our results indicate that c-di-GMP directly controls MshE activity, thus regulating MSHA pilus extension and retraction dynamics, and modulating V. cholerae surface attachment and colonization.
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Affiliation(s)
- Kyle A Floyd
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA
| | - Calvin K Lee
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Wujing Xian
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Mahmoud Nametalla
- Department of Biology, Brooklyn College, Room 307NE, 2900 Bedford Ave., Brooklyn, NY, 11210, USA
- CUNY Graduate Center, 365 5th Ave., New York, NY, 10016, USA
| | - Aneesa Valentine
- Department of Biology, Brooklyn College, Room 307NE, 2900 Bedford Ave., Brooklyn, NY, 11210, USA
- CUNY Graduate Center, 365 5th Ave., New York, NY, 10016, USA
| | - Benjamin Crair
- Department of Microbial Pathogenesis, Yale University, 840 West Campus Drive, Advanced Biosciences Center 211, West Haven, CT, 06516, USA
| | - Shiwei Zhu
- Department of Microbial Pathogenesis, Yale University, 840 West Campus Drive, Advanced Biosciences Center 211, West Haven, CT, 06516, USA
| | - Hannah Q Hughes
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
| | - Jennifer L Chlebek
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
| | - Daniel C Wu
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA
| | - Jin Hwan Park
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA
| | - Ali M Farhat
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Charles J Lomba
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Courtney K Ellison
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, 355 Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - Yves V Brun
- Department of Microbiology, Infectious Diseases, and Immunology, Faculty of Medicine, University of Montreal, Pavillon Roger-Gaudry, 2900, boulevard Édouard-Montpetit, C.P. 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Javier Campos-Gomez
- Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1918 University Blvd., MCLM 702, Birmingham, AL, 35233, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University, 840 West Campus Drive, Advanced Biosciences Center 211, West Haven, CT, 06516, USA
| | - Nicolas Biais
- Department of Biology, Brooklyn College, Room 307NE, 2900 Bedford Ave., Brooklyn, NY, 11210, USA
- CUNY Graduate Center, 365 5th Ave., New York, NY, 10016, USA
| | - Gerard C L Wong
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA.
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA.
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56
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Lomovatskaya LA, Romanenko AS. Secretion Systems of Bacterial Phytopathogens and Mutualists (Review). APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820020106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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57
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Crawshaw AD, Baslé A, Salgado PS. A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study. Acta Crystallogr D Struct Biol 2020; 76:261-271. [PMID: 32133990 PMCID: PMC7057214 DOI: 10.1107/s2059798320000467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/14/2020] [Indexed: 12/02/2022] Open
Abstract
Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.
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Affiliation(s)
- Adam D. Crawshaw
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
| | - Arnaud Baslé
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
| | - Paula S. Salgado
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
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58
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Silva YRDO, Contreras-Martel C, Macheboeuf P, Dessen A. Bacterial secretins: Mechanisms of assembly and membrane targeting. Protein Sci 2020; 29:893-904. [PMID: 32020694 DOI: 10.1002/pro.3835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Secretion systems are employed by bacteria to transport macromolecules across membranes without compromising their integrities. Processes including virulence, colonization, and motility are highly dependent on the secretion of effector molecules toward the immediate cellular environment, and in some cases, into the host cytoplasm. In Type II and Type III secretion systems, as well as in Type IV pili, homomultimeric complexes known as secretins form large pores in the outer bacterial membrane, and the localization and assembly of such 1 MDa molecules often relies on pilotins or accessory proteins. Significant progress has been made toward understanding details of interactions between secretins and their partner proteins using approaches ranging from bacterial genetics to cryo electron microscopy. This review provides an overview of the mode of action of pilotins and accessory proteins for T2SS, T3SS, and T4PS secretins, highlighting recent near-atomic resolution cryo-EM secretin complex structures and underlining the importance of these interactions for secretin functionality.
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Affiliation(s)
- Yuri Rafael de Oliveira Silva
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, São Paulo, Brazil.,Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Carlos Contreras-Martel
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Pauline Macheboeuf
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, São Paulo, Brazil.,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
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59
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Soncini SR, Hartman AH, Gallagher TM, Camper GJ, Jensen RV, Melville SB. Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces. BMC Genomics 2020; 21:45. [PMID: 31937237 PMCID: PMC6958937 DOI: 10.1186/s12864-020-6453-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Clostridium perfringens is a Gram-positive anaerobic pathogen that causes multiple diseases in humans and animals. C. perfringens lack flagella but have type IV pili (TFP) and can glide on agar surfaces. When C. perfringens bacteria are placed on surfaces, they become elongated, flexible and have TFP on their surface, traits not seen in liquid-grown cells. In addition, the main pilin in C. perfringens TFP, PilA2, undergoes differential post-translational modification when grown in liquid or on plates. To understand the mechanisms underlying these phenotypes, bacteria were grown in three types of liquid media and on agar plates with the same medium to compare gene expression using RNA-Seq. RESULTS Hundreds of genes were differentially expressed, including transcriptional regulatory protein-encoding genes and genes associated with TFP functions, which were higher on plates than in liquid. Transcript levels of TFP genes reflected the proportion of each protein predicted to reside in a TFP assembly complex. To measure differences in rates of translation, the Escherichia coli reporter gene gusA gene (encoding β-glucuronidase) was inserted into the chromosome downstream of TFP promoters and in-frame with the first gene of the operon. β-glucuronidase expression was then measured in cells grown in liquid or on plates. β-glucuronidase activity was proportional to mRNA levels in liquid-grown cells, but not plate-grown cells, suggesting significant levels of post-transcriptional regulation of these TFP-associated genes occurs when cells are grown on surfaces. CONCLUSIONS This study reveals insights into how a non-flagellated pathogenic rod-shaped bacterium senses and responds to growth on surfaces, including inducing transcriptional regulators and activating multiple post-transcriptional regulatory mechanisms associated with TFP functions.
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Affiliation(s)
- Samantha R Soncini
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.,Current address: UPMC Genome Center, Pittsburgh, PA, USA
| | - Andrea H Hartman
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Tara M Gallagher
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.,Current address: Department of Molecular Biology & Biochemistry, University of California, Irvine, USA
| | - Gary J Camper
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Stephen B Melville
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
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60
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Pyclik M, Srutkova D, Schwarzer M, Górska S. Bifidobacteria cell wall-derived exo-polysaccharides, lipoteichoic acids, peptidoglycans, polar lipids and proteins - their chemical structure and biological attributes. Int J Biol Macromol 2019; 147:333-349. [PMID: 31899242 DOI: 10.1016/j.ijbiomac.2019.12.227] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
A variety of health benefits has been documented to be associated with the consumption of probiotic bacteria, namely bifidobacteria and lactobacilli. Thanks to the scientific advances in recent years we are beginning to understand the molecular mechanisms by which bacteria in general and probiotic bacteria in particular act as host physiology and immune system modulators. More recently, the focus has shifted from live bacteria towards bacteria-derived defined molecules, so called postbiotics. These molecules may represent safer alternative compared to the live bacteria while retaining the desired effects on the host. The excellent source of effector macromolecules is the bacterial envelope. It contains compounds that are pivotal in the adhesion phenomenon, provide direct bacteria-to-host signaling capacity and the associated physiological impact and immunomodulatory properties of bacteria. Here we comprehensively review the structure and biological role of Bifidobacterium surface and cell wall molecules: exopolysaccharides, cell wall polysaccharides, lipoteichoic acids, polar lipids, peptidoglycans and proteins. We discuss their involvement in direct signaling to the host cells and their described immunomodulatory effects.
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Affiliation(s)
- Marcelina Pyclik
- Laboratory of Microbiome Immunobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic.
| | - Sabina Górska
- Laboratory of Microbiome Immunobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland.
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61
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Engel M, Gemünde A, Holtmann D, Müller‐Renno C, Ziegler C, Tippkötter N, Ulber R. Clostridium Acetobutylicum
’s Connecting World: Cell Appendage Formation in Bioelectrochemical Systems. ChemElectroChem 2019. [DOI: 10.1002/celc.201901656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mareike Engel
- Bioprocess EngineeringUniversity of Kaiserslautern 67663 Kaiserslautern Germany
| | - André Gemünde
- Bioprocess EngineeringUniversity of Kaiserslautern 67663 Kaiserslautern Germany
| | - Dirk Holtmann
- Industrial BiotechnologyDECHEMA Research Institute 60486 Frankfurt am Main Germany
| | | | - Christiane Ziegler
- Department of PhysicsUniversity of Kaiserslautern 67663 Kaiserslautern Germany
| | - Nils Tippkötter
- Bioprocess EngineeringUniversity of Applied Science Aachen 52428 Jülich Germany
| | - Roland Ulber
- Bioprocess EngineeringUniversity of Kaiserslautern 67663 Kaiserslautern Germany
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62
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Abstract
Transformation is a widespread mechanism of horizontal gene transfer in bacteria. DNA uptake to the periplasmic compartment requires a DNA-uptake pilus and the DNA-binding protein ComEA. In the gram-negative bacteria, DNA is first pulled toward the outer membrane by retraction of the pilus and then taken up by binding to periplasmic ComEA, acting as a Brownian ratchet to prevent backward diffusion. A similar mechanism probably operates in the gram-positive bacteria as well, but these systems have been less well characterized. Transport, defined as movement of a single strand of transforming DNA to the cytosol, requires the channel protein ComEC. Although less is understood about this process, it may be driven by proton symport. In this review we also describe various phenomena that are coordinated with the expression of competence for transformation, such as fratricide, the kin-discriminatory killing of neighboring cells, and competence-mediated growth arrest.
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Affiliation(s)
- David Dubnau
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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63
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Pelicic V. Monoderm bacteria: the new frontier for type IV pilus biology. Mol Microbiol 2019; 112:1674-1683. [PMID: 31556183 PMCID: PMC6916266 DOI: 10.1111/mmi.14397] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
In the diverse world of bacterial pili, type IV pili (Tfp) are unique for two reasons: their multifunctionality and ubiquity. This latter feature offers an extraordinary possibility, that is, to perform comparative studies in evolutionarily distant species in order to improve our fragmentary understanding of Tfp biology. Regrettably, such potential has remained largely untapped, because, for 20 years, Tfp have only been characterised in diderm bacteria. However, recent studies of Tfp in monoderms have started closing the gap, revealing many interesting commonalities and a few significant differences, extending the frontiers of knowledge of Tfp biology. Here, I review the current state of the art of the Tfp field in monoderm bacteria and discuss resulting implications for our general understanding of the assembly and function of these widespread filamentous nanomachines.
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Affiliation(s)
- Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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64
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Sánchez P, Oliver C, Hernández M, Cortés M, Cecilia Rauch M, Valenzuela K, Garduño RA, Avendaño-Herrera R, Yáñez AJ. In vitro genomic and proteomic evidence of a type IV pili-like structure in the fish pathogen Piscirickettsia salmonis. FEMS Microbiol Lett 2019; 365:5050058. [PMID: 29986002 DOI: 10.1093/femsle/fny169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/04/2018] [Indexed: 01/24/2023] Open
Abstract
Piscirickettsia salmonis is an intracellular γ-proteobacteria and the etiological agent of piscirickettsiosis, which causes massive economic losses in the Chilean salmon industry. The type IV pili (T4P) play an important role in adherence to host cell surfaces and bacterial pathogenicity. T4P contains a variable number of components, as predicted in P. salmonis genomes. However, no studies have determined if P. salmonis possesses T4P. The aims of this investigation were to identify T4P components in the P. salmonis type strain LF-89T, evaluate respective transcript expressions, and analyze the main putative T4P proteins using bioinformatics and proteomic approaches. Two main clusters of P. salmonis T4P genes were found. Expression of the pilA gene was upregulated at 4 h post-infection (hpi), while pilQ was upregulated 4 days post-infection. At 16 hpi, pilB and pilD were strongly upregulated. The PilA amino acid sequence analysis showed a conserved N-terminal domain and sequence motifs critical for T4P biosynthesis. MudPIT analysis revealed PilA in the P. salmonis LF-89T proteome, and TEM showed pili-like filamentous structures on the P. salmonis surface. These results strongly suggest the presence of a T4P-like structure in P. salmonis.
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Affiliation(s)
- Patricio Sánchez
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile
| | - Cristian Oliver
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile.,Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Viña del Mar 8370146, Chile
| | - Mauricio Hernández
- Austral-OMICS, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile
| | - Marcos Cortés
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile
| | - María Cecilia Rauch
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile
| | - Karla Valenzuela
- Microbiology and Immunology Department, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Rafael A Garduño
- Microbiology and Immunology Department, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,Canadian Food Inspection Agency, Dartmouth Laboratory, Dartmouth, Nova Scotia B3B 1Y9, Canada
| | - Rubén Avendaño-Herrera
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile.,Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Viña del Mar 8370146, Chile
| | - Alejandro J Yáñez
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile.,Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile
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65
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Méheust R, Burstein D, Castelle CJ, Banfield JF. The distinction of CPR bacteria from other bacteria based on protein family content. Nat Commun 2019; 10:4173. [PMID: 31519891 PMCID: PMC6744442 DOI: 10.1038/s41467-019-12171-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/22/2019] [Indexed: 11/26/2022] Open
Abstract
Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria. Recent studies have identified a large, phylogenetically distinct clade of bacteria, the candidate phyla radiation (CPR). Here, Méheust and colleagues analyze almost 3600 genomes to characterize the protein family content of CPR versus other bacteria and archaea.
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Affiliation(s)
- Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94704, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, 94720, USA.,School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94704, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Innovative Genomics Institute, Berkeley, CA, 94704, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA. .,University of Melbourne, Melbourne, VIC, 3010, Australia. .,Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720, USA.
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66
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Gutierrez-Rodarte M, Kolappan S, Burrell BA, Craig L. The Vibrio cholerae minor pilin TcpB mediates uptake of the cholera toxin phage CTXφ. J Biol Chem 2019; 294:15698-15710. [PMID: 31471320 DOI: 10.1074/jbc.ra119.009980] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Virulent strains of the bacterial pathogen Vibrio cholerae cause the diarrheal disease cholera by releasing cholera toxin into the small intestine. V. cholerae acquired its cholera toxin genes by lysogenic infection with the filamentous bacteriophage CTXφ. CTXφ uses its minor coat protein pIII, located in multiple copies at the phage tip, to bind to the V. cholerae toxin-coregulated pilus (TCP). However, the molecular details of this interaction and the mechanism of phage internalization are not well-understood. The TCP filament is a polymer of major pilins, TcpA, and one or more minor pilin, TcpB. TCP are retractile, with both retraction and assembly initiated by TcpB. Consistent with these roles in pilus dynamics, we hypothesized that TcpB controls both binding and internalization of CTXφ. To test this hypothesis, we determined the crystal structure of the C-terminal half of TcpB and characterized its interactions with CTXφ pIII. We show that TcpB is a homotrimer in its crystallographic form as well as in solution and is present in multiple copies at the pilus tip, which likely facilitates polyvalent binding to pIII proteins at the phage tip. We further show that recombinant forms of TcpB and pIII interact in vitro, and both TcpB and anti-TcpB antibodies block CTXφ infection of V. cholerae Finally, we show that CTXφ uptake requires TcpB-mediated retraction. Our data support a model whereby CTXφ and TCP bind in a tip-to-tip orientation, allowing the phage to be drawn into the V. cholerae periplasm as an extension of the pilus filament.
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Affiliation(s)
- Miguel Gutierrez-Rodarte
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Subramania Kolappan
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Bailey A Burrell
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Lisa Craig
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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67
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Dyksma S, Gallert C. Candidatus Syntrophosphaera thermopropionivorans: a novel player in syntrophic propionate oxidation during anaerobic digestion. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:558-570. [PMID: 30985964 DOI: 10.1111/1758-2229.12759] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Propionate is an important intermediate in the anaerobic mineralization of organic matter. In methanogenic environments, its degradation relies on syntrophic associations between syntrophic propionate-oxidizing bacteria (SPOB) and Archaea. However, only 10 isolated species have been identified as SPOB so far. We report syntrophic propionate oxidation in thermophilic enrichments of Candidatus Syntrophosphaera thermopropionivorans, a novel representative of the candidate phylum Cloacimonetes. In enrichment culture, methane was produced from propionate, while Ca. S. thermopropionivorans contributed 63% to total bacterial cells. The draft genome of Ca. S. thermopropionivorans encodes genes for propionate oxidation via methymalonyl-CoA. Phylogenetically, Ca. S. thermopropionivorans affiliates with the uncultured Cloacimonadaceae W5 and is more distantly related (86.4% 16S rRNA gene identity) to Ca. Cloacimonas acidaminovorans. Although Ca. S. thermopropionivorans was enriched from a thermophilic biogas reactor, Ca. Syntrophosphaera was in particular associated with mesophilic anaerobic digestion systems. 16S rRNA gene amplicon sequencng and a novel genus-specific quantitative PCR assay consistently identified Ca. Syntrophosphaera/Cloacimonadaceae W5 in 9 of 12 tested full-scale biogas reactors thereby outnumbering other SPOB such as Pelotomaculum, Smithella and Syntrophobacter. Taken together the ubiquity and abundance of Ca. Syntrophosphaera, those SPOB might be key players for syntrophic propionate metabolism that have been overlooked before.
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Affiliation(s)
- Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
| | - Claudia Gallert
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
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68
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Tamai E, Katayama S, Sekiya H, Nariya H, Kamitori S. Structures of major pilins in Clostridium perfringens demonstrate dynamic conformational change. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:718-732. [PMID: 31373571 DOI: 10.1107/s2059798319009689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022]
Abstract
Pili in Gram-positive bacteria are flexible rod proteins associated with the bacterial cell surface, and they play important roles in the initial adhesion to host tissues and colonization. The pilus shaft is formed by the covalent polymerization of major pilins, catalyzed by sortases, a family of cysteine transpeptidases. Here, X-ray structures of the major pilins from Clostridium perfringens strains 13 and SM101 and of sortase from strain SM101 are presented with biochemical analysis to detect the formation of pili in vivo. The major pilin from strain 13 adopts an elongated structure to form noncovalently linked polymeric chains in the crystal, yielding a practical model of the pilus fiber structure. The major pilin from strain SM101 adopts a novel bent structure and associates to form a left-handed twist like an antiparallel double helix in the crystal, which is likely to promote bacterial cell-cell interactions. A modeling study showed that pilin with a bent structure interacts favorably with sortase. The major pilin from strain SM101 was considered to be in an equilibrium state between an elongated and a bent structure through dynamic conformational change, which may be involved in pili-mediated colonization and sortase-mediated polymerization of pili.
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Affiliation(s)
- Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Seiichi Katayama
- Department of Life Science, Faculty of Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Hirofumi Nariya
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama-cho, Higashihiroshima, Hiroshima 739-8528, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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69
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Liu X, Zhan J, Jing X, Zhou S, Lovley DR. A pilin chaperone required for the expression of electrically conductive
Geobacter sulfurreducens
pili. Environ Microbiol 2019; 21:2511-2522. [DOI: 10.1111/1462-2920.14638] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and EnvironmentFujian Agriculture and Forestry University Fuzhou China
| | - Ji Zhan
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and EnvironmentFujian Agriculture and Forestry University Fuzhou China
| | - Xianyue Jing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and EnvironmentFujian Agriculture and Forestry University Fuzhou China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and EnvironmentFujian Agriculture and Forestry University Fuzhou China
| | - Derek R. Lovley
- Department of MicrobiologyUniversity of Massachusetts Amherst Amherst MA USA
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70
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Kosaka T, Goda M, Inoue M, Yakushi T, Yamada M. Flagellum-mediated motility in Pelotomaculum thermopropionicum SI. Biosci Biotechnol Biochem 2019; 83:1362-1371. [PMID: 30919743 DOI: 10.1080/09168451.2019.1597618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The basic functions of a propionate-oxidizing bacterium Pelotomaculum thermopropionicum flagellum, such as motility and chemotaxis, have not been studied. To investigate its motility, we compared with that of Syntrophobacter fumaroxidans, an aflagellar propionate-oxidizing bacterium, in soft agar medium. P. thermopropionicum cells spread, while S. fumaroxidans cells moved downward slightly, indicating flagellum-dependent motility in P. thermopropionicum SI. The motility of P. thermopropionicum was inhibited by the addition of carbonyl cyanide m-chlorophenyl hydrazone, a proton uncoupler, which is consistent with the fact that stator protein, MotB of P. thermopropionicum, shared sequence homology with proton-type stators. In addition, 5-N-ethyl-N-isopropyl amiloride, an Na+ channel blocker, showed no inhibitory effect on the motility. Furthermore, motAB of P. thermopropionicum complemented the defective swimming ability of Escherichia coli ∆motAB. These results suggest that the motility of P. thermopropionicum SI depends on the proton-type flagellar motor.
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Affiliation(s)
- Tomoyuki Kosaka
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan.,b Research Center for Thermotolerant Microbial Resources , Yamaguchi University , Yamaguchi , Japan
| | - Mutsumi Goda
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan
| | - Manami Inoue
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan
| | - Toshiharu Yakushi
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan.,b Research Center for Thermotolerant Microbial Resources , Yamaguchi University , Yamaguchi , Japan
| | - Mamoru Yamada
- a Department of Biological Chemistry, College of Agriculture, Graduate school of Science and Technology for Innovation , Yamaguchi University , Yamaguchi , Japan.,b Research Center for Thermotolerant Microbial Resources , Yamaguchi University , Yamaguchi , Japan
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71
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Molecular and Functional Analysis of the Type IV Pilus Gene Cluster in Streptococcus sanguinis SK36. Appl Environ Microbiol 2019; 85:AEM.02788-18. [PMID: 30635384 DOI: 10.1128/aem.02788-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/04/2019] [Indexed: 12/11/2022] Open
Abstract
Streptococcus sanguinis, dominant in the oral microbiome, is the only known streptococcal species possessing a pil gene cluster for the biosynthesis of type IV pili (Tfp). Although this cluster is commonly present in the genome of S. sanguinis, most of the strains do not express Tfp-mediated twitching motility. Thus, this study was designed to investigate the biological functions encoded by the cluster in the twitching-negative strain S. sanguinis SK36. We found that the cluster was transcribed as an operon, with three promoters located 5' to the cluster and one in the intergenic region between SSA_2307 and SSA_2305. Studies using promoter-cat fusion strains revealed that the transcription of the cluster was mainly driven by the distal 5' promoter, which is located more than 800 bases 5' to the first gene of the cluster, SSA_2318. Optimal expression of the cluster occurred at the early stationary growth phase in a CcpA-dependent manner, although a CcpA-binding consensus is absent in the promoter region. Expression of the cluster resulted in a short hairlike surface structure under transmission electron microscopy. Deletion of the putative pilin genes (SSA_2313 to SSA_2315) abolished the biosynthesis of this structure and significantly reduced the adherence of SK36 to HeLa and SCC-4 cells. Mutations in the pil genes downregulated biofilm formation by S. sanguinis SK36. Taken together, the results demonstrate that Tfp of SK36 are important for host cell adherence, but not for motility, and that expression of the pil cluster is subject to complex regulation.IMPORTANCE The proteins and assembly machinery of the type IV pili (Tfp) are conserved throughout bacteria and archaea, and yet the function of this surface structure differs from species to species and even from strain to strain. As seen in Streptococcus sanguinis SK36, the expression of the Tfp gene cluster results in a hairlike surface structure that is much shorter than the typical Tfp. This pilus is essential for the adherence of SK36 but is not involved in motility. Being a member of the highly diverse dental biofilm, perhaps S. sanguinis could more effectively utilize this structure to adhere to host cells and to interact with other microbes within the same niche.
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72
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Berry JL, Gurung I, Anonsen JH, Spielman I, Harper E, Hall AMJ, Goosens VJ, Raynaud C, Koomey M, Biais N, Matthews S, Pelicic V. Global biochemical and structural analysis of the type IV pilus from the Gram-positive bacterium Streptococcus sanguinis. J Biol Chem 2019; 294:6796-6808. [PMID: 30837269 PMCID: PMC6497953 DOI: 10.1074/jbc.ra118.006917] [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: 11/30/2018] [Revised: 02/27/2019] [Indexed: 11/06/2022] Open
Abstract
Type IV pili (Tfp) are functionally versatile filaments, widespread in prokaryotes, that belong to a large class of filamentous nanomachines known as type IV filaments (Tff). Although Tfp have been extensively studied in several Gram-negative pathogens where they function as key virulence factors, many aspects of their biology remain poorly understood. Here, we performed a global biochemical and structural analysis of Tfp in a recently emerged Gram-positive model, Streptococcus sanguinis In particular, we focused on the five pilins and pilin-like proteins involved in Tfp biology in S. sanguinis We found that the two major pilins, PilE1 and PilE2, (i) follow widely conserved principles for processing by the prepilin peptidase PilD and for assembly into filaments; (ii) display only one of the post-translational modifications frequently found in pilins, i.e. a methylated N terminus; (iii) are found in the same heteropolymeric filaments; and (iv) are not functionally equivalent. The 3D structure of PilE1, solved by NMR, revealed a classical pilin-fold with a highly unusual flexible C terminus. Intriguingly, PilE1 more closely resembles pseudopilins forming shorter Tff than bona fide Tfp-forming major pilins, underlining the evolutionary relatedness among different Tff. Finally, we show that S. sanguinis Tfp contain a low abundance of three additional proteins processed by PilD, the minor pilins PilA, PilB, and PilC. These findings provide the first global biochemical and structural picture of a Gram-positive Tfp and have fundamental implications for our understanding of a widespread class of filamentous nanomachines.
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Affiliation(s)
- Jamie-Lee Berry
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ishwori Gurung
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jan Haug Anonsen
- the Department of Biological Sciences, Proteomics and Mass Spectrometry Unit, University of Oslo, 0371 Oslo, Norway.,the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Ingrid Spielman
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Elliot Harper
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alexander M J Hall
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vivianne J Goosens
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claire Raynaud
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Michael Koomey
- the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Nicolas Biais
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Steve Matthews
- the Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vladimir Pelicic
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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73
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Abstract
ABSTRACT
Type IV pili (T4P) are remarkable bacterial surface appendages that carry out a range of functions. Various types of T4P have been identified in bacteria and archaea, making them almost universal structures in prokaryotes. T4P are best characterized in Gram-negative bacteria, in which pilus biogenesis and T4P-mediated functions have been studied for decades. Recent advances in microbial whole-genome sequencing have provided ample evidence for the existence of T4P also in many Gram-positive species. However, comparatively little is known, and T4P in Gram-positive bacteria are just beginning to be dissected. So far, they have mainly been studied in
Clostridium
and
Streptococcus
spp. and are involved in diverse cellular processes such as adhesion, motility, and horizontal gene transfer. Here we summarize the current understanding of T4P in Gram-positive species and their functions, with particular focus on the type IV competence pilus produced by the human pathogen
Streptococcus pneumoniae
and its role in natural transformation.
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74
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Abstract
Bacterial uptake of DNA through type IV filaments is an essential component of natural competence in numerous gram-positive and gram-negative species. Recent advances in the field have broadened our understanding of the structures used to take up extracellular DNA. Here, we review seminal experiments in the literature describing DNA binding by type IV pili, competence pili and the flp pili of Micrococcus luteus; collectively referred to here as type IV filaments. We compare the current state of the field on mechanisms of DNA uptake for these three appendage systems and describe the current mechanistic understanding of both DNA-binding and DNA-uptake by these versatile molecular machines.
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Affiliation(s)
- Kurt H Piepenbrink
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States.,Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, United States
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75
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Abstract
Microbial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a representative set of microorganisms. Our results uncovered important trends. First, microbes with different lifestyles are differentially impacted, with endosymbionts and obligate pathogens being those less prone to undergo this process. Second, certain genetic elements such as restriction-modification systems seem to be associated with higher rates of recombination. Most importantly, recombined genomes show the footprints of natural selection in which recombined regions preferentially contain genes that can be related to specific ecological adaptations. Taken together, our results clarify the relative contributions of factors modulating homologous recombination and show evidence for a clear a role of this process in shaping microbial genomes and driving ecological adaptations. Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes.
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76
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Luna Rico A, Zheng W, Petiot N, Egelman EH, Francetic O. Functional reconstitution of the type IVa pilus assembly system from enterohaemorrhagic Escherichia coli. Mol Microbiol 2019; 111:732-749. [PMID: 30561149 DOI: 10.1111/mmi.14188] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2018] [Indexed: 12/17/2022]
Abstract
Type 4a pili (T4aP) are long, thin and dynamic fibres displayed on the surface of diverse bacteria promoting adherence, motility and transport functions. Genomes of many Enterobacteriaceae contain conserved gene clusters encoding putative T4aP assembly systems. However, their expression has been observed only in few strains including Enterohaemorrhagic Escherichia coli (EHEC) and their inducers remain unknown. Here we used EHEC genomic DNA as a template to amplify and assemble an artificial operon composed of four gene clusters encoding 13 pilus assembly proteins. Controlled expressions of this operon in nonpathogenic E. coli strains led to efficient assembly of T4aP composed of the major pilin PpdD, as shown by shearing assays and immunofluorescence microscopy. When compared with PpdD pili assembled in a heterologous Klebsiella T2SS type 2 secretion system (T2SS) by using cryo-electron microscopy (cryoEM), these pili showed indistinguishable helical parameters, emphasizing that major pilins are the principal determinants of the fibre structure. Bacterial two-hybrid analysis identified several interactions of PpdD with T4aP assembly proteins, and with components of the T2SS that allow for heterologous fibre assembly. These studies lay ground for further characterization of the T4aP structure, function and biogenesis in enterobacteria.
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Affiliation(s)
- Areli Luna Rico
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France.,Structural Bioinformatics Unit and NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France
| | - Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nathalie Petiot
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, Paris, 75724, France
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77
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Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
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Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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78
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Trifonova A, Strateva T. Stenotrophomonas maltophilia – a low-grade pathogen with numerous virulence factors. Infect Dis (Lond) 2018; 51:168-178. [DOI: 10.1080/23744235.2018.1531145] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Angelina Trifonova
- Laboratory of Microbiology, Department of Military Epidemiology and Hygiene, Military Medical Academy, Sofia, Bulgaria
| | - Tanya Strateva
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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79
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Poquet I, Saujet L, Canette A, Monot M, Mihajlovic J, Ghigo JM, Soutourina O, Briandet R, Martin-Verstraete I, Dupuy B. Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture. Front Microbiol 2018; 9:2084. [PMID: 30258415 PMCID: PMC6143707 DOI: 10.3389/fmicb.2018.02084] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA1, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA1 in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA1. dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA1. Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.
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Affiliation(s)
- Isabelle Poquet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France
| | - Laure Saujet
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Alexis Canette
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | | | - Jean-Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, Paris, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Romain Briandet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
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80
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González-Torres P, Gabaldón T. Genome Variation in the Model Halophilic Bacterium Salinibacter ruber. Front Microbiol 2018; 9:1499. [PMID: 30072959 PMCID: PMC6060240 DOI: 10.3389/fmicb.2018.01499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/18/2018] [Indexed: 01/08/2023] Open
Abstract
The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by horizontal gene transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes potentially relevant for environmental interactions and adaptation to extremophilic conditions. Altogether, our results support scenarios that conciliate “Neutral” and “Constant Diversity” models of bacterial evolution.
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Affiliation(s)
- Pedro González-Torres
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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81
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Chaurasia P, Pratap S, Palva A, von Ossowski I, Krishnan V. Bent conformation of a backbone pilin N-terminal domain supports a three-stage pilus assembly mechanism. Commun Biol 2018; 1:94. [PMID: 30271975 PMCID: PMC6123636 DOI: 10.1038/s42003-018-0100-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/21/2018] [Indexed: 12/31/2022] Open
Abstract
Effective colonization of host cells by some Gram-positive bacteria often involves using lengthy, adhesive macromolecular structures called sortase-dependent pili. Among commensals, the gut-adapted Lactobacillus rhamnosus GG strain encodes the operons for two varieties of these pili (SpaCBA and SpaFED), with each structure consisting of backbone, tip, and basal pilin subunits. Although the tertiary structure was recently solved for the backbone subunit (SpaA) of the SpaCBA pilus, no structural information exists for its counterpart in the SpaFED pilus. Here, we report several crystal structures for the SpaD backbone pilin, two of which capture the N-terminal domain in either the closed (linear) or open (bent) conformation. To our knowledge, this is the first observation of the bent conformation in Gram-positive pilin structures. Based on this bent conformation, we suggest a three-stage model, which we call the expose-ligate-seal mechanism, for the docking and assembly of backbone pilins into the sortase-dependent pilus. Priyanka Chaurasia et al. report crystal structures of the SpaD backbone pilin from a gut-adapted bacteria, Lactobacillus rhamnosus. The observed bent conformation of the N-terminal domain has not been seen in other Gram-positive pilin structures.
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Affiliation(s)
- Priyanka Chaurasia
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India.,Department of Biotechnology, Manipal University, Manipal, Karnataka, 576104, India
| | - Shivendra Pratap
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, FIN-00014, Helsinki, Finland
| | - Ingemar von Ossowski
- Department of Veterinary Biosciences, University of Helsinki, FIN-00014, Helsinki, Finland
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India.
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82
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Nguyen Y, Boulton S, McNicholl ET, Akimoto M, Harvey H, Aidoo F, Melacini G, Burrows LL. A Highly Dynamic Loop of the Pseudomonas aeruginosa PA14 Type IV Pilin Is Essential for Pilus Assembly. ACS Infect Dis 2018; 4:936-943. [PMID: 29342354 DOI: 10.1021/acsinfecdis.7b00229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type IVa pili (T4aP) are long, thin surface filaments involved in attachment, motility, biofilm formation, and DNA uptake. They are important virulence factors for many bacteria, including Pseudomonas aeruginosa, an opportunistic pathogen and common cause of hospital-acquired infections. Each helical filament contains thousands of monomers of the major pilin subunit, PilA. Each P. aeruginosa strain expresses one of five phylogenetically distinct major pilins, which vary in sequence and the nature of their associated accessory protein(s). Here, we present the backbone resonance assignment of the C-terminal domain of the group III PilA from strain PA14, a highly virulent, globally distributed clone. Secondary structure probabilities calculated from chemical shifts were in excellent agreement with previous homology modeling using a group V pilin structural template. The analysis revealed that the distal segment of the αβ loop had high microsecond-millisecond dynamics compared with other loop regions. Shortening of this segment by internal deletion abrogated pilus assembly in a dominant negative manner, suggesting a potential role in pilin polymerization. Pilin conformations that support optimal interactions of both the conserved hydrophobic N-termini in the pilus core and hydrophilic loops creating the filament surface may be necessary to produce stable filaments.
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83
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Type IV Pili Promote Clostridium difficile Adherence and Persistence in a Mouse Model of Infection. Infect Immun 2018; 86:IAI.00943-17. [PMID: 29483294 DOI: 10.1128/iai.00943-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 12/16/2022] Open
Abstract
Cyclic diguanylate (c-di-GMP) is a second messenger that regulates the transition from motile to sessile lifestyles in numerous bacteria and controls virulence factor production in a variety of pathogens. In Clostridium difficile, c-di-GMP negatively regulates flagellum biosynthesis and swimming motility and promotes the production of type IV pili (TFP), biofilm formation, and surface motility in vitro Flagella have been identified as colonization factors in C. difficile, but the role of TFP in adherence to host cells and in colonization of the mammalian gut is unknown. Here we show that c-di-GMP promotes adherence to epithelial cells in vitro, which can be partly attributed to the loss of flagella. Using TFP-null mutants, we demonstrate that adherence to epithelial cells is partially mediated by TFP and that this TFP-mediated adherence requires c-di-GMP regulation. In a mouse model of colonization, the TFP-null mutants initially colonized the intestine as well as the parental strain but were cleared more quickly. Moreover, compared to the parent strain, C. difficile strains lacking TFP were particularly deficient in association with the cecal mucosa. Together these data indicate that TFP and their positive regulation by c-di-GMP promote attachment of C. difficile to the intestinal epithelium and contribute to persistence of C. difficile in the host intestine.
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84
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Low LY, Harrison PF, Gould J, Powell DR, Choo JM, Forster SC, Chapman R, Gearing LJ, Cheung JK, Hertzog P, Rood JI. Concurrent Host-Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection. mBio 2018; 9:e00473-18. [PMID: 29588405 PMCID: PMC5874911 DOI: 10.1128/mbio.00473-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 11/20/2022] Open
Abstract
To obtain an insight into host-pathogen interactions in clostridial myonecrosis, we carried out comparative transcriptome analysis of both the bacterium and the host in a murine Clostridium perfringens infection model, which is the first time that such an investigation has been conducted. Analysis of the host transcriptome from infected muscle tissues indicated that many genes were upregulated compared to the results seen with mock-infected mice. These genes were enriched for host defense pathways, including Toll-like receptor (TLR) and Nod-like receptor (NLR) signaling components. Real-time PCR confirmed that host TLR2 and NLRP3 inflammasome genes were induced in response to C. perfringens infection. Comparison of the transcriptome of C. perfringens cells from the infected tissues with that from broth cultures showed that host selective pressure induced a global change in C. perfringens gene expression. A total of 33% (923) of C. perfringens genes were differentially regulated, including 10 potential virulence genes that were upregulated relative to their expression in vitro These genes encoded putative proteins that may be involved in the synthesis of cell wall-associated macromolecules, in adhesion to host cells, or in protection from host cationic antimicrobial peptides. This report presents the first successful expression profiling of coregulated transcriptomes of bacterial and host genes during a clostridial myonecrosis infection and provides new insights into disease pathogenesis and host-pathogen interactions.IMPORTANCEClostridium perfringens is the causative agent of traumatic clostridial myonecrosis, or gas gangrene. In this study, we carried out transcriptional analysis of both the host and the bacterial pathogen in a mouse myonecrosis infection. The results showed that in comparison to mock-infected control tissues, muscle tissues from C. perfringens-infected mice had a significantly altered gene expression profile. In particular, the expression of many genes involved in the innate immune system was upregulated. Comparison of the expression profiles of C. perfringens cells isolated from the infected tissues with those from equivalent broth cultures identified many potential virulence genes that were significantly upregulated in vivo These studies have provided a new understanding of the range of factors involved in host-pathogen interactions in a myonecrosis infection.
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Affiliation(s)
- Lee-Yean Low
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Clayton, Australia
| | - Jodee Gould
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Clayton, Australia
| | - Jocelyn M Choo
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Samuel C Forster
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Ross Chapman
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Linden J Gearing
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Jackie K Cheung
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Paul Hertzog
- Department of Molecular and Translational Science, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, School of Clinical Science, Monash University, Clayton, Australia
| | - Julian I Rood
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
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85
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Bacteriocinogenic Enterococcus faecium inhibits the virulence property of Listeria monocytogenes. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.10.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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86
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Streptococcus sanguinis Noncoding cia-Dependent Small RNAs Negatively Regulate Expression of Type IV Pilus Retraction ATPase PilT and Biofilm Formation. Infect Immun 2018; 86:IAI.00894-17. [PMID: 29263111 DOI: 10.1128/iai.00894-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/18/2022] Open
Abstract
Small noncoding RNAs (sRNAs) have been identified as important regulators of gene expression in various cellular processes. cia-dependent small RNAs (csRNAs), a group of sRNAs that are controlled by the two-component regulatory system CiaRH, are widely conserved in streptococci, but their targets have been identified only in Streptococcus pneumoniaeStreptococcus sanguinis, a pioneer colonizer of teeth and one of the most predominant bacteria in the early oral biofilm, has been shown to have six csRNAs. Using computational target prediction and the luciferase reporter assay, we identified pilT, a constituent of the type IV pilus operon, as a negative regulatory target for one of the csRNAs, namely, csRNA1-1, in S. sanguinis RNA-RNA electrophoretic mobility shift assay using a nucleotide exchange mutant of csRNA1-1 revealed that csRNA1-1 binds directly to pilT mRNA. In addition, csRNA1-1 and csRNA1-2, a putative gene duplication product of csRNA1-1 that is tandemly located in the S. sanguinis genome, negatively regulated S. sanguinis biofilm formation. These results suggest the involvement of csRNAs in the colonization step of S. sanguinis.
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87
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Desvaux M, Candela T, Serror P. Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. Front Microbiol 2018; 9:100. [PMID: 29491848 PMCID: PMC5817068 DOI: 10.3389/fmicb.2018.00100] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
The cell envelope of parietal monoderm bacteria (archetypal Gram-positive bacteria) is formed of a cytoplasmic membrane (CM) and a cell wall (CW). While the CM is composed of phospholipids, the CW is composed at least of peptidoglycan (PG) covalently linked to other biopolymers, such as teichoic acids, polysaccharides, and/or polyglutamate. Considering the CW is a porous structure with low selective permeability contrary to the CM, the bacterial cell surface hugs the molecular figure of the CW components as a well of the external side of the CM. While the surfaceome corresponds to the totality of the molecules found at the bacterial cell surface, the proteinaceous complement of the surfaceome is the proteosurfaceome. Once translocated across the CM, secreted proteins can either be released in the extracellular milieu or exposed at the cell surface by associating to the CM or the CW. Following the gene ontology (GO) for cellular components, cell-surface proteins at the CM can either be integral (GO: 0031226), i.e., the integral membrane proteins, or anchored to the membrane (GO: 0046658), i.e., the lipoproteins. At the CW (GO: 0009275), cell-surface proteins can be covalently bound, i.e., the LPXTG-proteins, or bound through weak interactions to the PG or wall polysaccharides, i.e., the cell wall binding proteins. Besides monopolypeptides, some proteins can associate to each other to form supramolecular protein structures of high molecular weight, namely the S-layer, pili, flagella, and cellulosomes. After reviewing the cell envelope components and the different molecular mechanisms involved in protein attachment to the cell envelope, perspectives in investigating the proteosurfaceome in parietal monoderm bacteria are further discussed.
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Affiliation(s)
- Mickaël Desvaux
- Université Clermont Auvergne, INRA, UMR454 MEDiS, Clermont-Ferrand, France
| | - Thomas Candela
- EA4043 Unité Bactéries Pathogènes et Santé, Châtenay-Malabry, France
| | - Pascale Serror
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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88
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89
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Electron microscopic observations of prokaryotic surface appendages. J Microbiol 2017; 55:919-926. [DOI: 10.1007/s12275-017-7369-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 12/21/2022]
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90
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More than a Tad: spatiotemporal control of Caulobacter pili. Curr Opin Microbiol 2017; 42:79-86. [PMID: 29161615 DOI: 10.1016/j.mib.2017.10.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 01/09/2023]
Abstract
The Type IV pilus (T4P) is a powerful and sophisticated bacterial nanomachine involved in numerous cellular processes, including adhesion, DNA uptake and motility. Aside from the well-described subtype T4aP of the Gram-negative genera, including Myxococcus, Pseudomonas and Neisseria, the Tad (tight adherence) pilus secretion system re-shuffles homologous parts from other secretion systems along with uncharacterized components into a new type of protein translocation apparatus. A representative of the Tad apparatus, the Caulobacter crescentus pilus assembly (Cpa) machine is built exclusively at the newborn cell pole once per cell cycle. Recent comprehensive genetic analyses unearthed a myriad of spatiotemporal determinants acting on the Tad/Cpa system, many of which are conserved in other α-proteobacteria, including obligate intracellular pathogens and symbionts.
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91
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Skive B, Rohde M, Molinari G, Braunstein TH, Bojesen AM. Streptococcus equi subsp. zooepidemicus Invades and Survives in Epithelial Cells. Front Cell Infect Microbiol 2017; 7:465. [PMID: 29164073 PMCID: PMC5681531 DOI: 10.3389/fcimb.2017.00465] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/20/2017] [Indexed: 12/22/2022] Open
Abstract
Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is an opportunistic pathogen of several species including humans. S. zooepidemicus is found on mucus membranes of healthy horses, but can cause acute and chronic endometritis. Recently S. zooepidemicus was found able to reside in the endometrium for prolonged periods of time. Thus, we hypothesized that an intracellular phase may be part of the S. zooepidemicus pathogenesis and investigated if S. zooepidemicus was able to invade and survive inside epithelial cells. HEp-2 and HeLa cell lines were co-cultured with two S. zooepidemicus strains (1-4a and S31A1) both originating from the uterus of mares suffering from endometritis. Cells were fixed at different time points during the 23 h infection assay and field emission scanning electron microscopy (FESEM) was used to characterize adhesion and invasion mechanisms. The FESEM images showed three morphologically different types of invasion for both bacterial strains. The main port of entry was through large invaginations in the epithelial cell membrane. Pili-like bacterial appendages were observed when the S. zooepidemicus cells were in close proximity to the epithelial cells indicating that attachment and invasion were active processes. Adherent and intracellular S. zooepidemicus, and bacteria in association with lysosomes was determined by immunofluorescence staining techniques and fluorescence microscopy. Quantification of intracellular bacteria was determined in penicillin protection assays. Both S. zooepidemicus strains investigated were able to invade epithelial cells although at different magnitudes. The immunofluorescence data showed significantly higher adhesion and invasion rates for strain 1-4a when compared to strain S31A1. S. zooepidemicus was able to survive intracellularly, but the survival rate decreased over time in the cell culture system. Phagosome-like compartments containing S. zooepidemicus at some stages fused with lysosomes to form a phagolysosome. The results indicate that an intracellular phase may be one way S. zooepidemicus survives in the host, and could in part explain how S. zooepidemicus can cause recurrent/persistent infections. Future studies should reveal the ability of S. zooepidemicus to internalize and survive in primary equine endometrial cells and during in vivo conditions.
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Affiliation(s)
- Bolette Skive
- Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Gabriella Molinari
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thomas Hartig Braunstein
- Core Facility for Integrated Microscopy, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders M Bojesen
- Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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92
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Aderibigbe BA. Metal-Based Nanoparticles for the Treatment of Infectious Diseases. Molecules 2017; 22:E1370. [PMID: 28820471 PMCID: PMC6152252 DOI: 10.3390/molecules22081370] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/15/2017] [Indexed: 11/16/2022] Open
Abstract
Infectious diseases can be transmitted and they cause a significant burden on public health globally. They are the greatest world killers and it is estimated that they are responsible for the demise of over 17 million people annually. The impact of these diseases is greater in the developing countries. People with compromised immune systems and children are the most affected. Infectious diseases may be caused by bacteria, viruses, and protozoa. The treatment of infectious diseases is hampered by simultaneous resistance to multiple drugs, indicating that there is a serious and pressing need to develop new therapeutics that can overcome drug resistance. This review will focus on the recent reports of metal-based nanoparticles that are potential therapeutics for the treatment of infectious diseases and their biological efficacy (in vitro and in vivo).
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Affiliation(s)
- Blessing Atim Aderibigbe
- Department of Chemistry, University of Fort Hare, Alice Campus, Eastern Cape 5700, South Africa.
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93
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Tsuchida S, Maruyama F, Ogura Y, Toyoda A, Hayashi T, Okuma M, Ushida K. Genomic Characteristics of Bifidobacterium thermacidophilum Pig Isolates and Wild Boar Isolates Reveal the Unique Presence of a Putative Mobile Genetic Element with tetW for Pig Farm Isolates. Front Microbiol 2017; 8:1540. [PMID: 28861055 PMCID: PMC5561799 DOI: 10.3389/fmicb.2017.01540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/31/2017] [Indexed: 01/16/2023] Open
Abstract
Genomic analysis was performed on seven strains of Bifidobacterium thermacidophilum, a Sus-associated Bifidobacterium. Three strains from the feces of domestic pigs (Sus scrofa domesticus) and four strains from the rectal feces of free-range Japanese wild boars (S. s. scrofa) were compared. The phylogenetic position of these isolates suggested by genomic analyses were not concordant with that suggested by 16S rRNA sequence. There was biased distribution of genes for virulence, phage, metabolism of aromatic compounds, iron acquisition, cell division, and DNA metabolism. In particular four wild boar isolates harbored fiber-degrading enzymes, such as endoglucanase, while two of the pig isolates obtained from those grown under an intensive feeding practice with routine use of antimicrobials, particularly tetracycline harbored a tetracycline resistance gene, which was further proved functional by disk diffusion test. The tetW gene is associated with a serine recombinase of an apparently non-bifidobacterial origin. The insertion site of the tetW cassette was precisely defined by analyzing the corresponding genomic regions in the other tetracycline-susceptible isolates. The cassette may have been transferred from some other bacteria in the pig gut.
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Affiliation(s)
- Sayaka Tsuchida
- Laboratory of Animal Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto UniversityKyoto, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of GeneticsMishima, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Moriya Okuma
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Japan
| | - Kazunari Ushida
- Laboratory of Animal Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural UniversityKyoto, Japan
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94
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Gurung I, Berry JL, Hall A, Pelicic V. Cloning-independent markerless gene editing in Streptococcus sanguinis: novel insights in type IV pilus biology. Nucleic Acids Res 2017; 45:e40. [PMID: 27903891 PMCID: PMC5389465 DOI: 10.1093/nar/gkw1177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/14/2016] [Indexed: 11/14/2022] Open
Abstract
Streptococcus sanguinis, a naturally competent opportunistic human pathogen, is a Gram-positive workhorse for genomics. It has recently emerged as a model for the study of type IV pili (Tfp)—exceptionally widespread and important prokaryotic filaments. To enhance genetic manipulation of Streptococcus sanguinis, we have developed a cloning-independent methodology, which uses a counterselectable marker and allows sophisticated markerless gene editing in situ. We illustrate the utility of this methodology by answering several questions regarding Tfp biology by (i) deleting single or mutiple genes, (ii) altering specific bases in genes of interest, and (iii) engineering genes to encode proteins with appended affinity tags. We show that (i) the last six genes in the pil locus harbouring all the genes dedicated to Tfp biology play no role in piliation or Tfp-mediated motility, (ii) two highly conserved Asp residues are crucial for enzymatic activity of the prepilin peptidase PilD and (iii) that pilin subunits with a C-terminally appended hexa-histidine (6His) tag are still assembled into functional Tfp. The methodology for genetic manipulation we describe here should be broadly applicable.
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Affiliation(s)
- Ishwori Gurung
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Jamie-Lee Berry
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Alexander M. J. Hall
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- To whom correspondence should be addressed. Tel: +44 20 7594 2080;
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95
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Motility and adhesion through type IV pili in Gram-positive bacteria. Biochem Soc Trans 2017; 44:1659-1666. [PMID: 27913675 DOI: 10.1042/bst20160221] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 12/23/2022]
Abstract
Type IV pili are hair-like bacterial surface appendages that play a role in diverse processes such as cellular adhesion, colonization, twitching motility, biofilm formation, and horizontal gene transfer. These extracellular fibers are composed exclusively or primarily of many copies of one or more pilin proteins, tightly packed in a helix so that the highly hydrophobic amino-terminus of the pilin is buried in the pilus core. Type IV pili have been characterized extensively in Gram-negative bacteria, and recent advances in high-throughput genomic sequencing have revealed that they are also widespread in Gram-positive bacteria. Here, we review the current state of knowledge of type IV pilus systems in Gram-positive bacterial species and discuss them in the broader context of eubacterial type IV pili.
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96
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Nagar E, Zilberman S, Sendersky E, Simkovsky R, Shimoni E, Gershtein D, Herzberg M, Golden SS, Schwarz R. Type 4 pili are dispensable for biofilm development in the cyanobacterium Synechococcus elongatus. Environ Microbiol 2017; 19:2862-2872. [PMID: 28585390 DOI: 10.1111/1462-2920.13814] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/23/2017] [Accepted: 05/30/2017] [Indexed: 11/30/2022]
Abstract
The hair-like cell appendages denoted as type IV pili are crucial for biofilm formation in diverse eubacteria. The protein complex responsible for type IV pilus assembly is homologous with the type II protein secretion complex. In the cyanobacterium Synechococcus elongatus PCC 7942, the gene Synpcc7942_2071 encodes an ATPase homologue of type II/type IV systems. Here, we report that inactivation of Synpcc7942_2071 strongly affected the suite of proteins present in the extracellular milieu (exo-proteome) and eliminated pili observable by electron microscopy. These results support a role for this gene product in protein secretion as well as in pili formation. As we previously reported, inactivation of Synpcc7942_2071 enables biofilm formation and suppresses the planktonic growth of S. elongatus. Thus, pili are dispensable for biofilm development in this cyanobacterium, in contrast to their biofilm-promoting function in type IV pili-producing heterotrophic bacteria. Nevertheless, pili removal is not required for biofilm formation as evident by a piliated mutant of S. elongatus that develops biofilms. We show that adhesion and timing of biofilm development differ between the piliated and non-piliated strains. The study demonstrates key differences in the process of biofilm formation between cyanobacteria and well-studied type IV pili-producing heterotrophic bacteria.
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Affiliation(s)
- Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Shaul Zilberman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eyal Shimoni
- Weizmann Institute of Science, Electron Microscopy Unit, Rehovot, 7610001 Israel
| | - Diana Gershtein
- The Department of Desalination & Water Treatment, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be'er Sheva 84990, Israel
| | - Moshe Herzberg
- The Department of Desalination & Water Treatment, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be'er Sheva 84990, Israel
| | - Susan S Golden
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
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97
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Bacterial Filamentous Appendages Investigated by Solid-State NMR Spectroscopy. Methods Mol Biol 2017. [PMID: 28667627 DOI: 10.1007/978-1-4939-7033-9_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The assembly of filamentous appendages at the surface of bacteria is essential in many infection mechanisms. The extent of mechanical, dynamical, and functional properties of such appendages is very diverse, ranging from a structural scaffold of the pathogen-host cell interaction to cell motility, surface adhesion, or the export of virulence effectors. In particular, the architectures of several bacterial secretion systems have revealed the presence of filamentous architectures, known as pili, fimbriae, andneedles. At the macroscopic level, filamentous bacterial appendages appear as thin extracellular filaments of several nanometers in diameter and up to several microns in length. The structural characterization of these appendages at atomic-scale resolution represents an extremely challenging task because of their inherent noncrystallinity and very poor solubility. Here, we describe protocols based on recent advances in solid-state NMR spectroscopy to investigate the secondary structure, subunit-subunit protein interactions, symmetry parameters, and atomic architecture of bacterial filaments.
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98
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Muschiol S, Erlendsson S, Aschtgen MS, Oliveira V, Schmieder P, de Lichtenberg C, Teilum K, Boesen T, Akbey U, Henriques-Normark B. Structure of the competence pilus major pilin ComGC in Streptococcus pneumoniae. J Biol Chem 2017; 292:14134-14146. [PMID: 28659339 PMCID: PMC5572924 DOI: 10.1074/jbc.m117.787671] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/14/2017] [Indexed: 01/23/2023] Open
Abstract
Type IV pili are important virulence factors on the surface of many pathogenic bacteria and have been implicated in a wide range of diverse functions, including attachment, twitching motility, biofilm formation, and horizontal gene transfer. The respiratory pathogen Streptococcus pneumoniae deploys type IV pili to take up DNA during transformation. These “competence pili” are composed of the major pilin protein ComGC and exclusively assembled during bacterial competence, but their biogenesis remains unclear. Here, we report the high resolution NMR structure of N-terminal truncated ComGC revealing a highly flexible and structurally divergent type IV pilin. It consists of only three α-helical segments forming a well-defined electronegative cavity and confined electronegative and hydrophobic patches. The structure is particularly flexible between the first and second α-helix with the first helical part exhibiting slightly slower dynamics than the rest of the pilin, suggesting that the first helix is involved in forming the pilus structure core and that parts of helices two and three are primarily surface-exposed. Taken together, our results provide the first structure of a type IV pilin protein involved in the formation of competence-induced pili in Gram-positive bacteria and corroborate the remarkable structural diversity among type IV pilin proteins.
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Affiliation(s)
- Sandra Muschiol
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden,.
| | - Simon Erlendsson
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Center for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Marie-Stephanie Aschtgen
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Vitor Oliveira
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Casper de Lichtenberg
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Center for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Center for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Umit Akbey
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark,; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark
| | - Birgitta Henriques-Normark
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden,; Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and Lee Kong Chian School of Medicine (LKC), Nanyang Technological University, Singapore 639798, Singapore.
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99
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Callegan MC, Parkunan SM, Randall CB, Coburn PS, Miller FC, LaGrow AL, Astley RA, Land C, Oh SY, Schneewind O. The role of pili in Bacillus cereus intraocular infection. Exp Eye Res 2017; 159:69-76. [PMID: 28336259 PMCID: PMC5492386 DOI: 10.1016/j.exer.2017.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/09/2017] [Accepted: 03/16/2017] [Indexed: 12/15/2022]
Abstract
Bacterial endophthalmitis is a potentially blinding intraocular infection. The bacterium Bacillus cereus causes a devastating form of this disease which progresses rapidly, resulting in significant inflammation and loss of vision within a few days. The outer surface of B. cereus incites the intraocular inflammatory response, likely through interactions with innate immune receptors such as TLRs. This study analyzed the role of B. cereus pili, adhesion appendages located on the bacterial surface, in experimental endophthalmitis. To test the hypothesis that the presence of pili contributed to intraocular inflammation and virulence, we analyzed the progress of experimental endophthalmitis in mouse eyes infected with wild type B. cereus (ATCC 14579) or its isogenic pilus-deficient mutant (ΔbcpA-srtD-bcpB or ΔPil). One hundred CFU were injected into the mid-vitreous of one eye of each mouse. Infections were analyzed by quantifying intraocular bacilli and retinal function loss, and by histology from 0 to 12 h postinfection. In vitro growth and hemolytic phenotypes of the infecting strains were also compared. There was no difference in hemolytic activity (1:8 titer), motility, or in vitro growth (p > 0.05, every 2 h, 0-18 h) between wild type B. cereus and the ΔPil mutant. However, infected eyes contained greater numbers of wild type B. cereus than ΔPil during the infection course (p ≤ 0.05, 3-12 h). Eyes infected with wild type B. cereus experienced greater losses in retinal function than eyes infected with the ΔPil mutant, but the differences were not always significant. Eyes infected with ΔPil or wild type B. cereus achieved similar degrees of severe inflammation. The results indicated that the intraocular growth of pilus-deficient B. cereus may have been better controlled, leading to a trend of greater retinal function in eyes infected with the pilus-deficient strain. Although this difference was not enough to significantly alter the severity of the inflammatory response, these results suggest a potential role for pili in protecting B. cereus from clearance during the early stages of endophthalmitis, which is a newly described virulence mechanism for this organism and this infection.
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Affiliation(s)
- Michelle C. Callegan
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA,Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 950 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA,Dean A. McGee Eye Institute, Oklahoma City Oklahoma USA,Corresponding author: DMEI PA-418, 608 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA. Phone: (405) 271-3674, Fax: (405) 271-8128,
| | - Salai Madhumathi Parkunan
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 950 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA
| | - C. Blake Randall
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA
| | - Phillip S. Coburn
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA
| | - Frederick C. Miller
- Department of Cell Biology, University of Oklahoma Health Sciences Center, 950 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA
| | - Austin L. LaGrow
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA
| | - Roger A. Astley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA
| | - Craig Land
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA
| | - So-Young Oh
- Department of Microbiology, University of Chicago, 920 East 58
| | - Olaf Schneewind
- Department of Microbiology, University of Chicago, 920 East 58
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100
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Simon L, Škraban J, Kyrpides NC, Woyke T, Shapiro N, Cleenwerck I, Vandamme P, Whitman WB, Trček J. Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater. Antonie van Leeuwenhoek 2017; 110:1189-1197. [PMID: 28555445 DOI: 10.1007/s10482-017-0891-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
Abstract
Strain 11T was isolated from water of an artificial lake accumulating industrial wastewater on the outskirts of Celje, Slovenia. Phenotypic characterisation showed strain 11T to be a Gram-stain positive, spore forming bacterium. The 16S rRNA gene sequence identified strain 11T as a member of the genus Paenibacillus, closely related to Paenibacillus alvei (96.2%). Genomic similarity with P. alvei 29T was 73.1% (gANI), 70.2% (ANIb), 86.7% (ANIm) and 21.7 ± 2.3% (GGDC). The DNA G+C content of strain 11T was determined to be 47.5%. The predominant menaquinone of strain 11T was identified as MK-7 and the major fatty acid as anteiso-C15:0. The peptidoglycan was found to contain meso-diaminopimelic acid. In contrast to its close relatives P. alvei DSM 29T, Paenibacillus apiarius DSM 5581T and Paenibacillus profundus NRIC 0885T, strain 11T was found to be able to ferment D-fructose, D-mannose and D-xylose. A draft genome of strain 11T contains a cluster of genes associated with type IV pilin synthesis usually found in clostridia, and only sporadically in other Gram-positive bacteria. Genotypic, chemotaxonomic, physiological and biochemical characteristics of strain 11T presented in this study support the creation of a novel species within the genus Paenibacillus, for which the name Paenibacillus aquistagni sp. nov. is proposed, with strain 11T (=ZIM B1027T =LMG 29561T =CCM 8679T ) as the type strain.
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Affiliation(s)
- Lučka Simon
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | - Jure Škraban
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | | | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia. .,Department of Biology, Faculty of Chemistry and Chemical Engineering, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia.
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