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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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52
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Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. J Phys Chem B 2020; 124:3283-3290. [DOI: 10.1021/acs.jpcb.0c00167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
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53
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Malik A, Kim YR, Jang IH, Hwang S, Oh DC, Kim SB. Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium. BMC Genomics 2020; 21:118. [PMID: 32013859 PMCID: PMC6998099 DOI: 10.1186/s12864-020-6468-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. RESULTS A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. CONCLUSIONS This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.
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Affiliation(s)
- Adeel Malik
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yu Ri Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - In Hee Jang
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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54
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Mu D, Luan Y, Wang L, Gao Z, Yang P, Jing S, Wang Y, Xiang H, Wang T, Wang D. The combination of salvianolic acid A with latamoxef completely protects mice against lethal pneumonia caused by methicillin-resistant Staphylococcus aureus. Emerg Microbes Infect 2020; 9:169-179. [PMID: 31969071 PMCID: PMC7006784 DOI: 10.1080/22221751.2020.1711817] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Staphylococcus aureus (S. aureus), especially methicillin-resistant Staphylococcus aureus (MRSA), is a major cause of pneumonia, resulting in severe morbidity and mortality in adults and children. Sortase A (SrtA), which mediates the anchoring of cell surface proteins in the cell wall, is an important virulence factor of S. aureus. Here, we found that salvianolic acid A (Sal A), which is a natural product that does not affect the growth of S. aureus, could inhibit SrtA activity (IC50 = 5.75 μg/ml) and repress the adhesion of bacteria to fibrinogen, the anchoring of protein A to cell wall, the biofilm formation, and the ability of S. aureus to invade A549 cells. Furthermore, in vivo studies demonstrated that Sal A treatment reduced inflammation and protected mice against lethal pneumonia caused by MRSA. More significantly, full protection (a survival rate of 100%) was achieved when Sal A was administered in combination with latamoxef. Together, these results indicate that Sal A could be developed into a promising therapeutic drug to combat MRSA infections while limiting resistance development.
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Affiliation(s)
- Dan Mu
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Yongxin Luan
- Department of Neurosurgery, First Hospital of Jilin University, Jilin University, Changchun, People's Republic of China
| | - Lin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Zeyuan Gao
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Panpan Yang
- Department of Pharmacology, College of Basic Medical Science, Jilin University, Changchun, People's Republic of China
| | - Shisong Jing
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Yanling Wang
- College of Animal Science, Jilin University, Changchun, People's Republic of China.,Qingdao Vland biological Limited co., LTD, Qingdao, People's Republic of China
| | - Hua Xiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, People's Republic of China
| | - Tiedong Wang
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Dacheng Wang
- College of Animal Science, Jilin University, Changchun, People's Republic of China
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55
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Wehrli PM, Uzelac I, Olsson T, Jacso T, Tietze D, Gottfries J. Discovery and development of substituted thiadiazoles as inhibitors of Staphylococcus aureus Sortase A. Bioorg Med Chem 2019; 27:115043. [PMID: 31420255 DOI: 10.1016/j.bmc.2019.115043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/08/2019] [Accepted: 08/06/2019] [Indexed: 12/27/2022]
Abstract
High-throughput screening of small-molecule libraries has led to the identification of thiadiazoles as a new class of inhibitors against Staphylococcus aureus sortase A (SrtA). N-(5-((4-nitrobenzyl)thio)-1,3,4-thiadiazol-2-yl)nicotinamide (IC50 = 3.8 µM) was identified as a potent inhibitor of SrtA after synthetic modification of hit compounds. Additional ligands developed in this study displayed affinities in the low micromolar range without affecting bacterial growth in vitro. The study also suggest a new mode of action through covalent binding to the active site cysteine.
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Affiliation(s)
- Patrick M Wehrli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Ivana Uzelac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Tomas Jacso
- Structure & Biophysics, Discovery Sciences, AstraZeneca R&D, Sweden; Early Discovery, Department of Biology, Nuevolution AB, Denmark
| | - Daniel Tietze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Gottfries
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
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56
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Maitz MF, Martins MCL, Grabow N, Matschegewski C, Huang N, Chaikof EL, Barbosa MA, Werner C, Sperling C. The blood compatibility challenge. Part 4: Surface modification for hemocompatible materials: Passive and active approaches to guide blood-material interactions. Acta Biomater 2019; 94:33-43. [PMID: 31226481 DOI: 10.1016/j.actbio.2019.06.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/29/2019] [Accepted: 06/13/2019] [Indexed: 12/22/2022]
Abstract
Biomedical devices in the blood flow disturb the fine-tuned balance of pro- and anti-coagulant factors in blood and vessel wall. Numerous technologies have been suggested to reduce coagulant and inflammatory responses of the body towards the device material, ranging from camouflage effects to permanent activity and further to a responsive interaction with the host systems. However, not all types of modification are suitable for all types of medical products. This review has a focus on application-oriented considerations of hemocompatible surface fittings. Thus, passive versus bioactive modifications are discussed along with the control of protein adsorption, stability of the immobilization, and the type of bioactive substance, biological or synthetic. Further considerations are related to the target system, whether enzymes or cells should be addressed in arterial or venous system, or whether the blood vessel wall is addressed. Recent developments like feedback controlled or self-renewing systems for drug release or addressing cellular regulation pathways of blood platelets and endothelial cells are paradigms for a generation of blood contacting devices, which are hemocompatible by cooperation with the host system. STATEMENT OF SIGNIFICANCE: This paper is part 4 of a series of 4 reviews discussing the problem of biomaterial associated thrombogenicity. The objective was to highlight features of broad agreement and provide commentary on those aspects of the problem that were subject to dispute. We hope that future investigators will update these reviews as new scholarship resolves the uncertainties of today.
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Affiliation(s)
- Manfred F Maitz
- Institute Biofunctional Polymer Materials, Max Bergmann Center of Biomaterials, Leibniz-Institut für Polymerforschung Dresden e.V., Dresden, Germany; Key Laboratory of Advanced Technology for Materials of Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - M Cristina L Martins
- i3S, Instituto de Investigação e Inovação em Saúde, Portugal; INEB, Instituto de Engenharia Biomédica, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Niels Grabow
- Institut für Biomedizinische Technik, Universitätsmedizin Rostock, Friedrich-Barnewitz-Str. 4, 18119 Rostock, Germany
| | - Claudia Matschegewski
- Institut für Biomedizinische Technik, Universitätsmedizin Rostock, Friedrich-Barnewitz-Str. 4, 18119 Rostock, Germany; Institute for ImplantTechnology and Biomaterials (IIB) e.V., Friedrich-Barnewitz-Str. 4, 18119 Rostock, Germany
| | - Nan Huang
- Key Laboratory of Advanced Technology for Materials of Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02115, United States; Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Circle, Boston, MA 02115, United States; Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Mário A Barbosa
- i3S, Instituto de Investigação e Inovação em Saúde, Portugal; INEB, Instituto de Engenharia Biomédica, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Carsten Werner
- Institute Biofunctional Polymer Materials, Max Bergmann Center of Biomaterials, Leibniz-Institut für Polymerforschung Dresden e.V., Dresden, Germany
| | - Claudia Sperling
- Institute Biofunctional Polymer Materials, Max Bergmann Center of Biomaterials, Leibniz-Institut für Polymerforschung Dresden e.V., Dresden, Germany
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57
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A comprehensive in silico analysis of sortase superfamily. J Microbiol 2019; 57:431-443. [DOI: 10.1007/s12275-019-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/22/2022]
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58
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Hatlem D, Trunk T, Linke D, Leo JC. Catching a SPY: Using the SpyCatcher-SpyTag and Related Systems for Labeling and Localizing Bacterial Proteins. Int J Mol Sci 2019; 20:E2129. [PMID: 31052154 PMCID: PMC6539128 DOI: 10.3390/ijms20092129] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/05/2023] Open
Abstract
The SpyCatcher-SpyTag system was developed seven years ago as a method for protein ligation. It is based on a modified domain from a Streptococcus pyogenes surface protein (SpyCatcher), which recognizes a cognate 13-amino-acid peptide (SpyTag). Upon recognition, the two form a covalent isopeptide bond between the side chains of a lysine in SpyCatcher and an aspartate in SpyTag. This technology has been used, among other applications, to create covalently stabilized multi-protein complexes, for modular vaccine production, and to label proteins (e.g., for microscopy). The SpyTag system is versatile as the tag is a short, unfolded peptide that can be genetically fused to exposed positions in target proteins; similarly, SpyCatcher can be fused to reporter proteins such as GFP, and to epitope or purification tags. Additionally, an orthogonal system called SnoopTag-SnoopCatcher has been developed from an S. pneumoniae pilin that can be combined with SpyCatcher-SpyTag to produce protein fusions with multiple components. Furthermore, tripartite applications have been produced from both systems allowing the fusion of two peptides by a separate, catalytically active protein unit, SpyLigase or SnoopLigase. Here, we review the current state of the SpyCatcher-SpyTag and related technologies, with a particular emphasis on their use in vaccine development and in determining outer membrane protein localization and topology of surface proteins in bacteria.
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Affiliation(s)
- Daniel Hatlem
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Thomas Trunk
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Dirk Linke
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Jack C Leo
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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59
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Megta AK, Mishra AK, Palva A, von Ossowski I, Krishnan V. Crystal structure of basal pilin SpaE reveals the molecular basis of its incorporation in the lactobacillar SpaFED pilus. J Struct Biol 2019; 207:74-84. [PMID: 31026587 DOI: 10.1016/j.jsb.2019.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 11/16/2022]
Abstract
For some Gram-positive genera and species, the long-extended and adhesive sortase-dependent pilus plays an essential role during host colonization, biofilm formation, and immune modulation. Lactobacillus rhamnosus GG is a gut-adapted commensal strain that harbors the operonic genes for the SpaCBA and SpaFED pili, both being comprised of three different protein subunits termed the backbone, tip, and basal pilins. Crystal structures of the backbone pilins (SpaA and SpaD) have recently been solved, and here we describe the high-resolution (1.5 Å) structural determination of the SpaE basal pilin. SpaE consists of two immunoglobulin-like CnaB domains, with each displaying a spontaneously formed internal isopeptide bond, though apparently slow forming in the N-terminal domain. Remarkably, SpaE contains an atypically lengthy unstructured C-terminal tail, along with an YPKN pilin motif peptide, which is normally reserved for backbone subunits. Based on our analysis of the crystal structure data, we provide a molecular model for the basal positioning of the SpaE pilin within the SpaFED pilus.
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Affiliation(s)
- Abhin Kumar Megta
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India; School of Biotechnology, KIIT University, Odisha 751024, India
| | - Arjun K Mishra
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Vengadesan Krishnan
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India.
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60
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Xu B, Zhang P, Zhou H, Sun Y, Tang J, Fan H. Identification of novel genes associated with anti-phagocytic functions in Streptococcus equi subsp. zooepidemicus. Vet Microbiol 2019; 233:28-38. [PMID: 31176409 DOI: 10.1016/j.vetmic.2019.04.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 01/13/2023]
Abstract
The anti-phagocytic abilities of bacteria often affect bacterial pathogenicity. Here, random mutant library of Streptococcus equi subsp. zooepidemicus (SEZ) was constructed using transposon mutagenesis. After careful screening, 30 transposon mutants with different transposon insertion sites were identified by conducting quantitative phagocytosis and insertion-site confirmation assays, whose anti-phagocytic abilities were significantly reduced relative to the wild-type strain. Insertion sites of 19 strains were monocistronic, including genes coding membrane proteins, transporters, and enzymes with unknown pathological function, such as sadM, adhP, purD, guaA, alpha-galactosidase coding gene, ABC transporter permease coding gene, metallo-beta-lactamase coding gene, and three secreted enzyme coding genes spuZ, slaB, and endoS, as well as known virulence factor coding genes, such as hasA and szM. The insertion sites of another 11 strains were polycistronic. We focused on four monocistronic-mutant strains: MhtpZ, MspuZ, MslaB, and MendoS. The anti-phagocytic abilities of not only the mutants that were precoincubated with the recombinant proteins, but also the complement strains were significantly more pronounced than those of all four corresponding mutants. The polyclonal antiserum against SlaB or EndoS also significantly decreased the anti-phagocytic capacity of wild-type SEZ. All four mutants exhibited significantly decreased viability in whole blood and reduced lethality in mice relative to the wild-type strain. Thus, we identified a variety of new anti-phagocytic factors, particularly multiple SEZ secreted enzymes. These factors are instrumental in the phagocytic resistance of SEZ in the absence of opsonin. Our results provide a framework for further studies of SEZ pathogenesis and relevant vaccine development for novel potential targets.
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Affiliation(s)
- Bin Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China; National Research Center of Veterinary Biologicals engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ping Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China; Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Hong Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yu Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jinsheng Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hongjie Fan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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61
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Sortases, Surface Proteins, and Their Roles in Staphylococcus aureus Disease and Vaccine Development. Microbiol Spectr 2019; 7. [PMID: 30737913 DOI: 10.1128/microbiolspec.psib-0004-2018] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Sortases cleave short peptide motif sequences at the C-terminal end of secreted surface protein precursors and either attach these polypeptides to the peptidoglycan of Gram-positive bacteria or promote their assembly into pilus structures that are also attached to peptidoglycan. Sortase A, the enzyme first identified in the human pathogen Staphylococcus aureus, binds LPXTG motif sorting signals, cleaves between threonine (T) and glycine (G) residues, and forms an acyl enzyme between its active-site cysteine thiol and the carboxyl group of threonine (T). Sortase A acyl enzyme is relieved by the nucleophilic attack of the cross bridge amino group within lipid II, thereby generating surface protein linked to peptidoglycan precursor. Such products are subsequently incorporated into the cell wall envelope by enzymes of the peptidoglycan synthesis pathway. Surface proteins linked to peptidoglycan may be released from the bacterial envelope to diffuse into host tissues and fulfill specific biological functions. S. aureus sortase A is essential for host colonization and for the pathogenesis of invasive diseases. Staphylococcal sortase-anchored surface proteins fulfill key functions during the infectious process, and vaccine-induced antibodies targeting surface proteins may provide protection against S. aureus. Alternatively, small-molecule inhibitors of sortase may be useful agents for the prevention of S. aureus colonization and invasive disease.
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62
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Micoli F, Costantino P, Adamo R. Potential targets for next generation antimicrobial glycoconjugate vaccines. FEMS Microbiol Rev 2018; 42:388-423. [PMID: 29547971 PMCID: PMC5995208 DOI: 10.1093/femsre/fuy011] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/13/2018] [Indexed: 12/21/2022] Open
Abstract
Cell surface carbohydrates have been proven optimal targets for vaccine development. Conjugation of polysaccharides to a carrier protein triggers a T-cell-dependent immune response to the glycan moiety. Licensed glycoconjugate vaccines are produced by chemical conjugation of capsular polysaccharides to prevent meningitis caused by meningococcus, pneumococcus and Haemophilus influenzae type b. However, other classes of carbohydrates (O-antigens, exopolysaccharides, wall/teichoic acids) represent attractive targets for developing vaccines. Recent analysis from WHO/CHO underpins alarming concern toward antibiotic-resistant bacteria, such as the so called ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) and additional pathogens such as Clostridium difficile and Group A Streptococcus. Fungal infections are also becoming increasingly invasive for immunocompromised patients or hospitalized individuals. Other emergencies could derive from bacteria which spread during environmental calamities (Vibrio cholerae) or with potential as bioterrorism weapons (Burkholderia pseudomallei and mallei, Francisella tularensis). Vaccination could aid reducing the use of broad-spectrum antibiotics and provide protection by herd immunity also to individuals who are not vaccinated. This review analyzes structural and functional differences of the polysaccharides exposed on the surface of emerging pathogenic bacteria, combined with medical need and technological feasibility of corresponding glycoconjugate vaccines.
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Affiliation(s)
- Francesca Micoli
- GSK Vaccines Institute for Global Health (GVGH), Via Fiorentina 1, 53100 Siena
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63
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Milles LF, Unterauer EM, Nicolaus T, Gaub HE. Calcium stabilizes the strongest protein fold. Nat Commun 2018; 9:4764. [PMID: 30420680 PMCID: PMC6232131 DOI: 10.1038/s41467-018-07145-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022] Open
Abstract
Staphylococcal pathogens adhere to their human targets with exceptional resilience to mechanical stress, some propagating force to the bacterium via small, Ig-like folds called B domains. We examine the mechanical stability of these folds using atomic force microscopy-based single-molecule force spectroscopy. The force required to unfold a single B domain is larger than 2 nN – the highest mechanostability of a protein to date by a large margin. B domains coordinate three calcium ions, which we identify as crucial for their extreme mechanical strength. When calcium is removed through chelation, unfolding forces drop by a factor of four. Through systematic mutations in the calcium coordination sites we can tune the unfolding forces from over 2 nN to 0.15 nN, and dissect the contribution of each ion to B domain mechanostability. Their extraordinary strength, rapid refolding and calcium-tunable force response make B domains interesting protein design targets. Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.
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Affiliation(s)
- Lukas F Milles
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
| | - Eduard M Unterauer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Thomas Nicolaus
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
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64
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van Hensbergen VP, Movert E, de Maat V, Lüchtenborg C, Le Breton Y, Lambeau G, Payré C, Henningham A, Nizet V, van Strijp JAG, Brügger B, Carlsson F, McIver KS, van Sorge NM. Streptococcal Lancefield polysaccharides are critical cell wall determinants for human Group IIA secreted phospholipase A2 to exert its bactericidal effects. PLoS Pathog 2018; 14:e1007348. [PMID: 30321240 PMCID: PMC6201954 DOI: 10.1371/journal.ppat.1007348] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 10/25/2018] [Accepted: 09/20/2018] [Indexed: 12/21/2022] Open
Abstract
Human Group IIA secreted phospholipase A2 (hGIIA) is an acute phase protein with bactericidal activity against Gram-positive bacteria. Infection models in hGIIA transgenic mice have suggested the importance of hGIIA as an innate defense mechanism against the human pathogens Group A Streptococcus (GAS) and Group B Streptococcus (GBS). Compared to other Gram-positive bacteria, GAS is remarkably resistant to hGIIA activity. To identify GAS resistance mechanisms, we exposed a highly saturated GAS M1 transposon library to recombinant hGIIA and compared relative mutant abundance with library input through transposon-sequencing (Tn-seq). Based on transposon prevalence in the output library, we identified nine genes, including dltA and lytR, conferring increased hGIIA susceptibility. In addition, seven genes conferred increased hGIIA resistance, which included two genes, gacH and gacI that are located within the Group A Carbohydrate (GAC) gene cluster. Using GAS 5448 wild-type and the isogenic gacI mutant and gacI-complemented strains, we demonstrate that loss of the GAC N-acetylglucosamine (GlcNAc) side chain in the ΔgacI mutant increases hGIIA resistance approximately 10-fold, a phenotype that is conserved across different GAS serotypes. Increased resistance is associated with delayed penetration of hGIIA through the cell wall. Correspondingly, loss of the Lancefield Group B Carbohydrate (GBC) rendered GBS significantly more resistant to hGIIA-mediated killing. This suggests that the streptococcal Lancefield antigens, which are critical determinants for streptococcal physiology and virulence, are required for the bactericidal enzyme hGIIA to exert its bactericidal function.
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Affiliation(s)
- Vincent P. van Hensbergen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Elin Movert
- Department of Experimental Medical Science, Section for Immunology, Lund University, Lund, Sweden
| | - Vincent de Maat
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States of America
| | - Gérard Lambeau
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Department of Biochemistry, Valbonne, France
| | - Christine Payré
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Department of Biochemistry, Valbonne, France
| | - Anna Henningham
- Department of Pediatrics and Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Jos A. G. van Strijp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Britta Brügger
- Heidelberg University, Biochemistry Center (BZH), Heidelberg, Germany
| | - Fredric Carlsson
- Department of Experimental Medical Science, Section for Immunology, Lund University, Lund, Sweden
- Department of Biology, Section for Molecular Cell Biology, Lund University, Lund, Sweden
| | - Kevin S. McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States of America
| | - Nina M. van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Qian Y, Zhang Y, Yu Y, Li Q, Guo G, Fu Y, Yao H, Lu C, Zhang W. SBP1 is an adhesion-associated factor without the involvement of virulence in Streptococcus suis serotype 2. Microb Pathog 2018; 122:90-97. [DOI: 10.1016/j.micpath.2018.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/22/2018] [Accepted: 06/06/2018] [Indexed: 11/29/2022]
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66
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Molecular strategy for blocking isopeptide bond formation in nascent pilin proteins. Proc Natl Acad Sci U S A 2018; 115:9222-9227. [PMID: 30150415 DOI: 10.1073/pnas.1807689115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria anchor to their host cells through their adhesive pili, which must resist the large mechanical stresses induced by the host as it attempts to dislodge the pathogens. The pili of gram-positive bacteria are constructed as a single polypeptide made of hundreds of pilin repeats, which contain intramolecular isopeptide bonds strategically located in the structure to prevent their unfolding under force, protecting the pilus from degradation by extant proteases and oxygen radicals. Here, we demonstrate the design of a short peptide that blocks the formation of the isopeptide bond present in the pilin Spy0128 from the human pathogen Streptococcus pyogenes, resulting in mechanically labile pilin domains. We use a combination of protein engineering and atomic-force microscopy force spectroscopy to demonstrate that the peptide blocks the formation of the native isopeptide bond and compromises the mechanics of the domain. While an intact Spy0128 is inextensible at any force, peptide-modified Spy0128 pilins readily unfold at very low forces, marking the abrogation of the intramolecular isopeptide bond as well as the absence of a stable pilin fold. We propose that isopeptide-blocking peptides could be further developed as a type of highly specific antiadhesive antibiotics to treat gram-positive pathogens.
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67
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Song Y, He JZ, Wang RK, Ma JZ, Zou L. Effect of SrtA on Interspecies Adherence of Oral Bacteria. Curr Med Sci 2018; 38:160-166. [PMID: 30074166 DOI: 10.1007/s11596-018-1860-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 12/05/2017] [Indexed: 02/05/2023]
Abstract
This study aimed to study whether the Sortase A (srtA) gene helps mediate coaggregation and co-adherence between Streptococcus mutans (S. mutans) and other salivary bacteria. S. mutans UA159 and srtA-deficient mutant served as "bait" in classical co-aggregation assays and membrane-based co-adherence assays were used to examine interactions of S. mutans with Fusobacterium nucleatum (F. nucleatum), Streptococcus mitis (S. mitis), Streptococcus gordonii (S. gordonii), Streptococcus sanguis (S. sanguis), Actinomyces naeslundii (A. naeslundii) and Lactobacillus. Co-adherence assays were also performed using unfractionated saliva from healthy individuals. Co-adhering partners of S. mutans were sensitively detected using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Both UA159 and its srtA-deficient mutant bound to F. nucleatum but not to any of the other five salivary bacteria. The srtA-deficient mutant showed lower co-adherence with F.nucleatum. The two S. mutans strains also showed similar co-adherence profiles against unfractionated salivary bacteria, except that UA159 S. mutans but not the srtA-deficient bound to a Neisseria sp. under the same conditions. Deleting srtA reduces the ability of S. mutans to bind to F.nucleatum, but it does not appear to significantly affect the binding profile of S. mutans to bulk salivary bacteria.
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Affiliation(s)
- Ying Song
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Conservation Dentistry and Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, 401147, China
| | - Jin-Zhi He
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Conservation Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Ren-Ke Wang
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, China.,Department of Conservation Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jing-Zhi Ma
- Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Ling Zou
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, 610041, China. .,Department of Conservation Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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68
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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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69
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Engineering E. coli cell surface in order to develop a one-step purification method for recombinant proteins. AMB Express 2018; 8:107. [PMID: 29961206 PMCID: PMC6026487 DOI: 10.1186/s13568-018-0638-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Sortases are enzymes mostly found in Gram-positive bacteria which cleave proteins site-specifically. This feature makes them a promising tool in molecular biology and biotechnology. In this study, using bacterial surface display of recombinant proteins and ability of sortase A in site-specifically cleavage of the amino acid sequences, a novel method for one-step purification of recombinant proteins was developed. Using computational program tools, a chimeric protein containing a metallothionein (mt) and chitin binding domain (ChBD) was attached to the C-terminal domain of the truncated outer membrane protein A (Lpp'-ompA) using sortase recognition site (amino acid residues: LPQTG) as a separator. The structure of the chimeric protein was simulated using molecular dynamics to determine if the LPQTG motif is accessible to the sortase active site. The designed chimeric protein was expressed and purified. The purified chimeric protein was also displayed on the surface of E. coli cells. Both purified chimeric protein and the E. coli cells displaying Lpp'-ompA-mt-ChBD carrier protein were then treated with sortase to evaluate the efficiency of sortase-mediated cleavage of purified chimeric protein as well as surface displayed-chimeric protein. It is shown that mt-ChBD protein was successfully cleaved and dissociated from Lpp'-ompA carrier and released into the medium after treatment with sortase in both recombinant protein and surface displayed-chimeric protein. The experimental results confirmed the molecular dynamics analysis results. The presented method could be regarded as a novel strategy for one step expression and purification of recombinant proteins.
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70
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Schönfelder J, Alonso-Caballero A, De Sancho D, Perez-Jimenez R. The life of proteins under mechanical force. Chem Soc Rev 2018; 47:3558-3573. [PMID: 29473060 DOI: 10.1039/c7cs00820a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Although much of our understanding of protein folding comes from studies of isolated protein domains in bulk, in the cellular environment the intervention of external molecular machines is essential during the protein life cycle. During the past decade single molecule force spectroscopy techniques have been extremely useful to deepen our understanding of these interventional molecular processes, as they allow for monitoring and manipulating mechanochemical events in individual protein molecules. Here, we review some of the critical steps in the protein life cycle, starting with the biosynthesis of the nascent polypeptide chain in the ribosome, continuing with the folding supported by chaperones and the translocation into different cell compartments, and ending with proteolysis in the proteasome. Along these steps, proteins experience molecular forces often combined with chemical transformations, affecting their folding and structure, which are measured or mimicked in the laboratory by the application of force with a single molecule apparatus. These mechanochemical reactions can potentially be used as targets for fighting against diseases. Inspired by these insightful experiments, we devise an outlook on the emerging field of mechanopharmacology, which reflects an alternative paradigm for drug design.
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71
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Marín E, Haesaert A, Padilla L, Adán J, Hernáez ML, Monteoliva L, Gil C. Unraveling Gardnerella vaginalis Surface Proteins Using Cell Shaving Proteomics. Front Microbiol 2018; 9:975. [PMID: 29867878 PMCID: PMC5962675 DOI: 10.3389/fmicb.2018.00975] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/25/2018] [Indexed: 12/17/2022] Open
Abstract
Gardnerella vaginalis is one of the main etiologic agents of bacterial vaginosis (BV). This infection is responsible for a wide range of public health costs and is associated with several adverse outcomes during pregnancy. Improving our understanding of G. vaginalis protein cell surface will assist in BV diagnosis. This study represents the first proteomic approach that has analyzed the exposed proteins on G. vaginalis cell surface using a shaving approach. The 261 G. vaginalis proteins identified using this approach were analyzed with bioinformatic tools to detect characteristic motifs from surface-exposed proteins, such as signal peptides (36 proteins), lipobox domains (17 proteins), LPXTG motifs (5 proteins) and transmembrane alpha-helices (66 proteins). One third of the identified proteins were found to have at least one typical motif of surface-exposed proteins. Furthermore, the subcellular location was examined using two predictors (PSORT and Gpos-mPLoc). These bioinformatic tools classified 17% of the identified proteins as surface-associated proteins. Interestingly, we identified 13 members of the ATP-binding cassette (ABC) superfamily, which were mainly involved in the translocation of various substrates across membranes. To validate the location of the G. vaginalis surface-exposed proteins, an immunofluorescence assay with antibodies against Escherichia coli GroEL was performed to reveal the extracellular location of the moonlighting GroEL. In addition, monoclonal antibodies (mAb) against G. vaginalis Cna protein were produced and used to validate the location of Cna on the surface of the G. vaginalis. These high affinity anti-Cna mAb represent a useful tool for the study of this pathogenic microorganism and the BV.
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Affiliation(s)
- Elvira Marín
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Annelies Haesaert
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Laura Padilla
- Health and Biomed Division, LEITAT Technological Center, Barcelona, Spain
| | - Jaume Adán
- Health and Biomed Division, LEITAT Technological Center, Barcelona, Spain
| | - María L Hernáez
- Unidad de Proteómica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucía Monteoliva
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Concha Gil
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.,Unidad de Proteómica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
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72
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Engholm DH, Kilian M, Goodsell DS, Andersen ES, Kjærgaard RS. A visual review of the human pathogen Streptococcus pneumoniae. FEMS Microbiol Rev 2018; 41:854-879. [PMID: 29029129 DOI: 10.1093/femsre/fux037] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
Abstract
Being the principal causative agent of bacterial pneumonia, otitis media, meningitis and septicemia, the bacterium Streptococcus pneumoniae is a major global health problem. To highlight the molecular basis of this problem, we have portrayed essential biological processes of the pneumococcal life cycle in eight watercolor paintings. The paintings are done to a consistent nanometer scale based on currently available data from structural biology and proteomics. In this review article, the paintings are used to provide a visual review of protein synthesis, carbohydrate metabolism, cell wall synthesis, cell division, teichoic acid synthesis, virulence, transformation and pilus synthesis based on the available scientific literature within the field of pneumococcal biology. Visualization of the molecular details of these processes reveals several scientific questions about how molecular components of the pneumococcal cell are organized to allow biological function to take place. By the presentation of this visual review, we intend to stimulate scientific discussion, aid in the generation of scientific hypotheses and increase public awareness. A narrated video describing the biological processes in the context of a whole-cell illustration accompany this article.
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Affiliation(s)
- Ditte Høyer Engholm
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Rutgers, the State University of New Jersey, NJ 08901, USA
| | - Ebbe Sloth Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark
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73
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Tsolis KC, Tsare EP, Orfanoudaki G, Busche T, Kanaki K, Ramakrishnan R, Rousseau F, Schymkowitz J, Rückert C, Kalinowski J, Anné J, Karamanou S, Klapa MI, Economou A. Comprehensive subcellular topologies of polypeptides in Streptomyces. Microb Cell Fact 2018; 17:43. [PMID: 29544487 PMCID: PMC5853079 DOI: 10.1186/s12934-018-0892-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. Results Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible. We first introduced a uniform, improved nomenclature that re-annotated the names of ~ 4000 proteins based on functional and structural information. Then protein localization was assigned de novo using prediction tools and edited by manual curation for 7494 proteins, including information for 183 proteins that resulted from a recent genome re-annotation and are not available in current databases. The S. lividans proteome was also linked with those of other model bacterial strains including Streptomyces coelicolor A3(2) and Escherichia coli K-12, based on protein homology, and can be accessed through an open web interface. Finally, experimental data derived from proteomics experiments have been incorporated and provide validation for protein existence or topology for 579 proteins. Proteomics also reveals proteins released from vesicles that bleb off the membrane. All export systems known in S. lividans are also presented and exported proteins assigned export routes, where known. Conclusions SToPSdb provides an updated and comprehensive protein localization annotation resource for S. lividans and other streptomycetes. It forms the basis for future linking to databases containing experimental data of proteomics, genomics and metabolomics studies for this organism. Electronic supplementary material The online version of this article (10.1186/s12934-018-0892-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantinos C Tsolis
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Evridiki-Pandora Tsare
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece.,Department of General Biology, School of Medicine, University of Patras, Patras, Greece
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology-FoRTH, P.O. Box 1385, Iraklio, Crete, Greece
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Katerina Kanaki
- Institute of Molecular Biology and Biotechnology-FoRTH, P.O. Box 1385, Iraklio, Crete, Greece
| | - Reshmi Ramakrishnan
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Spyridoula Karamanou
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Maria I Klapa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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74
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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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75
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Wagachchi D, Tsai JYC, Chalmers C, Blanchett S, Loh JMS, Proft T. PilVax - a novel peptide delivery platform for the development of mucosal vaccines. Sci Rep 2018; 8:2555. [PMID: 29416095 PMCID: PMC5803258 DOI: 10.1038/s41598-018-20863-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/25/2018] [Indexed: 02/02/2023] Open
Abstract
Peptide vaccines are an attractive strategy to engineer the induction of highly targeted immune responses and avoid potentially allergenic and/or reactogenic protein regions. However, peptides by themselves are often unstable and poorly immunogenic, necessitating the need for an adjuvant and a specialised delivery system. We have developed a novel peptide delivery platform (PilVax) that allows the presentation of a stabilised and highly amplified peptide as part of the group A streptococcus serotype M1 pilus structure (PilM1) on the surface of the non-pathogenic bacterium Lactococcus lactis. To show proof of concept, we have successfully inserted the model peptide Ova324–339 into 3 different loop regions of the backbone protein Spy0128, which resulted in the assembly of the pilus containing large numbers of peptide on the surface of L. lactis. Intranasal immunisation of mice with L. lactis PilM1-Ova generated measurable Ova-specific systemic and mucosal responses (IgA and IgG). Furthermore, we show that multiple peptides can be inserted into the PilVax platform and that peptides can also be incorporated into structurally similar, but antigenically different pilus structures. PilVax may be useful as a cost-effective platform for the development of peptide vaccines against a variety of important human pathogens.
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Affiliation(s)
- Dasun Wagachchi
- Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, 1023, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1023, New Zealand
| | - Jia-Yun C Tsai
- Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, 1023, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1023, New Zealand
| | - Callum Chalmers
- Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, 1023, New Zealand
| | - Sam Blanchett
- Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, 1023, New Zealand
| | - Jacelyn M S Loh
- Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, 1023, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1023, New Zealand.
| | - Thomas Proft
- Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, 1023, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1023, New Zealand.
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76
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Mercier-Bonin M, Chapot-Chartier MP. Surface Proteins of Lactococcus lactis: Bacterial Resources for Muco-adhesion in the Gastrointestinal Tract. Front Microbiol 2017; 8:2247. [PMID: 29218032 PMCID: PMC5703838 DOI: 10.3389/fmicb.2017.02247] [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: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 01/13/2023] Open
Abstract
Food and probiotic bacteria, in particular lactic acid bacteria, are ingested in large amounts by humans and are part of the transient microbiota which is increasingly considered to be able to impact the resident microbiota and thus possibly the host health. The lactic acid bacterium Lactococcus lactis is extensively used in starter cultures to produce dairy fermented food. Also because of a generally recognized as safe status, L. lactis has been considered as a possible vehicle to deliver in vivo therapeutic molecules with anti-inflammatory properties in the gastrointestinal tract. One of the key factors that may favor health effects of beneficial bacteria to the host is their capacity to colonize transiently the gut, notably through close interactions with mucus, which covers and protects the intestinal epithelium. Several L. lactis strains have been shown to exhibit mucus-binding properties and bacterial surface proteins have been identified as key determinants of such capacity. In this review, we describe the different types of surface proteins found in L. lactis, with a special focus on mucus-binding proteins and pili. We also review the different approaches used to investigate the adhesion of L. lactis to mucus, and particularly to mucins, one of its major components, and we present how these approaches allowed revealing the role of surface proteins in muco-adhesion.
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Affiliation(s)
- Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
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77
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The Staphylococcus aureus Cell Wall-Anchored Protein Clumping Factor A Is an Important T Cell Antigen. Infect Immun 2017; 85:IAI.00549-17. [PMID: 28947645 PMCID: PMC5695125 DOI: 10.1128/iai.00549-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus aureus has become increasingly resistant to antibiotics, and vaccines offer a potential solution to this epidemic of antimicrobial resistance. Targeting of specific T cell subsets is now considered crucial for next-generation anti-S. aureus vaccines; however, there is a paucity of information regarding T cell antigens of S. aureus. This study highlights the importance of cell wall-anchored proteins as human CD4+ T cell activators capable of driving antigen-specific Th1 and Th17 cell activation. Clumping factor A (ClfA), which contains N1, N2, and N3 binding domains, was found to be a potent human T cell activator. We further investigated which subdomains of ClfA were involved in T cell activation and found that the full-length ClfA N123 and N23 were potent Th1 and Th17 activators. Interestingly, the N1 subdomain was capable of exclusively activating Th1 cells. Furthermore, when these subdomains were used in a model vaccine, N23 and N1 offered Th1- and Th17-mediated systemic protection in mice upon intraperitoneal challenge. Overall, however, full-length ClfA N123 is required for maximal protection both locally and systemically.
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78
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Molecular Mechanisms of the Binding and Specificity of Streptococcus Pneumoniae Sortase C Enzymes for Pilin Subunits. Sci Rep 2017; 7:13119. [PMID: 29030637 PMCID: PMC5640630 DOI: 10.1038/s41598-017-13135-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/19/2017] [Indexed: 02/05/2023] Open
Abstract
Pili are elongated structures that protrude from bacteria and increase their virulence. The Streptococcus pnuenomae pilus island 1 pili are composed of three subunits, RrgA, RrgB, and RrgC, and are assembled by three class C sortase C (SrtC) enzymes: SrtC-1, SrtC-2, and SrtC-3. Pilin subunits are recognized by SrtC proteins through a pentapeptide sorting signal, and while previous studies have sought to characterize the selectivities of SrtC isoforms for these subunits, the molecular mechanisms underlying these interactions remain unclear. Here, we report a series of molecular dynamics simulations of each SrtC enzyme with the sorting signals of RrgA, RrgB, and RrgC to determine the structural and thermodynamic basis of pilin recognition. Results show that, in accordance with previous studies, both SrtC-1 and SrtC-3 are selective for RrgB, while SrtC-2 is selective for RrgA. This specificity is tuned by the sorting signal binding conformation in which the first two residue sidechains complement hydrophobic residues around the active site, while the third residue projects away from the catalytic triad and makes specific interactions based on its charge and reach. Together, these results provided atomic-scale descriptions of the SrtC substrate selectivity mechanisms and extend the emerging model of pilin construction in S. pnuenomae.
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79
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Suliman M, Santosh V, Seegar TCM, Dalton AC, Schultz KM, Klug CS, Barton WA. Directed evolution provides insight into conformational substrate sampling by SrtA. PLoS One 2017; 12:e0184271. [PMID: 28859178 PMCID: PMC5578623 DOI: 10.1371/journal.pone.0184271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/21/2017] [Indexed: 11/19/2022] Open
Abstract
The Sortase family of transpeptidases are found in numerous gram-positive bacteria and involved in divergent physiological processes including anchoring of surface proteins to the cell wall as well as pili assembly. As essential proteins, sortase enzymes have been the focus of considerable interest for the development of novel anti-microbials, however, more recently their function as unique transpeptidases has been exploited for the synthesis of novel bio-conjugates. Yet, for synthetic purposes, SrtA-mediated conjugation suffers from the enzyme's inherently poor catalytic efficiency. Therefore, to identify SrtA variants with improved catalytic efficiency, we used directed evolution to select a catalytically enhanced SrtA enzyme. An analysis of improved SrtA variants in the context of sequence conservation, NMR and x-ray crystal structures, and kinetic data suggests a novel mechanism for catalysis involving large conformational changes that delivers substrate to the active site pocket. Indeed, using DEER-EPR spectroscopy, we reveal that upon substrate binding, SrtA undergoes a large scissors-like conformational change that simultaneously translates the sort-tag substrate to the active site in addition to repositioning key catalytic residues for esterification. A better understanding of Sortase dynamics will significantly enhance future engineering and drug discovery efforts.
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Affiliation(s)
- Muna Suliman
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Vishaka Santosh
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Tom C. M. Seegar
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Annamarie C. Dalton
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kathryn M. Schultz
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Candice S. Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - William A. Barton
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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80
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Sabulski MJ, Pidgeon SE, Pires MM. Immuno-targeting of Staphylococcus aureus via surface remodeling complexes. Chem Sci 2017; 8:6804-6809. [PMID: 29147504 PMCID: PMC5643955 DOI: 10.1039/c7sc02721d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/20/2017] [Indexed: 12/28/2022] Open
Abstract
Agents with novel mechanisms of action are needed to complement traditional antibiotics. Towards these goals, we have exploited the surface-homing properties of vancomycin to tag the surface of Gram-positive pathogens with immune cell attractants in two unique modes. First, vancomycin was conjugated to the small molecule hapten 2,4-dinitrophenol (DNP) to promote bacterial opsonization. Second, we built on these results by improving the tagging specificity and mechanism of incorporation by coupling it to a sortase A substrate peptide. We demonstrated, for the first time, that the surface of Staphylococcus aureus (S. aureus) can be metabolically labeled in live Caenorhabditis elegans hosts. These constructs represent a class of promising narrow-spectrum agents that target S. aureus for opsonization and establish a new surface labeling modality in live host organisms, which should be a powerful tool in dissecting features of host-pathogen interactions.
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Affiliation(s)
- Mary J Sabulski
- Department of Chemistry , Lehigh University , 6 E Packer Ave. , Bethlehem , PA 18015 , USA .
| | - Sean E Pidgeon
- Department of Chemistry , Lehigh University , 6 E Packer Ave. , Bethlehem , PA 18015 , USA .
| | - Marcos M Pires
- Department of Chemistry , Lehigh University , 6 E Packer Ave. , Bethlehem , PA 18015 , USA .
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81
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Pidgeon SE, Pires MM. Cell Wall Remodeling of Staphylococcus aureus in Live Caenorhabditis elegans. Bioconjug Chem 2017; 28:2310-2315. [DOI: 10.1021/acs.bioconjchem.7b00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sean E. Pidgeon
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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82
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Steward KF, Robinson C, Maskell DJ, Nenci C, Waller AS. Investigation of the Fim1 putative pilus locus of Streptococcus equi subspecies equi. MICROBIOLOGY-SGM 2017; 163:1217-1228. [PMID: 28749324 DOI: 10.1099/mic.0.000506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Gram-positive bacterium Streptococcus equi subspecies equi (S. equi) is the causative agent of strangles, among the most frequently diagnosed infectious diseases of horses worldwide. Genome analysis of S. equi strain 4047 (Se4047) identified a putative operon, Fim1, with similarity to the pilus loci of other Gram-positive bacteria. The Fim1 locus was present in all strains of S. equi and its close relative S. equi subspecies zooepidemicus (S. zooepidemicus) that have been studied to date. In this study we provide evidence that the putative structural pilus proteins, SEQ_0936 and CNE, are produced on the cell surface during in vitro growth and in vivo infection. Although the proteins encoded within the Fim1 locus are not essential for attachment or biofilm formation, over-transcription of SEQ_0936 and CNE enhanced attachment to equine tissue in vitro. Our data suggest that whilst the Fim1 locus does not produce a polymerized pilus structure, the products of the Fim1 locus may fulfil an adhesive function. The putative pilus-associated regulator, tetR, which contains a nonsense mutation in S. equi, was able to regulate transcription of the Fim1 locus following repair and over-transcription, confirming its predicted role in the operon.
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Affiliation(s)
- Karen Frances Steward
- Centre of Preventative Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
| | - Carl Robinson
- Centre of Preventative Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Chiara Nenci
- Elanco Animal Health, c/o Novartis Animal Health, Inc., Schwarzwaldallee 215, 4058 Basel, Swizerland
| | - Andrew Stephen Waller
- Centre of Preventative Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
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83
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von Ossowski I. Novel Molecular Insights about Lactobacillar Sortase-Dependent Piliation. Int J Mol Sci 2017; 18:ijms18071551. [PMID: 28718795 PMCID: PMC5536039 DOI: 10.3390/ijms18071551] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 01/09/2023] Open
Abstract
One of the more conspicuous structural features that punctuate the outer cell surface of certain bacterial Gram-positive genera and species is the sortase-dependent pilus. As these adhesive and variable-length protrusions jut outward from the cell, they provide a physically expedient and useful means for the initial contact between a bacterium and its ecological milieu. The sortase-dependent pilus displays an elongated macromolecular architecture consisting of two to three types of monomeric protein subunits (pilins), each with their own specific function and location, and that are joined together covalently by the transpeptidyl activity of a pilus-specific C-type sortase enzyme. Sortase-dependent pili were first detected among the Gram-positive pathogens and subsequently categorized as an essential virulence factor for host colonization and tissue invasion by these harmful bacteria. However, the sortase-dependent pilus was rebranded as also a niche-adaptation factor after it was revealed that “friendly” Gram-positive commensals exhibit the same kind of pilus structures, which includes two contrasting gut-adapted species from the Lactobacillus genus, allochthonous Lactobacillus rhamnosus and autochthonous Lactobacillus ruminis. This review will highlight and discuss what has been learned from the latest research carried out and published on these lactobacillar pilus types.
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Affiliation(s)
- Ingemar von Ossowski
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki FIN-00014, Finland.
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84
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Cavallari M. Rapid and Direct VHH and Target Identification by Staphylococcal Surface Display Libraries. Int J Mol Sci 2017; 18:ijms18071507. [PMID: 28704956 PMCID: PMC5535997 DOI: 10.3390/ijms18071507] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 01/01/2023] Open
Abstract
Unbiased and simultaneous identification of a specific antibody and its target antigen has been difficult without prior knowledge of at least one interaction partner. Immunization with complex mixtures of antigens such as whole organisms and tissue extracts including tumoral ones evokes a highly diverse immune response. During such a response, antibodies are generated against a variety of epitopes in the mixture. Here, we propose a surface display design that is suited to simultaneously identify camelid single domain antibodies and their targets. Immune libraries of single-domain antigen recognition fragments from camelid heavy chain-only antibodies (VHH) were attached to the peptidoglycan of Gram-positive Staphylococcus aureus employing its endogenous housekeeping sortase enzyme. The sortase transpeptidation reaction covalently attached the VHH to the bacterial peptidoglycan. The reversible nature of the reaction allowed the recovery of the VHH from the bacterial surface and the use of the VHH in downstream applications. These staphylococcal surface display libraries were used to rapidly identify VHH as well as their targets by immunoprecipitation (IP). Our novel bacterial surface display platform was stable under harsh screening conditions, allowed fast target identification, and readily permitted the recovery of the displayed VHH for downstream analysis.
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Affiliation(s)
- Marco Cavallari
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestrasse 18, 79104 Freiburg, Germany.
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85
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Probing the potential of CnaB-type domains for the design of tag/catcher systems. PLoS One 2017; 12:e0179740. [PMID: 28654665 PMCID: PMC5487036 DOI: 10.1371/journal.pone.0179740] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 06/02/2017] [Indexed: 01/06/2023] Open
Abstract
Building proteins into larger, post-translational assemblies in a defined and stable way is still a challenging task. A promising approach relies on so-called tag/catcher systems that are fused to the proteins of interest and allow a durable linkage via covalent intermolecular bonds. Tags and catchers are generated by splitting protein domains that contain intramolecular isopeptide or ester bonds that form autocatalytically under physiological conditions. There are already numerous biotechnological and medical applications that demonstrate the usefulness of covalent linkages mediated by these systems. Additional covalent tag/catcher systems would allow creating more complex and ultra-stable protein architectures and networks. Two of the presently available tag/catcher systems were derived from closely related CnaB-domains of Streptococcus pyogenes and Streptococcus dysgalactiae proteins. However, it is unclear whether domain splitting is generally tolerated within the CnaB-family or only by a small subset of these domains. To address this point, we have selected a set of four CnaB domains of low sequence similarity and characterized the resulting tag/catcher systems by computational and experimental methods. Experimental testing for intermolecular isopeptide bond formation demonstrated two of the four systems to be functional. For these two systems length and sequence variations of the peptide tags were investigated revealing only a relatively small effect on the efficiency of the reaction. Our study suggests that splitting into tag and catcher moieties is tolerated by a significant portion of the naturally occurring CnaB-domains, thus providing a large reservoir for the design of novel tag/catcher systems.
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86
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Jacobitz AW, Kattke MD, Wereszczynski J, Clubb RT. Sortase Transpeptidases: Structural Biology and Catalytic Mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:223-264. [PMID: 28683919 DOI: 10.1016/bs.apcsb.2017.04.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent because of its ability to ligate biomolecules together in vitro via a covalent peptide bond. Here we review what is known about the structures and catalytic mechanism of sortase enzymes. Based on their primary sequences, most sortase homologs can be classified into six distinct subfamilies, called class A-F enzymes. Atomic structures reveal unique, class-specific variations that support alternate substrate specificities, while structures of sortase enzymes bound to sorting signal mimics shed light onto the molecular basis of substrate recognition. The results of computational studies are reviewed that provide insight into how key reaction intermediates are stabilized during catalysis, as well as the mechanism and dynamics of substrate recognition. Lastly, the reported in vitro activities of sortases are compared, revealing that the transpeptidation activity of SaSrtA is at least 20-fold faster than other sortases that have thus far been characterized. Together, the results of the structural, computational, and biochemical studies discussed in this review begin to reveal how sortases decorate the microbial surface with proteins and pili, and may facilitate ongoing efforts to discover therapeutically useful small molecule inhibitors.
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Affiliation(s)
- Alex W Jacobitz
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Michele D Kattke
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Jeff Wereszczynski
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - Robert T Clubb
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States.
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87
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Moonens K, Remaut H. Evolution and structural dynamics of bacterial glycan binding adhesins. Curr Opin Struct Biol 2017; 44:48-58. [DOI: 10.1016/j.sbi.2016.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 01/25/2023]
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88
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Burke HM, McSweeney L, Scanlan EM. Exploring chemoselective S-to-N acyl transfer reactions in synthesis and chemical biology. Nat Commun 2017; 8:15655. [PMID: 28537277 PMCID: PMC5458133 DOI: 10.1038/ncomms15655] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/13/2017] [Indexed: 12/16/2022] Open
Abstract
S -to-N acyl transfer is a high-yielding chemoselective process for amide bond formation. It is widely utilized by chemists for synthetic applications, including peptide and protein synthesis, chemical modification of proteins, protein-protein ligation and the development of probes and molecular machines. Recent advances in our understanding of S -to-N acyl transfer processes in biology and innovations in methodology for thioester formation and desulfurization, together with an extension of the size of cyclic transition states, have expanded the boundaries of this process well beyond peptide ligation. As the field develops, this chemistry will play a central role in our molecular understanding of Biology. The conversion of thioesters to amides via acyl transfer has become one of the most important synthetic techniques for the chemical synthesis and modification of proteins. This review discusses this S-to-N acyl transfer process, and highlights some of the key applications across chemistry and biology.
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Affiliation(s)
- Helen M. Burke
- School of Chemistry, Trinity College Dublin, Dublin D2, Ireland
| | | | - Eoin M. Scanlan
- School of Chemistry, Trinity College Dublin, Dublin D2, Ireland
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89
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Khare B, V L Narayana S. Pilus biogenesis of Gram-positive bacteria: Roles of sortases and implications for assembly. Protein Sci 2017; 26:1458-1473. [PMID: 28493331 DOI: 10.1002/pro.3191] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/26/2022]
Abstract
Successful adherence, colonization, and survival of Gram-positive bacteria require surface proteins, and multiprotein assemblies called pili. These surface appendages are attractive pharmacotherapeutic targets and understanding their assembly mechanisms is essential for identifying a new class of 'anti-infectives' that do not elicit microbial resistance. Molecular details of the Gram-negative pilus assembly are available indepth, but the Gram-positive pilus biogenesis is still an emerging field and investigations continue to reveal novel insights into this process. Pilus biogenesis in Gram-positive bacteria is a biphasic process that requires enzymes called pilus-sortases for assembly and a housekeeping sortase for covalent attachment of the assembled pilus to the peptidoglycan cell wall. Emerging structural and functional data indicate that there are at least two groups of Gram-positive pili, which require either the Class C sortase or Class B sortase in conjunction with LepA/SipA protein for major pilin polymerization. This observation suggests two distinct modes of sortase-mediated pilus biogenesis in Gram-positive bacteria. Here we review the structural and functional biology of the pilus-sortases from select streptococcal pilus systems and their role in Gram-positive pilus assembly.
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Affiliation(s)
- Baldeep Khare
- Center for Structural Biology, School of Optometry, University of Alabama at Birmingham, Birmingham, USA
| | - Sthanam V L Narayana
- Center for Structural Biology, School of Optometry, University of Alabama at Birmingham, Birmingham, USA
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90
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Tso D, Peebles CL, Maurer JB, Duda RL, Hendrix RW. On the catalytic mechanism of bacteriophage HK97 capsid crosslinking. Virology 2017; 506:84-91. [PMID: 28359902 DOI: 10.1016/j.virol.2017.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
Abstract
During maturation of the phage HK97 capsid, each of the 415 capsid subunits forms covalent bonds to neighboring subunits, stabilizing the capsid. Crosslinking is catalyzed not by a separate enzyme but by subunits of the assembled capsid in response to conformational rearrangements during maturation. This report investigates the catalytic mechanism. Earlier work established that the crosslinks are isopeptide (amide) bonds between side chains of a lysine on one subunit and an asparagine on another subunit, aided by a catalytic glutamate on a third subunit. The mature capsid structure suggests that the reaction may be facilitated by the arrival of a valine with the lysine to complete a hydrophobic pocket surrounding the glutamate, lysine and asparagine. We show that this valine has an essential role for efficient crosslinking, and that any of six other amino acids can successfully substitute for valine. Evidently none of the remaining 13 amino acids will work.
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Affiliation(s)
- DanJu Tso
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Craig L Peebles
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joshua B Maurer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert L Duda
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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91
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Chalupowicz L, Barash I, Reuven M, Dror O, Sharabani G, Gartemann K, Eichenlaub R, Sessa G, Manulis‐Sasson S. Differential contribution of Clavibacter michiganensis ssp. michiganensis virulence factors to systemic and local infection in tomato. MOLECULAR PLANT PATHOLOGY 2017; 18:336-346. [PMID: 26992141 PMCID: PMC6638269 DOI: 10.1111/mpp.12400] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 05/03/2023]
Abstract
Clavibacter michiganensis ssp. michiganensis (Cmm) causes substantial economic losses in tomato production worldwide. The disease symptoms observed in plants infected systemically by Cmm are wilting and canker on the stem, whereas blister-like spots develop in locally infected leaves. A wide repertoire of serine proteases and cell wall-degrading enzymes has been implicated in the development of wilt and canker symptoms. However, virulence factors involved in the formation of blister-like spots, which play an important role in Cmm secondary spread in tomato nurseries, are largely unknown. Here, we demonstrate that Cmm virulence factors play different roles during blister formation relative to wilting. Inoculation with a green fluorescent protein (GFP)-labelled Cmm382 indicates that penetration occurs mainly through trichomes. When spray inoculated on tomato leaves, the wild-type Cmm382 and Cmm100 (lacking plasmids pCM1 and pCM2) strains form blister-like spots on leaves, whereas Cmm27 (lacking the chp/tomA pathogenicity island) is non-pathogenic, indicating that plasmid-borne genes, which have a crucial role in wilting, are not required for blister formation. Conversely, mutations in chromosomal genes encoding serine proteases (chpC and sbtA), cell wall-degrading enzymes (pgaA and endX/Y), a transcriptional regulator (vatr2), a putative perforin (perF) and a putative sortase (srtA) significantly affect disease incidence and the severity of blister formation. The transcript levels of these genes, as measured by quantitative reverse transcription-polymerase chain reaction, showed that, during blister formation, they are expressed early at 8-16 h after inoculation, whereas, during wilting, they are expressed after 24-72 h or expressed at low levels. Plant gene expression studies suggest that chpC is involved in the suppression of host defence.
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Affiliation(s)
- Laura Chalupowicz
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
| | - Isaac Barash
- Department of Molecular Biology and Ecology of Plants, Faculty of Life SciencesTel Aviv UniversityTel Aviv69978Israel
| | - Michal Reuven
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
| | - Orit Dror
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
| | - Galit Sharabani
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
| | - Karl‐Heinz Gartemann
- Department of Genetechnology/MicrobiologyUniversity of BielefeldBielefeld33501Germany
| | - Rudolf Eichenlaub
- Department of Genetechnology/MicrobiologyUniversity of BielefeldBielefeld33501Germany
| | - Guido Sessa
- Department of Molecular Biology and Ecology of Plants, Faculty of Life SciencesTel Aviv UniversityTel Aviv69978Israel
| | - Shulamit Manulis‐Sasson
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
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92
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Raeeszadeh-Sarmazdeh M, Parthasarathy R, Boder ET. Fine-tuning sortase-mediated immobilization of protein layers on surfaces using sequential deprotection and coupling. Biotechnol Prog 2017; 33:824-831. [PMID: 28218499 DOI: 10.1002/btpr.2449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/08/2017] [Indexed: 12/23/2022]
Abstract
Increasing interest in protein immobilization on surfaces has heightened the need for techniques enabling layer-by-layer protein attachment. Here, we report a technique for controlling enzyme-mediated immobilization of layers of protein on the surface using a genetically encoded protecting group. An enterokinase-cleavable peptide sequence was inserted at the N-terminus of bifunctional fluorescent proteins containing Sortase A substrate recognition tags at both ends to control Sortase A-mediated protein immobilization on the surface layer-by-layer. Efficient, sequential immobilization of a second layer of protein using Sortase A required removal of the N-terminal protecting group, suggesting the method enables multilayer synthesis using cyclic deprotection and coupling steps. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:824-831, 2017.
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Affiliation(s)
| | | | - Eric T Boder
- Dept. of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996
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93
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Bonnet J, Cartannaz J, Tourcier G, Contreras-Martel C, Kleman JP, Morlot C, Vernet T, Di Guilmi AM. Autocatalytic association of proteins by covalent bond formation: a Bio Molecular Welding toolbox derived from a bacterial adhesin. Sci Rep 2017; 7:43564. [PMID: 28252635 PMCID: PMC5333627 DOI: 10.1038/srep43564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/25/2017] [Indexed: 11/26/2022] Open
Abstract
Unusual intramolecular cross-links present in adhesins from Gram-positive bacteria have been used to develop a generic process amenable to biotechnology applications. Based on the crystal structure of RrgA, the Streptococcus pneumoniae pilus adhesin, we provide evidence that two engineered protein fragments retain their ability to associate covalently with high specificity, in vivo and in vitro, once isolated from the parent protein. We determined the optimal conditions for the assembly of the complex and we solved its crystal structure at 2 Å. Furthermore, we demonstrate biotechnological applications related to antibody production, nanoassembly and cell-surface labeling based on this process we named Bio Molecular Welding.
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Affiliation(s)
- J Bonnet
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - J Cartannaz
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - G Tourcier
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - C Contreras-Martel
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - J P Kleman
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - C Morlot
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - T Vernet
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - A M Di Guilmi
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
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94
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Egan AJF, Cleverley RM, Peters K, Lewis RJ, Vollmer W. Regulation of bacterial cell wall growth. FEBS J 2017; 284:851-867. [PMID: 27862967 DOI: 10.1111/febs.13959] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/28/2016] [Accepted: 11/09/2016] [Indexed: 12/19/2022]
Abstract
During growth and propagation, a bacterial cell enlarges and subsequently divides its peptidoglycan (PG) sacculus, a continuous mesh-like layer that encases the cell membrane to confer mechanical strength and morphological robustness. The mechanism of sacculus growth, how it is regulated and how it is coordinated with other cellular processes is poorly understood. In this article, we will discuss briefly the current knowledge of how cell wall synthesis is regulated, on multiple levels, from both sides of the cytoplasmic membrane. According to the current knowledge, cytosolic scaffolding proteins connect PG synthases with cytoskeletal elements, and protein phosphorylation regulates cell wall growth in Gram-positive species. PG-active enzymes engage in multiple protein-protein interactions within PG synthesis multienzyme complexes, and some of the interactions modulate activities. PG synthesis is also regulated by central metabolism, and by PG maturation through the action of PG hydrolytic enzymes. Only now are we beginning to appreciate how these multiple levels of regulating PG synthesis enable the cell to propagate robustly with a defined cell shape under different and variable growth conditions.
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Affiliation(s)
- Alexander J F Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK
| | - Robert M Cleverley
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK
| | - Richard J Lewis
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK
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95
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van Harten RM, Willems RJL, Martin NI, Hendrickx APA. Multidrug-Resistant Enterococcal Infections: New Compounds, Novel Antimicrobial Therapies? Trends Microbiol 2017; 25:467-479. [PMID: 28209400 DOI: 10.1016/j.tim.2017.01.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/14/2016] [Accepted: 01/18/2017] [Indexed: 02/08/2023]
Abstract
Over the past two decades infections due to antibiotic-resistant bacteria have escalated world-wide, affecting patient morbidity, mortality, and health care costs. Among these bacteria, Enterococcus faecium and Enterococcus faecalis represent opportunistic nosocomial pathogens that cause difficult-to-treat infections because of intrinsic and acquired resistance to a plethora of antibiotics. In recent years, a number of novel antimicrobial compound classes have been discovered and developed that target Gram-positive bacteria, including E. faecium and E. faecalis. These new antibacterial agents include teixobactin (targeting lipid II and lipid III), lipopeptides derived from nisin (targeting lipid II), dimeric vancomycin analogues (targeting lipid II), sortase transpeptidase inhibitors (targeting the sortase enzyme), alanine racemase inhibitors, lipoteichoic acid synthesis inhibitors (targeting LtaS), various oxazolidinones (targeting the bacterial ribosome), and tarocins (interfering with teichoic acid biosynthesis). The targets of these novel compounds and mode of action make them very promising for further antimicrobial drug development and future treatment of Gram-positive bacterial infections. Here we review current knowledge of the most favorable anti-enterococcal compounds along with their implicated modes of action and efficacy in animal models to project their possible future use in the clinical setting.
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Affiliation(s)
- Roel M van Harten
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.
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96
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Abstract
Bacterial pathogens utilize a multitude of methods to invade mammalian hosts, damage tissue sites, and thwart the immune system from responding. One essential component of these strategies for many bacterial pathogens is the secretion of proteins across phospholipid membranes. Secreted proteins can play many roles in promoting bacterial virulence, from enhancing attachment to eukaryotic cells, to scavenging resources in an environmental niche, to directly intoxicating target cells and disrupting their functions. Many pathogens use dedicated protein secretion systems to secrete virulence factors from the cytosol of the bacteria into host cells or the host environment. In general, bacterial protein secretion apparatuses can be divided into classes, based on their structures, functions, and specificity. Some systems are conserved in all classes of bacteria and secrete a broad array of substrates, while others are only found in a small number of bacterial species and/or are specific to only one or a few proteins. In this chapter, we review the canonical features of several common bacterial protein secretion systems, as well as their roles in promoting the virulence of bacterial pathogens. Additionally, we address recent findings that indicate that the innate immune system of the host can detect and respond to the presence of protein secretion systems during mammalian infection.
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97
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Kattke MD, Chan AH, Duong A, Sexton DL, Sawaya MR, Cascio D, Elliot MA, Clubb RT. Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal. PLoS One 2016; 11:e0167763. [PMID: 27936128 PMCID: PMC5148588 DOI: 10.1371/journal.pone.0167763] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/18/2016] [Indexed: 01/17/2023] Open
Abstract
Many species of Gram-positive bacteria use sortase transpeptidases to covalently affix proteins to their cell wall or to assemble pili. Sortase-displayed proteins perform critical and diverse functions for cell survival, including cell adhesion, nutrient acquisition, and morphological development, among others. Based on their amino acid sequences, there are at least six types of sortases (class A to F enzymes); however, class E enzymes have not been extensively studied. Class E sortases are used by soil and freshwater-dwelling Actinobacteria to display proteins that contain a non-canonical LAXTG sorting signal, which differs from 90% of known sorting signals by substitution of alanine for proline. Here we report the first crystal structure of a class E sortase, the 1.93 Å resolution structure of the SrtE1 enzyme from Streptomyces coelicolor. The active site is bound to a tripeptide, providing insight into the mechanism of substrate binding. SrtE1 possesses β3/β4 and β6/β7 active site loops that contact the LAXTG substrate and are structurally distinct from other classes. We propose that SrtE1 and other class E sortases employ a conserved tyrosine residue within their β3/β4 loop to recognize the amide nitrogen of alanine at position P3 of the sorting signal through a hydrogen bond, as seen here. Incapability of hydrogen-bonding with canonical proline-containing sorting signals likely contributes to class E substrate specificity. Furthermore, we demonstrate that surface anchoring of proteins involved in aerial hyphae formation requires an N-terminal segment in SrtE1 that is presumably positioned within the cytoplasm. Combined, our results reveal unique features within class E enzymes that enable them to recognize distinct sorting signals, and could facilitate the development of substrate-based inhibitors of this important enzyme family.
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Affiliation(s)
- Michele D. Kattke
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Albert H. Chan
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Andrew Duong
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Danielle L. Sexton
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Michael R. Sawaya
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Duilio Cascio
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Marie A. Elliot
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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98
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Calkins S, Couger M, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. GENOMICS DATA 2016; 10:91-96. [PMID: 27766204 PMCID: PMC5065635 DOI: 10.1016/j.gdata.2016.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/29/2016] [Accepted: 10/05/2016] [Indexed: 11/26/2022]
Abstract
Staphylococcus hominis is a predominant member of the human skin microbiome. We here report on the genomic analysis of Staphylococcus hominis strain Hudgins that was isolated from the wrist area of human skin. The partial genome assembly of S. hominis Hudgins consists of 2,211,863 bp of DNA with 2174 protein-coding genes and 90 RNA genes. Based on the genomic analysis of KEGG pathways, the organism is expected to be a versatile heterotroph potentially capable of hydrolyzing the sugars glucose, fructose, mannose, and the amino acids alanine, aspartate, glutamate, glycine, threonine, cysteine, methionine, valine, isoleucine, leucine, lysine, arginine, phenylalanine, tyrosine, and tryptophan for energy production through aerobic respiration, with occasional lactate and acetate fermentation. Evidence for poly-gamma glutamate capsule and type IV Com system pili were identified in the genome. Based on COG analysis, the genome of S. hominis Hudgins clusters away from the previously published S. hominis genome ZBW5.
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Affiliation(s)
- Shelby Calkins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - M.B. Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Colin Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Jordan Zandler
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Garett C. Hudgins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Radwa A. Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Connie Budd
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Donald P. French
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, United States
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Noha Youssef
- 1110 S Innovation way, Stillwater, OK 74074, United States
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99
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Staphylococcus epidermidis ΔSortase A strain elicits protective immunity against Staphylococcus aureus infection. Antonie van Leeuwenhoek 2016; 110:133-143. [PMID: 27757703 DOI: 10.1007/s10482-016-0784-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
Abstract
Staphylococcus aureus and Staphylococcus epidermidis are two of the most significant opportunistic human pathogens, causing medical implant and nosocomial infections worldwide. These bacteria contain surface proteins that play crucial roles in multiple biological processes. It has become apparent that they have evolved a number of unique mechanisms by which they can immobilise proteins on their surface. Notably, a conserved cell membrane-anchored enzyme, sortase A (SrtA), can catalyse the covalent attachment of precursor bacterial cell wall-attached proteins to peptidoglycan. Considering its indispensable role in anchoring substrates to the cell wall and its effects on virulence, SrtA has attracted great attention. In this study, a 549-bp gene was cloned from a pathogenic S. epidermidis strain, YC-1, which shared high identity with srtA from other Staphylococcus spp. A mutant strain, YC-1ΔsrtA, was then constructed by allelic exchange mutagenesis. The direct survival rate assay suggested that YC-1ΔsrtA had a lower survival capacity in healthy mice blood compare with the wild-type strain, indicating that the deletion of srtA affects the virulence and infectious capacity of S. epidermidis YC-1. YC-1ΔsrtA was then administered via intraperitoneal injection and it provided a relative percent survival value of 72.7 % in mice against S. aureus TC-1 challenge. These findings demonstrate the possbility that YC-1ΔsrtA might be used as a live attenuated vaccine to produce cross-protection against S. aureus.
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100
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Castelain M, Duviau MP, Oxaran V, Schmitz P, Cocaign-Bousquet M, Loubière P, Piard JC, Mercier-Bonin M. Oligomerized backbone pilin helps piliated Lactococcus lactis to withstand shear flow. BIOFOULING 2016; 32:911-923. [PMID: 27472256 DOI: 10.1080/08927014.2016.1213817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
The present work focuses on the role of pili present at the cell surface of Lactococcus lactis in bacterial adhesion to abiotic (hydrophobic polystyrene) and biotic (mucin-coated polystyrene) surfaces. Native pili-displaying strains and isogenic derivatives in which pilins or sortase C structural genes had been modified were used. Surface physico-chemistry, morphology and shear-flow-induced detachment of lactococcal cells were evaluated. The involvement of pili in L. lactis adhesion was clearly demonstrated, irrespective of the surface characteristics (hydrophobic/hydrophilic, presence or not of specific binding sites). The accessory pilin, PilC, and the backbone pilin, PilB, were revealed to play a major role in adhesion, provided that the PilB was present in its polymerized form. Within the population fraction that remained attached to the surface under increasing shear flow, different association behaviors were observed, showing that pili could serve as anchoring sites thus hampering the effect of shear flow on cell orientation and detachment.
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Affiliation(s)
- Mickaël Castelain
- a LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | | | - Virginie Oxaran
- b Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Philippe Schmitz
- a LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | | | - Pascal Loubière
- a LISBP, Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | - Jean-Christophe Piard
- b Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
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