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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. Evolution of a small phage protein overcomes antiphage defense in Enterococcus faecalis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567456. [PMID: 38014348 PMCID: PMC10680825 DOI: 10.1101/2023.11.16.567456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of new antibiotics needed to combat these infections remains stagnant. MDR enterococci, which are a common cause of hospital-acquired infections, are emerging as one of the major contributors to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which entails the use of lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of phage resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from vancomycin-resistant Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) and we show that this enzyme is sufficient to restrict the replication of lytic phage phi47 in E. faecalis. We further find that phi47 can evolve to overcome restriction by acquiring a missense mutation in a novel TIV-RE inhibitor protein encoded by many enterococcal phages. We show that this inhibitor, which we have named type IV restriction inhibiting factor A (tifA), directly binds to and inactivates diverse TIV-REs. Overall, our findings significantly advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages can evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P. Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Shelby E. Andersen
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Sonia R. Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - John C. Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
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Priyanka, Sharma S, Joshi H, Kumar C, Waseem R, Sharma M. Mycobacterium tuberculosis protein PPE15 (Rv1039c) possesses eukaryote-like SH3 domain that interferes with NADPH Oxidase assembly and Reactive Oxygen Species production. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119702. [PMID: 38408543 DOI: 10.1016/j.bbamcr.2024.119702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Inhibition of Reactive Oxygen Species (ROS) is one of the strategies that Mycobacterium tuberculosis (Mtb) employs as its defence mechanism. In this study, the role of PPE15 (Rv1039c), a late-stage protein, has been investigated in modulating the cellular ROS. We discovered PPE15 to be a secretory protein that downregulates ROS generation in THP1 macrophages. Our in-silico analysis revealed the presence of a eukaryote-like SH3 (SH3e) domain in PPE15. The predicted SH3e-domain of PPE15 was found to interact with cytosolic components of NADPH Oxidase (NOX), p67phox and p47phox through molecular docking. In-vitro experiments using THP1 macrophages showed a diminished NADP/NADPH ratio, indicating reduced NOX activity. We also observed increased levels of p67phox and p47phox in the cytoplasmic fraction of PPE15 treated macrophages as compared to the plasma membrane fraction. To understand the role of the SH3e-domain in ROS modulation, this domain was deleted from the full-length PPE15 (PPE15-/-SH3). We observed an increase in cellular ROS and NADP/NADPH ratio in response to PPE15-/-SH3 protein. The interaction of PPE15-/-SH3 with p67phox or p47phox was also reduced in the cytoplasm, indicating migration of NOX subunits to the plasma membrane. Additionally, M. smegmatis expressing PPE15 was observed to be resistant to oxidative stress with significant intracellular survival in THP1 macrophages as compared to M. smegmatis expressing PPE15-/-SH3. These observations suggest that the SH3e-domain of PPE15 interferes with ROS generation by sequestering NOX components that inhibit NOX assembly at the cell membrane. Therefore, PPE15 acts like a molecular mimic of SH3-domain carrying eukaryotic proteins that can be employed by Mtb at late stages of infection for its survival. These findings give us new insights about the pathogen evading strategy of Mtb which may help in improving the therapeutics for TB treatment.
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Affiliation(s)
- Priyanka
- DSKC BioDiscovery Laboratory and Department of Zoology, Miranda House, University of Delhi, Delhi, India.
| | - Sadhna Sharma
- DSKC BioDiscovery Laboratory and Department of Zoology, Miranda House, University of Delhi, Delhi, India.
| | - Hemant Joshi
- School of Biotechnology, Jawaharlal Nehru University, Delhi, India
| | - Chanchal Kumar
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rashid Waseem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Monika Sharma
- DSKC BioDiscovery Laboratory and Department of Zoology, Miranda House, University of Delhi, Delhi, India.
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Pantiora PD, Georgakis ND, Premetis GE, Labrou NE. Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic. Appl Microbiol Biotechnol 2024; 108:163. [PMID: 38252132 PMCID: PMC10803476 DOI: 10.1007/s00253-023-12979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
The misuse and overuse of antibiotics have contributed to a rapid emergence of antibiotic-resistant bacterial pathogens. This global health threat underlines the urgent need for innovative and novel antimicrobials. Endolysins derived from bacteriophages or prophages constitute promising new antimicrobials (so-called enzybiotics), exhibiting the ability to break down bacterial peptidoglycan (PG). In the present work, metagenomic analysis of soil samples, collected from thermal springs, allowed the identification of a prophage-derived endolysin that belongs to the N-acetylmuramoyl-L-alanine amidase type 2 (NALAA-2) family and possesses a LysM (lysin motif) region as a cell wall binding domain (CWBD). The enzyme (Ami1) was cloned and expressed in Escherichia coli, and its bactericidal and lytic activity was characterized. The results indicate that Ami1 exhibits strong bactericidal and antimicrobial activity against a broad range of bacterial pathogens, as well as against isolated peptidoglycan (PG). Among the examined bacterial pathogens, Ami1 showed highest bactericidal activity against Staphylococcus aureus sand Staphylococcus epidermidis cells. Thermostability analysis revealed a melting temperature of 64.2 ± 0.6 °C. Overall, these findings support the potential that Ami1, as a broad spectrum antimicrobial agent, could be further assessed as enzybiotic for the effective treatment of bacterial infections. KEY POINTS: • Metagenomic analysis allowed the identification of a novel prophage endolysin • The endolysin belongs to type 2 amidase family with lysin motif region • The endolysin displays high thermostability and broad bactericidal spectrum.
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Affiliation(s)
- Panagiota D Pantiora
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos D Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Georgios E Premetis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece.
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Mikoulinskaia GV, Prokhorov DA, Chernyshov SV, Sitnikova DS, Arakelian AG, Uversky VN. Conservative Tryptophan Residue in the Vicinity of an Active Site of the M15 Family l,d-Peptidases: A Key Element in the Catalysis. Int J Mol Sci 2023; 24:13249. [PMID: 37686055 PMCID: PMC10487532 DOI: 10.3390/ijms241713249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Bioinformatics analysis of the sequences of orthologous zinc-containing peptidases of the M15_C subfamily revealed the presence of a conserved tryptophan residue near the active site, which is not involved in the formation of the protein core. Site-directed mutagenesis of this Trp114/109 residue using two representatives of the family, l-alanoyl-d-glutamate peptidases of bacteriophages T5 (calcium-activated EndoT5) and RB49 (EndoRB49, without ion regulation) as examples, and further analysis of the 1H NMR spectra of the mutants showed that a decrease in the volume of the W → F → A residue leads to changes in the hydrophobic core and active center of the protein, and also decreases the affinity for regulatory Ca2+ in the EndoT5 mutants. The inactive T5W114A mutant lacks the ability to bind the substrate. In general, the conserved Trp114/109 residue, due to the spatial restrictions of its side chain, significantly affects the formation of the catalytically active form of the enzyme and is critical for catalysis.
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Affiliation(s)
- Galina V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Dmitry A. Prokhorov
- Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul., 3, 142290 Pushchino, Moscow Region, Russia;
| | - Sergei V. Chernyshov
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Daria S. Sitnikova
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Arina G. Arakelian
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
- Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul., 3, 142290 Pushchino, Moscow Region, Russia;
| | - Vladimir N. Uversky
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow Region, Russia
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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5
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Mehrabipour M, Jasemi NSK, Dvorsky R, Ahmadian MR. A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling. Cells 2023; 12:2054. [PMID: 37626864 PMCID: PMC10453029 DOI: 10.3390/cells12162054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
SRC homology 3 (SH3) domains are fundamental modules that enable the assembly of protein complexes through physical interactions with a pool of proline-rich/noncanonical motifs from partner proteins. They are widely studied modular building blocks across all five kingdoms of life and viruses, mediating various biological processes. The SH3 domains are also implicated in the development of human diseases, such as cancer, leukemia, osteoporosis, Alzheimer's disease, and various infections. A database search of the human proteome reveals the existence of 298 SH3 domains in 221 SH3 domain-containing proteins (SH3DCPs), ranging from 13 to 720 kilodaltons. A phylogenetic analysis of human SH3DCPs based on their multi-domain architecture seems to be the most practical way to classify them functionally, with regard to various physiological pathways. This review further summarizes the achievements made in the classification of SH3 domain functions, their binding specificity, and their significance for various diseases when exploiting SH3 protein modular interactions as drug targets.
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Affiliation(s)
- Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, 040 01 Košice, Slovakia
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
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6
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Cifuente JO, Schulze J, Bethe A, Di Domenico V, Litschko C, Budde I, Eidenberger L, Thiesler H, Ramón Roth I, Berger M, Claus H, D'Angelo C, Marina A, Gerardy-Schahn R, Schubert M, Guerin ME, Fiebig T. A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule. Nat Chem Biol 2023; 19:865-877. [PMID: 37277468 PMCID: PMC10299916 DOI: 10.1038/s41589-023-01324-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 03/31/2023] [Indexed: 06/07/2023]
Abstract
Bacterial capsules have critical roles in host-pathogen interactions. They provide a protective envelope against host recognition, leading to immune evasion and bacterial survival. Here we define the capsule biosynthesis pathway of Haemophilus influenzae serotype b (Hib), a Gram-negative bacterium that causes severe infections in infants and children. Reconstitution of this pathway enabled the fermentation-free production of Hib vaccine antigens starting from widely available precursors and detailed characterization of the enzymatic machinery. The X-ray crystal structure of the capsule polymerase Bcs3 reveals a multi-enzyme machine adopting a basket-like shape that creates a protected environment for the synthesis of the complex Hib polymer. This architecture is commonly exploited for surface glycan synthesis by both Gram-negative and Gram-positive pathogens. Supported by biochemical studies and comprehensive 2D nuclear magnetic resonance, our data explain how the ribofuranosyltransferase CriT, the phosphatase CrpP, the ribitol-phosphate transferase CroT and a polymer-binding domain function as a unique multi-enzyme assembly.
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Affiliation(s)
- Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Julia Schulze
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Andrea Bethe
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Valerio Di Domenico
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - Christa Litschko
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Insa Budde
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Lukas Eidenberger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Hauke Thiesler
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Isabel Ramón Roth
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Monika Berger
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Heike Claus
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Cecilia D'Angelo
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Alberto Marina
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Rita Gerardy-Schahn
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.
- Ikerbasque Basque Foundation for Science, Bilbao, Spain.
| | - Timm Fiebig
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
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Ser/Thr Kinase-Dependent Phosphorylation of the Peptidoglycan Hydrolase CwlA Controls Its Export and Modulates Cell Division in Clostridioides difficile. mBio 2021; 12:mBio.00519-21. [PMID: 34006648 PMCID: PMC8262956 DOI: 10.1128/mbio.00519-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cell growth and division require a balance between synthesis and hydrolysis of the peptidoglycan (PG). Inhibition of PG synthesis or uncontrolled PG hydrolysis can be lethal for the cells, making it imperative to control peptidoglycan hydrolase (PGH) activity. The synthesis or activity of several key enzymes along the PG biosynthetic pathway is controlled by the Hanks-type serine/threonine kinases (STKs). In Gram-positive bacteria, inactivation of genes encoding STKs is associated with a range of phenotypes, including cell division defects and changes in cell wall metabolism, but only a few kinase substrates and associated mechanisms have been identified. We previously demonstrated that STK-PrkC plays an important role in cell division, cell wall metabolism, and resistance to antimicrobial compounds in the human enteropathogen Clostridioides difficile In this work, we characterized a PG hydrolase, CwlA, which belongs to the NlpC/P60 family of endopeptidases and hydrolyses cross-linked PG between daughter cells to allow cell separation. We identified CwlA as the first PrkC substrate in C. difficile We demonstrated that PrkC-dependent phosphorylation inhibits CwlA export, thereby controlling hydrolytic activity in the cell wall. High levels of CwlA at the cell surface led to cell elongation, whereas low levels caused cell separation defects. Thus, we provided evidence that the STK signaling pathway regulates PGH homeostasis to precisely control PG hydrolysis during cell division.IMPORTANCE Bacterial cells are encased in a PG exoskeleton that helps to maintain cell shape and confers physical protection. To allow bacterial growth and cell separation, PG needs to be continuously remodeled by hydrolytic enzymes that cleave PG at critical sites. How these enzymes are regulated remains poorly understood. We identify a new PG hydrolase involved in cell division, CwlA, in the enteropathogen C. difficile Lack or accumulation of CwlA at the bacterial surface is responsible for a division defect, while its accumulation in the absence of PrkC also increases susceptibility to antimicrobial compounds targeting the cell wall. CwlA is a substrate of the kinase PrkC in C. difficile PrkC-dependent phosphorylation controls the export of CwlA, modulating its levels and, consequently, its activity in the cell wall. This work provides a novel regulatory mechanism by STK in tightly controlling protein export.
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Lisboa J, Pereira C, Rifflet A, Ayala J, Terceti MS, Barca AV, Rodrigues I, Pereira PJB, Osorio CR, García-Del Portillo F, Gomperts Boneca I, do Vale A, Dos Santos NMS. A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria. mSphere 2021; 6:e00736-20. [PMID: 33536321 PMCID: PMC7860986 DOI: 10.1128/msphere.00736-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/08/2021] [Indexed: 11/20/2022] Open
Abstract
Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from Photobacterium damselae subsp. piscicida (Phdp), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( PhotobacteriumNlpC-like protein A) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the γ-d-glutamyl-meso-diaminopimelic acid bond. However, PnpA does not cleave the PG of Phdp or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the Phdp type II secretion system and degrades the PG of Vibrio anguillarum and Vibrio vulnificus This suggests that PnpA is used by Phdp to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG.IMPORTANCE Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that Photobacterium damselae subsp. piscicida, a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.
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Affiliation(s)
- Johnny Lisboa
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Cassilda Pereira
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Aline Rifflet
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Juan Ayala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mateus S Terceti
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alba V Barca
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inês Rodrigues
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- Biomolecular Structure Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Macromolecular Structure Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco García-Del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ivo Gomperts Boneca
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Nuno M S Dos Santos
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
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Jurėnas D, Van Melderen L. The Variety in the Common Theme of Translation Inhibition by Type II Toxin-Antitoxin Systems. Front Genet 2020; 11:262. [PMID: 32362907 PMCID: PMC7180214 DOI: 10.3389/fgene.2020.00262] [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] [Received: 10/15/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Type II Toxin–antitoxin (TA) modules are bacterial operons that encode a toxic protein and its antidote, which form a self-regulating genetic system. Antitoxins put a halter on toxins in many ways that distinguish different types of TA modules. In type II TA modules, toxin and antitoxin are proteins that form a complex which physically sequesters the toxin, thereby preventing its toxic activity. Type II toxins inhibit various cellular processes, however, the translation process appears to be their favorite target and nearly every step of this complex process is inhibited by type II toxins. The structural features, enzymatic activities and target specificities of the different toxin families are discussed. Finally, this review emphasizes that the structural folds presented by these toxins are not restricted to type II TA toxins or to one particular cellular target, and discusses why so many of them evolved to target translation as well as the recent developments regarding the role(s) of these systems in bacterial physiology and evolution.
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Affiliation(s)
- Dukas Jurėnas
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, Marseille, France
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Gosselies, Belgium
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10
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Kaur G, Burroughs AM, Iyer LM, Aravind L. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. eLife 2020; 9:52696. [PMID: 32101166 PMCID: PMC7159879 DOI: 10.7554/elife.52696] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
Social cellular aggregation or multicellular organization pose increased risk of transmission of infections through the system upon infection of a single cell. The generality of the evolutionary responses to this outside of Metazoa remains unclear. We report the discovery of several thematically unified, remarkable biological conflict systems preponderantly present in multicellular prokaryotes. These combine thresholding mechanisms utilizing NTPase chaperones (the MoxR-vWA couple), GTPases and proteolytic cascades with hypervariable effectors, which vary either by using a reverse transcriptase-dependent diversity-generating system or through a system of acquisition of diverse protein modules, typically in inactive form, from various cellular subsystems. Conciliant lines of evidence indicate their deployment against invasive entities, like viruses, to limit their spread in multicellular/social contexts via physical containment, dominant-negative interactions or apoptosis. These findings argue for both a similar operational 'grammar' and shared protein domains in the sensing and limiting of infections during the multiple emergences of multicellularity.
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Affiliation(s)
- Gurmeet Kaur
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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11
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Structural Basis for Cell-Wall Recognition by Bacteriophage PBC5 Endolysin. Structure 2019; 27:1355-1365.e4. [DOI: 10.1016/j.str.2019.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/04/2019] [Accepted: 07/05/2019] [Indexed: 11/20/2022]
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12
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Linkous RO, Sestok AE, Smith AT. The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein-protein interactions. Proteins 2019; 87:897-903. [PMID: 31162843 DOI: 10.1002/prot.25755] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/25/2019] [Accepted: 05/30/2019] [Indexed: 12/27/2022]
Abstract
In order to establish infection, pathogenic bacteria must obtain essential nutrients such as iron. Under acidic and/or anaerobic conditions, most bacteria utilize the Feo system in order to acquire ferrous iron (Fe2+ ) from their host environment. The mechanism of this process, including its regulation, remains poorly understood. In this work, we have determined the crystal structure of FeoA from the nosocomial agent Klebsiella pneumoniae (KpFeoA). Our structure reveals an SH3-like domain that mediates interactions between neighboring polypeptides via hydrophobic intercalations into a Leu-rich surface ridge. Using docking of a small peptide corresponding to a postulated FeoB partner binding site, we demonstrate that KpFeoA can assume both "open" and "closed" conformations, controlled by binding at this Leu-rich ridge. We propose a model in which a "C-shaped" clamp along the FeoA surface mediates interactions with its partner protein, FeoB. These findings are the first to demonstrate atomic-level details of FeoA-based protein-protein interactions and provide a framework for testing FeoA-FeoB interactions, which could be exploited for future antibiotic developments.
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Affiliation(s)
- Richard O Linkous
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, Maryland
| | - Alexandrea E Sestok
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, Maryland
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, Maryland
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13
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The Antistaphylococcal Lysin, CF-301, Activates Key Host Factors in Human Blood To Potentiate Methicillin-Resistant Staphylococcus aureus Bacteriolysis. Antimicrob Agents Chemother 2019; 63:AAC.02291-18. [PMID: 30670427 DOI: 10.1128/aac.02291-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteriophage-derived lysins are cell-wall-hydrolytic enzymes that represent a potential new class of antibacterial therapeutics in development to address burgeoning antimicrobial resistance. CF-301, the lead compound in this class, is in clinical development as an adjunctive treatment to potentially improve clinical cure rates of Staphylococcus aureus bacteremia and infective endocarditis (IE) when used in addition to antibiotics. In order to profile the activity of CF-301 in a clinically relevant milieu, we assessed its in vitro activity in human blood versus in a conventional testing medium (cation-adjusted Mueller-Hinton broth [caMHB]). CF-301 exhibited substantially greater potency (32 to ≥100-fold) in human blood versus caMHB in three standard microbiologic testing formats (e.g., broth dilution MICs, checkerboard synergy, and time-kill assays). We demonstrated that CF-301 acted synergistically with two key human blood factors, human serum lysozyme (HuLYZ) and human serum albumin (HSA), which normally have no nascent antistaphylococcal activity, against a prototypic methicillin-resistant S. aureus (MRSA) strain (MW2). Similar in vitro enhancement of CF-301 activity was also observed in rabbit, horse, and dog (but not rat or mouse) blood. Two well-established MRSA IE models in rabbit and rat were used to validate these findings in vivo by demonstrating comparable synergistic efficacy with standard-of-care anti-MRSA antibiotics at >100-fold lower lysin doses in the rabbit than in the rat model. The unique properties of CF-301 that enable bactericidal potentiation of antimicrobial activity via activation of "latent" host factors in human blood may have important therapeutic implications for durable improvements in clinical outcomes of serious antibiotic-resistant staphylococcal infections.
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14
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Seijsing J, Sobieraj AM, Keller N, Shen Y, Zinkernagel AS, Loessner MJ, Schmelcher M. Improved Biodistribution and Extended Serum Half-Life of a Bacteriophage Endolysin by Albumin Binding Domain Fusion. Front Microbiol 2018; 9:2927. [PMID: 30538696 PMCID: PMC6277698 DOI: 10.3389/fmicb.2018.02927] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022] Open
Abstract
The increasing number of multidrug-resistant bacteria intensifies the need to develop new antimicrobial agents. Endolysins are bacteriophage-derived enzymes that degrade the bacterial cell wall and hold promise as a new class of highly specific and versatile antimicrobials. One major limitation to the therapeutic use of endolysins is their often short serum circulation half-life, mostly due to kidney excretion and lysosomal degradation. One strategy to increase the half-life of protein drugs is fusion to the albumin-binding domain (ABD). By high-affinity binding to serum albumin, ABD creates a complex with large hydrodynamic volume, reducing kidney excretion and lysosomal degradation. The aim of this study was to investigate the in vitro antibacterial activity and in vivo biodistribution and half-life of an engineered variant of the Staphylococcus aureus phage endolysin LysK. The ABD sequence was introduced at different positions within the enzyme, and lytic activity of each variant was determined in vitro and ex vivo in human serum. Half-life and biodistribution were assessed in vivo by intravenous injection of europium-labeled proteins into C57BL/6 wild-type mice. Our data demonstrates that fusion of the endolysin to ABD improves its serum circulation half-life and reduces its deposition in the kidneys in vivo. The most active construct reduced S. aureus counts in human serum ex vivo by 3 logs within 60 min. We conclude that ABD fusions provide an effective strategy to extend the half-life of antibacterial enzymes, supporting their therapeutic potential for treatment of systemic bacterial infections.
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Affiliation(s)
- Johan Seijsing
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Anna M Sobieraj
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Nadia Keller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich - University of Zürich, Zürich, Switzerland
| | - Yang Shen
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Annelies S Zinkernagel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich - University of Zürich, Zürich, Switzerland
| | - Martin J Loessner
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Mathias Schmelcher
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
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15
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Gómez L, Alvarez F, Betancur D, Oñate A. Brucellosis vaccines based on the open reading frames from genomic island 3 of Brucella abortus. Vaccine 2018; 36:2928-2936. [PMID: 29685597 DOI: 10.1016/j.vaccine.2018.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/02/2018] [Accepted: 04/04/2018] [Indexed: 01/18/2023]
Abstract
Brucella abortus is the etiological agent of brucellosis, a zoonotic disease affecting cattle and humans. This disease has been partially controlled in cattle by immunization with live attenuated B. abortus S19 and RB51 strains. However, use of these vaccine strains has been associated with safety issues in animals and humans. New vaccines have since emerged in the prevention of brucellosis, particularly DNA vaccines, which have shown effectiveness and a good safety profile. Their protection efficacy in mice is associated with the induction of Th1 type and cytotoxic T cell mediated immune response against structural antigens and virulence factors expressed during B. abortus infection. Some antigenic candidate for vaccine design against brucellosis (mainly DNA vaccines) have been obtained from genomic island 3 (GI-3) of B. abortus, which encodes several open reading frames (ORFs) involved in the intracellular survival and virulence of this pathogen. The immunogenicity and protection conferred by these DNA vaccines in a murine model is reviewed in this article, suggesting that some of them could be safe and effective vaccine candidates against to prevent B. abortus infection.
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Affiliation(s)
- Leonardo Gómez
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - Francisco Alvarez
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - Daniel Betancur
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - Angel Oñate
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile.
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16
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Tossavainen H, Raulinaitis V, Kauppinen L, Pentikäinen U, Maaheimo H, Permi P. Structural and Functional Insights Into Lysostaphin-Substrate Interaction. Front Mol Biosci 2018; 5:60. [PMID: 30018958 PMCID: PMC6038053 DOI: 10.3389/fmolb.2018.00060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Lysostaphin from Staphylococcus simulans and its family enzymes rapidly acquire prominence as the next generation agents in treatment of S. aureus infections. The specificity of lysostaphin is promoted by its C-terminal cell wall targeting domain selectivity toward pentaglycine bridges in S. aureus cell wall. Scission of these cross-links is carried out by its N-terminal catalytic domain, a zinc-dependent endopeptidase. Understanding the determinants affecting the efficiency of catalysis and strength and specificity of interactions lies at the heart of all lysostaphin family enzyme applications. To this end, we have used NMR, SAXS and molecular dynamics simulations to characterize lysostaphin structure and dynamics, to address the inter-domain interaction, the enzyme-substrate interaction as well as the catalytic properties of pentaglycine cleavage in solution. Our NMR structure confirms the recent crystal structure, yet, together with the molecular dynamics simulations, emphasizes the dynamic nature of the loops embracing the catalytic site. We found no evidence for inter-domain interaction, but, interestingly, the SAXS data delineate two preferred conformation subpopulations. Catalytic H329 and H360 were observed to bind a second zinc ion, which reduces lysostaphin pentaglycine cleaving activity. Binding of pentaglycine or its lysine derivatives to the targeting domain was found to be of very low affinity. The pentaglycine interaction site was located to the N-terminal groove of the domain. Notably, the targeting domain binds the peptidoglycan stem peptide Ala-d-γ-Glu-Lys-d-Ala-d-Ala with a much higher, micromolar affinity. Binding site mapping reveals two interaction sites of different affinities on the surface of the domain for this peptide.
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Affiliation(s)
- Helena Tossavainen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vytas Raulinaitis
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Linda Kauppinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku Centre for Biotechnology, Turku, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
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17
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Romero P, Bartual SG, Schmelcher M, Glück C, Hermoso JA, Loessner MJ. Structural insights into the binding and catalytic mechanisms of the Listeria monocytogenes bacteriophage glycosyl hydrolase PlyP40. Mol Microbiol 2018; 108:128-142. [PMID: 29405497 DOI: 10.1111/mmi.13922] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2018] [Indexed: 01/16/2023]
Abstract
Endolysins are bacteriophage-encoded peptidoglycan hydrolases that specifically degrade the bacterial cell wall at the end of the phage lytic cycle. They feature a distinct modular architecture, consisting of enzymatically active domains (EADs) and cell wall-binding domains (CBDs). Structural analysis of the complete enzymes or individual domains is required for better understanding the mechanisms of peptidoglycan degradation and provides guidelines for the rational design of chimeric enzymes. We here report the crystal structure of the EAD of PlyP40, a member of the GH-25 family of glycosyl hydrolases, and the first muramidase reported for Listeria phages. Site-directed mutagenesis confirmed key amino acids (Glu98 and Trp10) involved in catalysis and substrate stabilization. In addition, we found that PlyP40 contains two heterogeneous CBD modules with homology to SH3 and LysM domains. Truncation analysis revealed that both domains are required for full activity but contribute to cell wall recognition and lysis differently. Replacement of CBDP40 with a corresponding domain from a different Listeria phage endolysin yielded an enzyme with a significant shift in pH optimum. Finally, domain swapping between PlyP40 and the streptococcal endolysin Cpl-1 produced an intergeneric chimera with activity against Listeria cells, indicating that structural similarity of individual domains determines enzyme function.
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Affiliation(s)
- Patricia Romero
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Sergio G Bartual
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, 28006 Madrid, Spain
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Chaim Glück
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, 28006 Madrid, Spain
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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18
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Romero Pastrana F, Neef J, Koedijk DGAM, de Graaf D, Duipmans J, Jonkman MF, Engelmann S, van Dijl JM, Buist G. Human antibody responses against non-covalently cell wall-bound Staphylococcus aureus proteins. Sci Rep 2018; 8:3234. [PMID: 29459694 PMCID: PMC5818649 DOI: 10.1038/s41598-018-21724-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/06/2018] [Indexed: 12/28/2022] Open
Abstract
Human antibody responses to pathogens, like Staphylococcus aureus, are important indicators for in vivo expression and immunogenicity of particular bacterial components. Accordingly, comparing the antibody responses to S. aureus components may serve to predict their potential applicability as antigens for vaccination. The present study was aimed at assessing immunoglobulin G (IgG) responses elicited by non-covalently cell surface-bound proteins of S. aureus, which thus far received relatively little attention. To this end, we applied plasma samples from patients with the genetic blistering disease epidermolysis bullosa (EB) and healthy S. aureus carriers. Of note, wounds of EB patients are highly colonized with S. aureus and accordingly these patients are more seriously exposed to staphylococcal antigens than healthy individuals. Ten non-covalently cell surface-bound proteins of S. aureus, namely Atl, Eap, Efb, EMP, IsaA, LukG, LukH, SA0710, Sle1 and SsaA2, were selected by bioinformatics and biochemical approaches. These antigens were recombinantly expressed, purified and tested for specific IgG responses using human plasma. We show that high exposure of EB patients to S. aureus is mirrored by elevated IgG levels against all tested non-covalently cell wall-bound staphylococcal antigens. This implies that these S. aureus cell surface proteins are prime targets for the human immune system.
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Affiliation(s)
- Francisco Romero Pastrana
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Jolanda Neef
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Dennis G A M Koedijk
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Douwe de Graaf
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - José Duipmans
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marcel F Jonkman
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Susanne Engelmann
- Institute of Microbiology, Technical University Braunschweig, Inhoffenstrasse 7, D-38124, Braunschweig, Germany.,Helmholtz Institute for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, D-38124, Braunschweig, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
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Corrected and Republished from: Identification of Peptidoglycan Hydrolase Constructs with Synergistic Staphylolytic Activity in Cow's Milk. Appl Environ Microbiol 2017; 84:AEM.02134-17. [PMID: 29320762 DOI: 10.1128/aem.02134-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/16/2017] [Indexed: 01/21/2023] Open
Abstract
Peptidoglycan hydrolases (PGHs) have been suggested as novel therapeutics for the treatment of bovine mastitis. However, activity in the presence of cow's milk is an important requirement for drugs administered into the bovine udder. We have used a microtiter plate-based protocol to screen a library of >170 recombinant PGHs, including engineered bacteriophage endolysins, for enzymes with activity against Staphylococcus aureus in milk. Eight suitable PGH constructs were identified by this approach, and their efficacies against S. aureus in heat-treated milk were compared by time-kill assays. The two most active enzymes (lysostaphin and CHAPK_CWT-LST) reduced S. aureus numbers in milk to undetectable levels within minutes at nanomolar concentrations. Due to their different peptidoglycan cleavage sites, these PGH constructs revealed synergistic activity, as demonstrated by checkerboard assays, spot assays, and time-kill experiments. Furthermore, they proved active against a selection of staphylococcal mastitis isolates from different geographical regions when applied individually or in synergistic combination. The PGH combination completely eradicated S. aureus from milk: no more bacteria were detected within 24 h after the addition of the enzymes, corresponding to a reduction of >9 log units from the level in the control. Efficacy was also retained at different inoculum levels (3 log versus 6 log CFU/ml) and when S. aureus was grown in milk as opposed to broth prior to the experiments. In raw cow's milk, CHAPK_CWT-LST showed reduced efficacy, whereas lysostaphin retained its activity, reducing bacterial numbers by >3.5 log units within 3 h.IMPORTANCE Staphylococci, and S. aureus in particular, are a major cause of bovine mastitis, an inflammation of the mammary gland in cows that is associated with high costs and risks for consumers of milk products. S. aureus-induced mastitis, commonly treated by intramammary infusion of antibiotics, is characterized by low cure rates and increasing antibiotic resistance in bacteria. Therefore, alternative treatment options are highly desirable. PGHs, including bacteriophage endolysins, rapidly and specifically kill selected pathogens by degrading their cell walls and are refractory to resistance development; thus, they have promise as novel antibacterial agents. This study employed a screening approach to identify PGH constructs with high staphylolytic activity in cow's milk among a large collection of enzymes. Our results suggest that the most promising enzymes identified by this strategy hold potential as novel mastitis therapeutics and thus support their further characterization in animal models.
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20
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Identification of Peptidoglycan Hydrolase Constructs with Synergistic Staphylolytic Activity in Cow's Milk. Appl Environ Microbiol 2017; 83:AEM.03445-16. [PMID: 28159785 DOI: 10.1128/aem.03445-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/26/2017] [Indexed: 01/21/2023] Open
Abstract
Peptidoglycan hydrolases (PGHs) have been suggested as novel therapeutics for the treatment of bovine mastitis. However, activity in the presence of cow's milk is an important requirement for drugs administered into the bovine udder. We have screened a library of >170 recombinant PGHs, including engineered bacteriophage endolysins, for enzymes with activity against Staphylococcus aureus in milk, using a microtiter plate-based protocol. Nine suitable PGH constructs were identified by this approach and further compared in time-kill assays for their efficacy against S. aureus in heat-treated milk. The three most active enzymes (lysostaphin, Ami2638A, and CHAPK_CWT-LST) reduced S. aureus in milk to undetectable numbers within minutes at nanomolar concentrations. Due to their different peptidoglycan cleavage sites, these PGH constructs revealed synergistic activity in most combinations, as demonstrated by checkerboard assays, spot assays, and time-kill experiments. Furthermore, they proved active against a selection of staphylococcal mastitis isolates from different geographical regions when applied individually or in synergistic combination. The most effective PGH combination completely eradicated S. aureus from milk, with no more bacteria being detected within 24 h after addition of the enzymes, corresponding to a reduction of >9 log units compared to the control. Efficacy was also retained at different inoculum levels (3 versus 6 log CFU/ml) and when S. aureus was grown in milk as opposed to broth prior to the experiments. In raw cow's milk, CHAPK_CWT-LST showed reduced efficacy, whereas both Ami2638A and lysostaphin retained their activity, reducing bacterial numbers by >3.5 log units within 3 h.IMPORTANCE Staphylococci and S. aureus in particular are a major cause of bovine mastitis, an inflammation of the mammary gland in cows associated with high costs and risks for consumers of milk products. S. aureus-induced mastitis, commonly treated by intramammary infusion of antibiotics, is characterized by low cure rates and increasing antibiotic resistance in bacteria. Therefore, alternative treatment options are highly desirable. PGHs, including bacteriophage endolysins, rapidly and specifically kill selected pathogens by degrading their cell wall and are refractory to resistance development, therefore holding promise as novel antibacterial agents. This study employed a screening approach to identify PGH constructs with high staphylolytic activity in cow's milk within a large collection of enzymes. Our results suggest that the most promising enzymes identified by this strategy hold potential as novel mastitis therapeutics and support their further characterization in animal models.
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21
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Charoensuk K, Sakurada T, Tokiyama A, Murata M, Kosaka T, Thanonkeo P, Yamada M. Thermotolerant genes essential for survival at a critical high temperature in thermotolerant ethanologenic Zymomonas mobilis TISTR 548. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:204. [PMID: 28855965 PMCID: PMC5571576 DOI: 10.1186/s13068-017-0891-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/18/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND High-temperature fermentation (HTF) technology is expected to reduce the cost of bioconversion of biomass to fuels or chemicals. For stable HTF, the development of a thermotolerant microbe is indispensable. Elucidation of the molecular mechanism of thermotolerance would enable the thermal stability of microbes to be improved. RESULTS Thermotolerant genes that are essential for survival at a critical high temperature (CHT) were identified via transposon mutagenesis in ethanologenic, thermotolerant Zymomonas mobilis TISTR 548. Surprisingly, no genes for general heat shock proteins except for degP were included. Cells with transposon insertion in these genes showed a defect in growth at around 39 °C but grew normally at 30 °C. Of those, more than 60% were found to be sensitive to ethanol at 30 °C, indicating that the mechanism of thermotolerance partially overlaps with that of ethanol tolerance in the organism. Products of these genes were classified into nine categories of metabolism, membrane stabilization, transporter, DNA repair, tRNA modification, protein quality control, translation control, cell division, and transcriptional regulation. CONCLUSIONS The thermotolerant genes of Escherichia coli and Acetobacter tropicalis that had been identified can be functionally classified into 9 categories according to the classification of those of Z. mobilis, and the ratio of thermotolerant genes to total genomic genes in Z. mobilis is nearly the same as that in E. coli, though the ratio in A. tropicalis is relatively low. There are 7 conserved thermotolerant genes that are shared by these three or two microbes. These findings suggest that Z. mobilis possesses molecular mechanisms for its survival at a CHT that are similar to those in E. coli and A. tropicalis. The mechanisms may mainly contribute to membrane stabilization, protection and repair of damage of macromolecules and maintenance of cellular metabolism at a CHT. Notably, the contribution of heat shock proteins to such survival seems to be very low.
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Affiliation(s)
- Kannikar Charoensuk
- Division of Product Development and Management Technology, Faculty of Agro-Industrial Technology, Rajamangala University of Technology Tawan-ok, Chanthaburi Campus, Chanthaburi, 22100 Thailand
| | - Tomoko Sakurada
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube, 755-8505 Japan
| | - Amina Tokiyama
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515 Japan
| | - Masayuki Murata
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube, 755-8505 Japan
| | - Tomoyuki Kosaka
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube, 755-8505 Japan
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515 Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8315 Japan
| | - Pornthap Thanonkeo
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002 Thailand
| | - Mamoru Yamada
- Life Science, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube, 755-8505 Japan
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515 Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8315 Japan
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22
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Faheem M, Martins-de-Sa D, Vidal JFD, Álvares ACM, Brandão-Neto J, Bird LE, Tully MD, von Delft F, Souto BM, Quirino BF, Freitas SM, Barbosa JARG. Functional and structural characterization of a novel putative cysteine protease cell wall-modifying multi-domain enzyme selected from a microbial metagenome. Sci Rep 2016; 6:38031. [PMID: 27934875 PMCID: PMC5146660 DOI: 10.1038/srep38031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022] Open
Abstract
A current metagenomics focus is to interpret and transform collected genomic data into biological information. By combining structural, functional and genomic data we have assessed a novel bacterial protein selected from a carbohydrate-related activity screen in a microbial metagenomic library from Capra hircus (domestic goat) gut. This uncharacterized protein was predicted as a bacterial cell wall-modifying enzyme (CWME) and shown to contain four domains: an N-terminal, a cysteine protease, a peptidoglycan-binding and an SH3 bacterial domain. We successfully cloned, expressed and purified this putative cysteine protease (PCP), which presented autoproteolytic activity and inhibition by protease inhibitors. We observed cell wall hydrolytic activity and ampicillin binding capacity, a characteristic of most bacterial CWME. Fluorimetric binding analysis yielded a Kb of 1.8 × 105 M-1 for ampicillin. Small-angle X-ray scattering (SAXS) showed a maximum particle dimension of 95 Å with a real-space Rg of 28.35 Å. The elongated molecular envelope corroborates the dynamic light scattering (DLS) estimated size. Furthermore, homology modeling and SAXS allowed the construction of a model that explains the stability and secondary structural changes observed by circular dichroism (CD). In short, we report a novel cell wall-modifying autoproteolytic PCP with insight into its biochemical, biophysical and structural features.
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Affiliation(s)
- Muhammad Faheem
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Diogo Martins-de-Sa
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Julia F. D. Vidal
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Alice C. M. Álvares
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - José Brandão-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, England
| | - Louise E. Bird
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, OX11 0FA, United Kingdom
| | - Mark D. Tully
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, England
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, England
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Betulia M. Souto
- Embrapa Agroenergia, Parque Estação Biológica - PqEB s/n°, Brasília, DF, 70770-901, Brazil
| | - Betania F. Quirino
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
- Embrapa Agroenergia, Parque Estação Biológica - PqEB s/n°, Brasília, DF, 70770-901, Brazil
| | - Sonia M. Freitas
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - João Alexandre R. G. Barbosa
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
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23
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Rozentur-Shkop E, Goobes G, Chill JH. A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP. JOURNAL OF BIOMOLECULAR NMR 2016; 66:243-257. [PMID: 27844185 DOI: 10.1007/s10858-016-0073-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J(15N,13Cα) couplings. This concept was realized using a unidirectional (H)NCO 13C-detected experiment suitable for poor spectral dispersion and optimized for maximum coverage of amino acid types. To demonstrate the utility of this approach we applied it to the disordered actin-binding N-terminal domain of WASp interacting protein (WIP), a ubiquitous key modulator of cytoskeletal changes in a range of biological systems. One- and two-bond J(15N,13Cα) couplings were acquired for WIP residues 2-65 at various temperatures, and in denaturing and crowding environments. Under native conditions fitted J-couplings identified in the WIP conformational ensemble a propensity for extended conformation at residues 16-23 and 45-60, and a helical tendency at residues 28-42. These findings are consistent with a previous study of the based upon chemical shift and RDC data and confirm that the WIP2-65 conformational ensemble is biased towards the structure assumed by this fragment in its actin-bound form. The effects of environmental changes upon this ensemble were readily apparent in the J-coupling data, which reflected a significant decrease in structural propensity at higher temperatures, in the presence of 8 M urea, and under the influence of a bacterial cell lysate. The latter suggests that crowding can cause protein unfolding through protein-protein interactions that stabilize the unfolded state. We conclude that J-couplings are a useful measureable in characterizing structural ensembles in IDPs, and that the proposed experiment provides a practical method for accurately performing such measurements, once again emphasizing the power of NMR in studying IDP behavior.
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Affiliation(s)
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, 52900, Ramat Gan, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, 52900, Ramat Gan, Israel.
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24
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Gómez LA, Alvarez FI, Fernández PA, Flores MR, Molina RE, Coloma RF, Oñate AA. Immunogenicity and Protective Response Induced by Recombinant Plasmids Based on the BAB1_0267 and BAB1_0270 Open Reading Frames of Brucella abortus 2308 in BALB/c Mice. Front Cell Infect Microbiol 2016; 6:117. [PMID: 27747197 PMCID: PMC5041321 DOI: 10.3389/fcimb.2016.00117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/16/2016] [Indexed: 01/05/2023] Open
Abstract
Immunogenicity induced by recombinant plasmids based on the BAB1_0267 and BAB1_0270 open reading frames (ORFs) of Brucella abortus 2308 was evaluated. Bioinformatics analyses indicate that the BAB1_0267 and BAB1_0270 ORFs encode a protein with a SH3 domain and a Zn-dependent metalloproteinase, respectively. Both ORFs have important effects on intracellular survival and replication of B. abortus 2308, mediated via professional and non-professional phagocytic cells. Our results show that immunization with the recombinant plasmid based on the BAB1_0267 ORF significantly increases the production of IgG1, levels of IFN-γ and the lymphoproliferative response of splenocytes. However, BAB1_0267 did not provide significant levels of protection. The plasmid based on the BAB1_0270 significantly increased IgG2a production, levels of IFN-γ and TNF-α, and the lymphoproliferative response of splenocytes. These results demonstrate that immunization with the BAB1_0270 derived recombinant plasmid induce a Th1-type immune response, correlated with a heightened resistance to B. abortus 2308 infection in mice. It is concluded that the Th1-type immune response against bacterial Zn-dependent metalloproteinase induces a protective response in mice, and that pV270 recombinant plasmid is an effective candidate microbicide against brucellosis.
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Affiliation(s)
- Leonardo A Gómez
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Francisco I Alvarez
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Pablo A Fernández
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Manuel R Flores
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Raúl E Molina
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Roberto F Coloma
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Angel A Oñate
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
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25
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Jarábková V, Tišáková L, Godány A. Phage Endolysin: A Way To Understand A Binding Function Of C-Terminal Domains A Mini Review. NOVA BIOTECHNOLOGICA ET CHIMICA 2015. [DOI: 10.1515/nbec-2015-0021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractEndolysins are bacteriophage-encoded peptidoglycan hydrolases, which are synthesized in the end of phage reproduction cycle, in an infected host cell. Usually, for endolysins from phages that infect Gram-positive bacteria, a modular structure is typical. Therefore, these are composed of at least two separate functional domains: an N-terminal catalytic domain (EAD) and a C-terminal cell wall binding domain (CBD). Specific ligand recognition of CBDs and following peptidoglycan (PG) binding mostly allows a rapid lytic activity of an EAD. Here we briefly characterize phage endolysin CBDs in conjuction with their domain architecture, (non)necessity for the following lytic activity and a high/low specificity of their ligands as well. Such an overall assessment of CBDs may help to find new ways to widen opportunities in their protein design to create ‛designer recombinant endolysins’ with diverse applications.
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26
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Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains. mBio 2015; 6:e02327-14. [PMID: 26374125 PMCID: PMC4600125 DOI: 10.1128/mbio.02327-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (or dl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.
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27
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Synergistic streptococcal phage λSA2 and B30 endolysins kill streptococci in cow milk and in a mouse model of mastitis. Appl Microbiol Biotechnol 2015; 99:8475-86. [PMID: 25895090 DOI: 10.1007/s00253-015-6579-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
Abstract
Bovine mastitis results in billion dollar losses annually in the USA alone. Streptococci are among the most relevant causative agents of this disease. Conventional antibiotic therapy is often unsuccessful and contributes to development of antibiotic resistance. Bacteriophage endolysins represent a new class of antimicrobials against these bacteria. In this work, we characterized the endolysins (lysins) of the streptococcal phages λSA2 and B30 and evaluated their potential as anti-mastitis agents. When tested in vitro against live streptococci, both enzymes exhibited near-optimum lytic activities at ionic strengths, pH, and Ca(2+) concentrations consistent with cow milk. When tested in combination in a checkerboard assay, the lysins were found to exhibit strong synergy. The λSA2 lysin displayed high activity in milk against Streptococcus dysgalactiae (reduction of CFU/ml by 3.5 log units at 100 μg/ml), Streptococcus agalactiae (2 log), and Streptococcus uberis (4 log), whereas the B30 lysin was less effective. In a mouse model of bovine mastitis, both enzymes significantly reduced intramammary concentrations of all three streptococcal species (except for B30 vs. S. dysgalactiae), and the effects on mammary gland wet weights and TNFα concentrations were consistent with these findings. Unexpectedly, the synergistic effect determined for the two enzymes in vitro was not observed in the mouse model. Overall, our results illustrate the potential of endolysins for treatment of Streptococcus-induced bovine mastitis.
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28
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Osipovitch DC, Therrien S, Griswold KE. Discovery of novel S. aureus autolysins and molecular engineering to enhance bacteriolytic activity. Appl Microbiol Biotechnol 2015; 99:6315-26. [PMID: 25690309 DOI: 10.1007/s00253-015-6443-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/24/2015] [Accepted: 01/26/2015] [Indexed: 01/21/2023]
Abstract
Staphylococcus aureus is a dangerous bacterial pathogen whose clinical impact has been amplified by the emergence and rapid spread of antibiotic resistance. In the search for more effective therapeutic strategies, great effort has been placed on the study and development of staphylolytic enzymes, which benefit from high potency activity toward drug-resistant strains, and a low inherent susceptibility to emergence of new resistance phenotypes. To date, the majority of therapeutic candidates have derived from either bacteriophage or environmental competitors of S. aureus. Little to no consideration has been given to cis-acting autolysins that represent key elements in the bacterium's endogenous cell wall maintenance and recycling machinery. In this study, five putative autolysins were cloned from the S. aureus genome, and their activities were evaluated. Four of these novel enzymes, or component domains thereof, demonstrated lytic activity toward live S. aureus cells, but their potencies were 10s to 1000s of times lower than that of the well-characterized therapeutic candidate lysostaphin. We hypothesized that their poor activities were due in part to suboptimal cell wall targeting associated with their native cell wall binding domains, and we sought to enhance their antibacterial potential via chimeragenesis with the peptidoglycan binding domain of lysostaphin. The most potent chimera exhibited a 140-fold increase in lytic rate, bringing it within 8-fold of lysostaphin. While this enzyme was sensitive to certain biologically relevant environmental factors and failed to exhibit a measurable minimal inhibitory concentration, it was able to kill lysostaphin-resistant S. aureus and ultimately proved active in lung surfactant. We conclude that the S. aureus proteome represents a rich and untapped reservoir of novel antibacterial enzymes, and we demonstrate enhanced bacteriolytic activity via improved cell wall targeting of autolysin catalytic domains.
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Affiliation(s)
- Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth College, Hanover, NH, 03755, USA
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29
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Schmelcher M, Shen Y, Nelson DC, Eugster MR, Eichenseher F, Hanke DC, Loessner MJ, Dong S, Pritchard DG, Lee JC, Becker SC, Foster-Frey J, Donovan DM. Evolutionarily distinct bacteriophage endolysins featuring conserved peptidoglycan cleavage sites protect mice from MRSA infection. J Antimicrob Chemother 2015; 70:1453-65. [PMID: 25630640 DOI: 10.1093/jac/dku552] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 12/09/2014] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES In the light of increasing drug resistance in Staphylococcus aureus, bacteriophage endolysins [peptidoglycan hydrolases (PGHs)] have been suggested as promising antimicrobial agents. The aim of this study was to determine the antimicrobial activity of nine enzymes representing unique homology groups within a diverse class of staphylococcal PGHs. METHODS PGHs were recombinantly expressed, purified and tested for staphylolytic activity in multiple in vitro assays (zymogram, turbidity reduction assay and plate lysis) and against a comprehensive set of strains (S. aureus and CoNS). PGH cut sites in the staphylococcal peptidoglycan were determined by biochemical assays (Park-Johnson and Ghuysen procedures) and MS analysis. The enzymes were tested for their ability to eradicate static S. aureus biofilms and compared for their efficacy against systemic MRSA infection in a mouse model. RESULTS Despite similar modular architectures and unexpectedly conserved cleavage sites in the peptidoglycan (conferred by evolutionarily divergent catalytic domains), the enzymes displayed varying degrees of in vitro lytic activity against numerous staphylococcal strains, including cell surface mutants and drug-resistant strains, and proved effective against static biofilms. In a mouse model of systemic MRSA infection, six PGHs provided 100% protection from death, with animals being free of clinical signs at the end of the experiment. CONCLUSIONS Our results corroborate the high potential of PGHs for treatment of S. aureus infections and reveal unique antimicrobial and biochemical properties of the different enzymes, suggesting a high diversity of potential applications despite highly conserved peptidoglycan target sites.
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Affiliation(s)
- Mathias Schmelcher
- Animal Biosciences and Biotechnology Laboratory, ANRI, NEA, ARS, USDA, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Daniel C Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA Department of Veterinary Medicine, University of Maryland, 8075 Greenmead Drive, College Park, MD 20742, USA
| | - Marcel R Eugster
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Fritz Eichenseher
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Daniela C Hanke
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Shengli Dong
- Department of Biochemistry and Molecular Genetics, MCLM 552, University of Alabama at Birmingham, 1530 3rd Ave., Birmingham, AL 35294-0005, USA
| | - David G Pritchard
- Department of Biochemistry and Molecular Genetics, MCLM 552, University of Alabama at Birmingham, 1530 3rd Ave., Birmingham, AL 35294-0005, USA
| | - Jean C Lee
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C Becker
- Animal Biosciences and Biotechnology Laboratory, ANRI, NEA, ARS, USDA, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA
| | - Juli Foster-Frey
- Animal Biosciences and Biotechnology Laboratory, ANRI, NEA, ARS, USDA, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA
| | - David M Donovan
- Animal Biosciences and Biotechnology Laboratory, ANRI, NEA, ARS, USDA, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA
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30
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Anzengruber J, Courtin P, Claes IJJ, Debreczeny M, Hofbauer S, Obinger C, Chapot-Chartier MP, Vanderleyden J, Messner P, Schäffer C. Biochemical characterization of the major N-acetylmuramidase from Lactobacillus buchneri. Microbiology (Reading) 2014; 160:1807-1819. [DOI: 10.1099/mic.0.078162-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial cell wall hydrolases are essential for peptidoglycan remodelling in regard to bacterial cell growth and division. In this study, peptidoglycan hydrolases (PGHs) of different Lactobacillus buchneri strains were investigated. First, the genome sequence of L. buchneri CD034 and L. buchneri NRRL B-30929 was analysed in silico for the presence of PGHs. Of 23 putative PGHs with different predicted hydrolytic specificities, the glycosyl hydrolase family 25 domain-containing homologues LbGH25B and LbGH25N from L. buchneri CD034 and NRRL B-30929, respectively, were selected and characterized in detail. Zymogram analysis confirmed hydrolysing activity on bacterial cell walls for both enzymes. Subsequent reversed-phase HPLC and MALDI-TOF MS analysis of the peptidoglycan breakdown products from L. buchneri strains CD034 and NRRL B-30929, and from Lactobacillus rhamnosus GG, which served as a reference, revealed that LbGH25B and LbGH25N have N-acetylmuramidase activity. Both enzymes were identified as cell wall-associated proteins by means of immunofluorescence microscopy and cellular fractionation, as well as by the ability of purified recombinant LbGH25B and LbGH25N to bind to L. buchneri cell walls in vitro. Moreover, similar secondary structures mainly composed of β-sheets and nearly identical thermal stabilities with T
m values around 49 °C were found for the two N-acetylmuramidases by far-UV circular dichroism spectroscopy. The functional and structural data obtained are discussed and compared to related PGHs. In this study, a major N-acetylmuramidase from L. buchneri was characterized in detail for the first time.
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Affiliation(s)
- Julia Anzengruber
- Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Pascal Courtin
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- INRA and AgroParisTech, UMR1319 Micalis, 78350 Jouy-en-Josas, France
| | - Ingmar J. J. Claes
- Center of Microbial and Plant Genetics, K.U. Leuven, 3001 Leuven, Belgium
| | - Monika Debreczeny
- VIBT Imaging Centre, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190 Vienna, Austria
| | - Marie-Pierre Chapot-Chartier
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- INRA and AgroParisTech, UMR1319 Micalis, 78350 Jouy-en-Josas, France
| | - Jos Vanderleyden
- Center of Microbial and Plant Genetics, K.U. Leuven, 3001 Leuven, Belgium
| | - Paul Messner
- Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
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Sanders AN, Wright LF, Pavelka MS. Genetic characterization of mycobacterial L,D-transpeptidases. MICROBIOLOGY-SGM 2014; 160:1795-1806. [PMID: 24855140 DOI: 10.1099/mic.0.078980-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
l,d-Transpeptidases (Ldts) catalyse the formation of 3-3 cross-links in peptidoglycans (PGs); however, the role of these enzymes in cell envelope physiology is not well understood. Mycobacterial PG contains a higher percentage of 3-3 cross-links (~30-80 %) than the PG in most other bacteria, suggesting that they are particularly important to mycobacterial cell wall biology. The genomes of Mycobacterium tuberculosis and Mycobacterium smegmatis encode multiple Ldt genes, but it is not clear if they are redundant. We compared the sequences of the Ldt proteins from 18 mycobacterial genomes and found that they can be grouped into six classes. We then constructed M. smegmatis strains lacking single or multiple Ldt genes to determine the physiological consequence of the loss of these enzymes. We report that of the single mutants, only one, ΔldtC (MSMEG_0929, class 5), displayed an increased susceptibility to imipenem - a carbapenem antibiotic that inhibits the Ldt enzymes. The invariant cysteine in the active site of LdtC was required for function, consistent with its role as an Ldt. A triple mutant missing ldtC and both of the class 2 genes displayed hypersusceptibility to antibiotics, lysozyme and d-methionine, and had an altered cellular morphology. These data demonstrated that the distinct classes of mycobacterial Ldts may reflect different, non-redundant functions and that the class 5 Ldt was peculiar in that its loss, alone and with the class 2 proteins, had the most profound effect on phenotype.
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Affiliation(s)
- Akeisha N Sanders
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Lori F Wright
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martin S Pavelka
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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Tamai E, Yoshida H, Sekiya H, Nariya H, Miyata S, Okabe A, Kuwahara T, Maki J, Kamitori S. X-ray structure of a novel endolysin encoded by episomal phage phiSM101 ofClostridium perfringens. Mol Microbiol 2014; 92:326-37. [DOI: 10.1111/mmi.12559] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Eiji Tamai
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Hiromi Yoshida
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Hirofumi Nariya
- Department of Microbiology; Faculty of Medicine; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Shigeru Miyata
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
- College of Bioscience and Biotechnology; Chubu University; 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
| | - Akinobu Okabe
- Department of Human Nutrition; Faculty of Contemporary Life Science; Chugokugakuen University; Niwase 83 Kita-ku Okayama 761-0197 Japan
| | - Tomomi Kuwahara
- Department of Microbiology; Faculty of Medicine; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Jun Maki
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Shigehiro Kamitori
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
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Huang Y, Qian H, Wang X, Cheng Z, Ren J, Zhao W, Xie Y. Expression, purification and preliminary crystallographic studies of the C-terminal SH3 domain of human Tks4. Acta Crystallogr F Struct Biol Commun 2014; 70:343-6. [PMID: 24598923 PMCID: PMC3944698 DOI: 10.1107/s2053230x14001952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/27/2014] [Indexed: 11/10/2022] Open
Abstract
The Src homology 3 (SH3) domain is a small, noncatalytic domain with a conserved sequence of about 60 amino-acid residues that interacts with proline-rich peptides to form a protein complex. In this study, the C-terminal SH3 domain of human Tks4 (residues 853-911) was expressed, purified and crystallized. X-ray diffraction data were collected to 2.3 Å resolution. The crystal belonged to the trigonal space group P3121 (or P3221), with unit-cell parameters a = b = 83.87, c = 108.44 Å, α = β = 90, γ = 120°. Calculating the self-rotation and the native Patterson function did not lead to the detection of any noncrystallographic translational symmetry. Six, seven or eight protein molecules are likely to be present in the asymmetric unit, resulting in a Matthews coefficient and approximate solvent content of 2.71 Å(3) Da(-1) and 55%, 2.32 Å(3) Da(-1) and 47%, and 2.03 Å(3) Da(-1) and 39%, respectively. To solve the crystal structure of the C-terminal SH3 domain of human Tks4, the isomorphous replacement method is presently being utilized.
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Affiliation(s)
- Yuxin Huang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People’s Republic of China
| | - Huolian Qian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People’s Republic of China
| | - Xiaoying Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People’s Republic of China
| | - Zhong Cheng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People’s Republic of China
| | - Jixia Ren
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People’s Republic of China
| | - Weichen Zhao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People’s Republic of China
| | - Yong Xie
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, People’s Republic of China
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34
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Maity A, Majumdar S, Priya P, De P, Saha S, Ghosh Dastidar S. Adaptability in protein structures: structural dynamics and implications in ligand design. J Biomol Struct Dyn 2014; 33:298-321. [PMID: 24433438 DOI: 10.1080/07391102.2013.873002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The basic framework of understanding the mechanisms of protein functions is achieved from the knowledge of their structures which can model the molecular recognition. Recent advancement in the structural biology has revealed that in spite of the availability of the structural data, it is nontrivial to predict the mechanism of the molecular recognition which progresses via situation-dependent structural adaptation. The mutual selectivity of protein-protein and protein-ligand interactions often depends on the modulations of conformations empowered by their inherent flexibility, which in turn regulates the function. The mechanism of a protein's function, which used to be explained by the ideas of 'lock and key' has evolved today as the concept of 'induced fit' as well as the 'population shift' models. It is felt that the 'dynamics' is an essential feature to take into account for understanding the mechanism of protein's function. The design principles of therapeutic molecules suffer from the problems of plasticity of the receptors whose binding conformations are accurately not predictable from the prior knowledge of a template structure. On the other hand, flexibility of the receptors provides the opportunity to improve the binding affinity of a ligand by suitable substitution that will maximize the binding by modulating the receptors surface. In this paper, we discuss with example how the protein's flexibility is correlated with its functions in various systems, revealing the importance of its understanding and for making applications. We also highlight the methodological challenges to investigate it computationally and to account for the flexible nature of the molecules in drug design.
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Affiliation(s)
- Atanu Maity
- a Bioinformatics Centre, Bose Institute , P-1/12, C.I.T. Scheme VII M, Kolkata 700054 , India
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35
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Schuch R, Lee HM, Schneider BC, Sauve KL, Law C, Khan BK, Rotolo JA, Horiuchi Y, Couto DE, Raz A, Fischetti VA, Huang DB, Nowinski RC, Wittekind M. Combination therapy with lysin CF-301 and antibiotic is superior to antibiotic alone for treating methicillin-resistant Staphylococcus aureus-induced murine bacteremia. J Infect Dis 2013; 209:1469-78. [PMID: 24286983 PMCID: PMC3982849 DOI: 10.1093/infdis/jit637] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Lysins are bacteriophage-derived enzymes that degrade bacterial peptidoglycans. Lysin CF-301 is being developed to treat Staphylococcus aureus because of its potent, specific, and rapid bacteriolytic effects. It also demonstrates activity on drug-resistant strains, has a low resistance profile, eradicates biofilms, and acts synergistically with antibiotics. CF-301 was bacteriolytic against 250 S. aureus strains tested including 120 methicillin-resistant S. aureus (MRSA) isolates. In time-kill studies with 62 strains, CF-301 reduced S. aureus by 3-log10 within 30 minutes compared to 6–12 hours required by antibiotics. In bacteremia, CF-301 increased survival by reducing blood MRSA 100-fold within 1 hour. Combinations of CF-301 with vancomycin or daptomycin synergized in vitro and increased survival significantly in staphylococcal-induced bacteremia compared to treatment with antibiotics alone (P < .0001). Superiority of CF-301 combinations with antibiotics was confirmed in 26 independent bacteremia studies. Combinations including CF-301 and antibiotics represent an attractive alternative to antibiotic monotherapies currently used to treat S. aureus bacteremia.
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DR1769, a protein with N-terminal beta propeller repeats and a low-complexity hydrophilic tail, plays a role in desiccation tolerance of Deinococcus radiodurans. J Bacteriol 2013; 195:3888-96. [PMID: 23794625 DOI: 10.1128/jb.00418-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Deinococcus radiodurans genome encodes five putative quinoproteins. Among these, the Δdr2518 and Δdr1769 mutants became sensitive to gamma radiation. DR2518 with beta propeller repeats in the C-terminal domain was characterized as a radiation-responsive serine/threonine protein kinase in this bacterium. DR1769 contains beta propeller repeats at the N terminus, while its C-terminal domain is a proline-rich disordered structure and constitutes a low-complexity hydrophilic region with aliphatic-proline dipeptide motifs. The Δdr1769 mutant showed nearly a 3-log cycle sensitivity to desiccation at 5% humidity compared to that of the wild type. Interestingly, the gamma radiation and mitomycin C (MMC) resistance in mutant cells also dropped by ∼1-log cycle at 10 kGy and ∼1.5-fold, respectively, compared to those in wild-type cells. But there was no effect of UV (254 nm) exposure up to 800 J · m(-2). These cells showed defective DNA double-strand break repair, and the average size of the nucleoid in desiccated wild-type and Δdr1769 cells was reduced by approximately 2-fold compared to that of respective controls. However, the nucleoid in wild-type cells returned to a size almost similar to that of the untreated control, which did not happen in mutant cells, at least up to 24 h postdesiccation. These results suggest that DR1769 plays an important role in desiccation and radiation resistance of D. radiodurans, possibly by protecting genome integrity under extreme conditions.
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37
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Schmelcher M, Donovan DM, Loessner MJ. Bacteriophage endolysins as novel antimicrobials. Future Microbiol 2013; 7:1147-71. [PMID: 23030422 DOI: 10.2217/fmb.12.97] [Citation(s) in RCA: 474] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endolysins are enzymes used by bacteriophages at the end of their replication cycle to degrade the peptidoglycan of the bacterial host from within, resulting in cell lysis and release of progeny virions. Due to the absence of an outer membrane in the Gram-positive bacterial cell wall, endolysins can access the peptidoglycan and destroy these organisms when applied externally, making them interesting antimicrobial candidates, particularly in light of increasing bacterial drug resistance. This article reviews the modular structure of these enzymes, in which cell wall binding and catalytic functions are separated, as well as their mechanism of action, lytic activity and potential as antimicrobials. It particularly focuses on molecular engineering as a means of optimizing endolysins for specific applications, highlights new developments that may render these proteins active against Gram-negative and intracellular pathogens and summarizes the most recent applications of endolysins in the fields of medicine, food safety, agriculture and biotechnology.
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Affiliation(s)
- Mathias Schmelcher
- Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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38
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Abstract
Peptidoglycan (PG) is the major structural component of the bacterial cell wall. Bacteria have autolytic PG hydrolases that allow the cell to grow and divide. A well-studied group of PG hydrolase enzymes are the bacteriophage endolysins. Endolysins are PG-degrading proteins that allow the phage to escape from the bacterial cell during the phage lytic cycle. The endolysins, when purified and exposed to PG externally, can cause "lysis from without." Numerous publications have described how this phenomenon can be used therapeutically as an effective antimicrobial against certain pathogens. Endolysins have a characteristic modular structure, often with multiple lytic and/or cell wall-binding domains (CBDs). They degrade the PG with glycosidase, amidase, endopeptidase, or lytic transglycosylase activities and have been shown to be synergistic with fellow PG hydrolases or a range of other antimicrobials. Due to the coevolution of phage and host, it is thought they are much less likely to invoke resistance. Endolysin engineering has opened a range of new applications for these proteins from food safety to environmental decontamination to more effective antimicrobials that are believed refractory to resistance development. To put phage endolysin work in a broader context, this chapter includes relevant studies of other well-characterized PG hydrolase antimicrobials.
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39
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Yoshimura H, Ikeuchi M, Ohomori M. Cell surface-associated proteins in the filamentous cyanobacterium Anabaena sp. strain PCC 7120. Microbes Environ 2012; 27:538-43. [PMID: 23059722 PMCID: PMC4103569 DOI: 10.1264/jsme2.me12091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The cell surface senses environmental changes first and transfers signals into the cell. To understand the response to environmental changes, it is necessary to analyze cell surface components, particularly cell surface-associated proteins. We therefore investigated cell surface-associated proteins from the filamentous cyanobacterium Anabaena sp. strain PCC 7120. The cell surface-associated proteins extracted by an acidic buffer were resolved by SDS-PAGE. Eighteen proteins were identified from resolved bands by amino-terminal sequencing. Analysis of cell surface-associated proteins indicated that several proteins among them were involved in nucleic acid binding, protein synthesis, proteolytic activity and electron transfer, and other proteins were involved in the stress response.
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Affiliation(s)
- Hidehisa Yoshimura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3–8–1 Komaba, Meguro-ku, Tokyo 153–8902, Japan.
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40
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Schmelcher M, Korobova O, Schischkova N, Kiseleva N, Kopylov P, Pryamchuk S, Donovan DM, Abaev I. Staphylococcus haemolyticus prophage ΦSH2 endolysin relies on cysteine, histidine-dependent amidohydrolases/peptidases activity for lysis 'from without'. J Biotechnol 2012; 162:289-98. [PMID: 23026556 DOI: 10.1016/j.jbiotec.2012.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/07/2012] [Accepted: 09/18/2012] [Indexed: 10/27/2022]
Abstract
Staphylococcus aureus is an important pathogen, with methicillin-resistant (MRSA) and multi-drug resistant strains becoming increasingly prevalent in both human and veterinary clinics. S. aureus causing bovine mastitis yields high annual losses to the dairy industry. Conventional treatment of mastitis by broad range antibiotics is often not successful and may contribute to development of antibiotic resistance. Bacteriophage endolysins present a promising new source of antimicrobials. The endolysin of prophage ΦSH2 of Staphylococcus haemolyticus strain JCSC1435 (ΦSH2 lysin) is a peptidoglycan hydrolase consisting of two catalytic domains (CHAP and amidase) and an SH3b cell wall binding domain. In this work, we demonstrated its lytic activity against live staphylococcal cells and investigated the contribution of each functional module to bacterial lysis by testing a series of deletion constructs in zymograms and turbidity reduction assays. The CHAP domain exhibited three-fold higher activity than the full length protein and optimum activity in physiological saline. This activity was further enhanced by the presence of bivalent calcium ions. The SH3b domain was shown to be required for full activity of the complete ΦSH2 lysin. The full length enzyme and the CHAP domain showed activity against multiple staphylococcal strains, including MRSA strains, mastitis isolates, and CoNS.
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Affiliation(s)
- Mathias Schmelcher
- ANRI, Agricultural Research Service, US Department of Agriculture, 10300 Baltimore Avenue, Building 230, BARC-EAST, Beltsville, MD 20705, USA
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41
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SH3 domains: modules of protein-protein interactions. Biophys Rev 2012; 5:29-39. [PMID: 28510178 DOI: 10.1007/s12551-012-0081-z] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/29/2012] [Indexed: 01/01/2023] Open
Abstract
Src homology 3 (SH3) domains are involved in the regulation of important cellular pathways, such as cell proliferation, migration and cytoskeletal modifications. Recognition of polyproline and a number of noncanonical sequences by SH3 domains has been extensively studied by crystallography, nuclear magnetic resonance and other methods. High-affinity peptides that bind SH3 domains are used in drug development as candidates for anticancer treatment. This review summarizes the latest achievements in deciphering structural determinants of SH3 function.
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Coggill P, Bateman A. The YARHG domain: an extracellular domain in search of a function. PLoS One 2012; 7:e35575. [PMID: 22615736 PMCID: PMC3355149 DOI: 10.1371/journal.pone.0035575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 03/19/2012] [Indexed: 11/30/2022] Open
Abstract
We have identified a new bacterial protein domain that we hypothesise binds to peptidoglycan. This domain is called the YARHG domain after the most highly conserved sequence-segment. The domain is found in the extracellular space and is likely to be composed of four alpha-helices. The domain is found associated with protein kinase domains, suggesting it is associated with signalling in some bacteria. The domain is also found associated with three different families of peptidases. The large number of different domains that are found associated with YARHG suggests that it is a useful functional module that nature has recombined multiple times.
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Affiliation(s)
- Penny Coggill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
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Sycuro LK, Wyckoff TJ, Biboy J, Born P, Pincus Z, Vollmer W, Salama NR. Multiple peptidoglycan modification networks modulate Helicobacter pylori's cell shape, motility, and colonization potential. PLoS Pathog 2012; 8:e1002603. [PMID: 22457625 PMCID: PMC3310797 DOI: 10.1371/journal.ppat.1002603] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 01/05/2012] [Indexed: 12/14/2022] Open
Abstract
Helical cell shape of the gastric pathogen Helicobacter pylori has been suggested to promote virulence through viscosity-dependent enhancement of swimming velocity. However, H. pylori csd1 mutants, which are curved but lack helical twist, show normal velocity in viscous polymer solutions and the reason for their deficiency in stomach colonization has remained unclear. Characterization of new rod shaped mutants identified Csd4, a DL-carboxypeptidase of peptidoglycan (PG) tripeptide monomers and Csd5, a putative scaffolding protein. Morphological and biochemical studies indicated Csd4 tripeptide cleavage and Csd1 crosslinking relaxation modify the PG sacculus through independent networks that coordinately generate helical shape. csd4 mutants show attenuation of stomach colonization, but no change in proinflammatory cytokine induction, despite four-fold higher levels of Nod1-agonist tripeptides in the PG sacculus. Motility analysis of similarly shaped mutants bearing distinct alterations in PG modifications revealed deficits associated with shape, but only in gel-like media and not viscous solutions. As gastric mucus displays viscoelastic gel-like properties, our results suggest enhanced penetration of the mucus barrier underlies the fitness advantage conferred by H. pylori's characteristic shape.
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Affiliation(s)
- Laura K. Sycuro
- Molecular and Cellular Biology Graduate Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Timna J. Wyckoff
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Division of Science and Mathematics, University of Minnesota, Morris, Minnesota, United States of America
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Petra Born
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Zachary Pincus
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nina R. Salama
- Molecular and Cellular Biology Graduate Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Regulski K, Courtin P, Meyrand M, Claes IJJ, Lebeer S, Vanderleyden J, Hols P, Guillot A, Chapot-Chartier MP. Analysis of the peptidoglycan hydrolase complement of Lactobacillus casei and characterization of the major γ-D-glutamyl-L-lysyl-endopeptidase. PLoS One 2012; 7:e32301. [PMID: 22384208 PMCID: PMC3288076 DOI: 10.1371/journal.pone.0032301] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/24/2012] [Indexed: 01/01/2023] Open
Abstract
Peptidoglycan (PG) is the major component of Gram positive bacteria cell wall and is essential for bacterial integrity and shape. Bacteria synthesize PG hydrolases (PGHs) which are able to cleave bonds in their own PG and play major roles in PG remodelling required for bacterial growth and division. Our aim was to identify the main PGHs in Lactobacillus casei BL23, a lactic acid bacterium with probiotic properties. The PGH complement was first identified in silico by amino acid sequence similarity searches of the BL23 genome sequence. Thirteen PGHs were detected with different predicted hydrolytic specificities. Transcription of the genes was confirmed by RT-PCR. A proteomic analysis combining the use of SDS-PAGE and LC-MS/MS revealed the main seven PGHs synthesized during growth of L. casei BL23. Among these PGHs, LCABL_02770 (renamed Lc-p75) was identified as the major one. This protein is the homolog of p75 (Msp1) major secreted protein of Lactobacillus rhamnosus GG, which was shown to promote survival and growth of intestinal epithelial cells. We identified its hydrolytic specificity on PG and showed that it is a γ-D-glutamyl-L-lysyl-endopeptidase. It has a marked specificity towards PG tetrapeptide chains versus tripeptide chains and for oligomers rather than monomers. Immunofluorescence experiments demonstrated that Lc-p75 localizes at cell septa in agreement with its role in daughter cell separation. It is also secreted under an active form as detected in zymogram. Comparison of the muropeptide profiles of wild type and Lc-p75-negative mutant revealed a decrease of the amount of disaccharide-dipeptide in the mutant PG in agreement with Lc-p75 activity. As a conclusion, Lc-p75 is the major L. casei BL23 PGH with endopeptidase specificity and a key role in daughter cell separation. Further studies will aim at investigating the role of Lc-p75 in the anti-inflammatory potential of L. casei BL23.
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Affiliation(s)
- Krzysztof Regulski
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Pascal Courtin
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Mickael Meyrand
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | | | - Sarah Lebeer
- Centre of Microbial and Plant Genetics, K.U. Leuven, Leuven, Belgium
| | - Jos Vanderleyden
- Centre of Microbial and Plant Genetics, K.U. Leuven, Leuven, Belgium
| | - Pascal Hols
- Biochimie et Génétique Moléculaire Bactérienne, Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Alain Guillot
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Marie-Pierre Chapot-Chartier
- Institut National de la Recherche Agronomique, UMR1319 Micalis, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- * E-mail:
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45
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Abstract
Complex glycoconjugates play critical roles in the biology of microorganisms. Despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. One of the primary pathways involves representatives of the ATP-binding cassette (ABC) transporter superfamily. These proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both Gram-positive and Gram-negative bacteria. Recent investigations of the structure and function of ABC transporters involved in the export of lipopolysaccharide O antigens have revealed two fundamentally different strategies for coupling glycan polymerization to export. These mechanisms are distinguished by the presence (or absence) of characteristic nonreducing terminal modifications on the export substrates, which serve as chain termination and/or export signals, and by the presence (or absence) of a discrete substrate-binding domain in the nucleotide-binding domain polypeptide of the ABC transporter. A bioinformatic survey examining ABC exporters from known oligo- and polysaccharide biosynthesis loci identifies conserved nucleotide-binding domain protein families that correlate well with themes in the structures and assembly of glycans. The familial relationships among the ABC exporters generate hypotheses concerning the biosynthesis of structurally diverse oligo- and polysaccharides, which play important roles in the biology of bacteria with different lifestyles.
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46
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Kondos SC, Hatfaludi T, Voskoboinik I, Trapani JA, Law RHP, Whisstock JC, Dunstone MA. The structure and function of mammalian membrane-attack complex/perforin-like proteins. ACTA ACUST UNITED AC 2010; 76:341-51. [PMID: 20860583 DOI: 10.1111/j.1399-0039.2010.01566.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The membrane-attack complex (MAC) of complement pathway and perforin (PF) are important tools deployed by the immune system to target pathogens. Both perforin and the C9 component of the MAC contain a common 'MACPF' domain and form pores in the cell membrane as part of their function. The MAC targets gram-negative bacteria and certain pathogenic parasites, while perforin, released by natural killer cells or cytotoxic T lymphocytes (CTLs), targets virus-infected and transformed host cells (1). Remarkably, recent structural studies show that the MACPF domain is homologous to the pore-forming portion of bacterial cholesterol-dependent cytolysins; these data have provided important insight into the mechanism of pore-forming MACPF proteins. In addition to their role in immunity, MACPF family members have been identified as animal venoms, factors required for pathogen migration across host cell membranes and factors that govern developmental processes such as embryonic patterning and neuronal guidance (2). While most MACPF proteins characterized to date either form pores or span lipid membranes, some do not (e.g. the C6 component of the MAC). A current challenge is thus to understand the role, pore forming or otherwise, of MACPF proteins in developmental biology. This review discusses structural and functional diversity of the mammalian MACPF proteins.
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Affiliation(s)
- S C Kondos
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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Su YC, Chin KH, Hung HC, Shen GH, Wang AHJ, Chou SH. Structure of Stenotrophomonas maltophilia FeoA complexed with zinc: a unique prokaryotic SH3-domain protein that possibly acts as a bacterial ferrous iron-transport activating factor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:636-42. [PMID: 20516589 DOI: 10.1107/s1744309110013941] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 04/15/2010] [Indexed: 11/10/2022]
Abstract
Iron is vital to the majority of prokaryotes, with ferrous iron believed to be the preferred form for iron uptake owing to its much better solubility. The major route for bacterial ferrous iron uptake is found to be via an Feo (ferrous iron-transport) system comprising the three proteins FeoA, FeoB and FeoC. Although the structure and function of FeoB have received much attention recently, the roles played by FeoA and FeoC have been little investigated to date. Here, the tertiary structure of FeoA from Stenotrophomonas maltophilia (Sm), a vital opportunistic pathogen in immunodepressed hosts, is reported. The crystal structure of SmFeoA has been determined to a resolution of 1.7 A using an Se single-wavelength anomalous dispersion (Se-SAD) approach. Although SmFeoA bears low sequence identity to eukaryotic proteins, its structure is found to adopt a eukaryotic SH3-domain-like fold. It also bears weak similarity to the C-terminal SH3 domain of bacterial DtxR (diphtheria toxin regulator), with some unique characteristics. Intriguingly, SmFeoA is found to adopt a unique dimer cross-linked by two zinc ions and six anions (chloride ions). Since FeoB has been found to contain a G-protein-like domain with low GTPase activity, FeoA may interact with FeoB through the SH3-G-protein domain interaction to act as a ferrous iron-transport activating factor.
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Affiliation(s)
- Yi Che Su
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
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48
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A role for the class A penicillin-binding protein PonA2 in the survival of Mycobacterium smegmatis under conditions of nonreplication. J Bacteriol 2010; 192:3043-54. [PMID: 20400545 DOI: 10.1128/jb.00025-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Class A penicillin-binding proteins (PBPs) are large, bifunctional proteins that are responsible for glycan chain assembly and peptide cross-linking of bacterial peptidoglycan. Bacteria in the genus Mycobacterium have been reported to have only two class A PBPs, PonA1 and PonA2, that are encoded in their genomes. We report here that the genomes of Mycobacterium smegmatis and other soil mycobacteria contain an additional gene encoding a third class A penicillin-binding protein, PonA3, which is a paralog of PonA2. Both the PonA2 and PonA3 proteins contain a penicillin-binding protein and serine/threonine protein kinase-associated (PASTA) domain that we propose may be involved in sensing the cell cycle and a C-terminal proline-rich region (PRR) that may have a role in protein-protein or protein-carbohydrate interactions. We show here that an M. smegmatis Delta ponA2 mutant has an unusual antibiotic susceptibility profile, exhibits a spherical morphology and an altered cell surface in stationary phase, and is defective for stationary-phase survival and recovery from anaerobic culture. In contrast, a Delta ponA3 mutant has no discernible phenotype under laboratory conditions. We demonstrate that PonA2 and PonA3 can bind penicillin and that PonA3 can partially substitute for PonA2 when ponA3 is expressed from a constitutive promoter on a multicopy plasmid. Our studies suggest that PonA2 is involved in adaptation to periods of nonreplication in response to starvation or anaerobiosis and that PonA3 may have a similar role. However, the regulation of PonA3 is likely different, suggesting that its importance could be related to stresses encountered in the environmental niches occupied by M. smegmatis and other soil-dwelling mycobacteria.
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Eldholm V, Johnsborg O, Straume D, Ohnstad HS, Berg KH, Hermoso JA, Håvarstein LS. Pneumococcal CbpD is a murein hydrolase that requires a dual cell envelope binding specificity to kill target cells during fratricide. Mol Microbiol 2010; 76:905-17. [PMID: 20384696 DOI: 10.1111/j.1365-2958.2010.07143.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pneumococci that are competent for natural genetic transformation express a number of proteins involved in binding, uptake, translocation and recombination of DNA. In addition, they attack and lyse non-competent sister cells present in the same environment. This phenomenon has been termed fratricide. The key effector of pneumococcal fratricide is CbpD, a secreted protein encompassing an N-terminal CHAP domain, two SH3b domains and a C-terminal choline-binding domain (CBD). CbpD is believed to degrade the cell wall of target cells, but experimental evidence supporting this hypothesis has been lacking. Here, we show that CbpD indeed has muralytic activity, and that this activity requires functional CBD and SH3b domains. To better understand the critical role played by the non-catalytic C-terminal region of CbpD, various translational fusions were constructed between the CBD and SH3b domains and green fluorescent protein (GFP). The results showed that the SH3b domains specifically recognize and bind peptidoglycan, while the CBD domain functions as a localization signal that directs CbpD to the septal region of the pneumococcal cell. Intriguingly, transmission electron microscopy analysis revealed that target cells attacked by CbpD ruptures at the septal region, in accordance with the binding specificity displayed by the CBD domain.
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Affiliation(s)
- Vegard Eldholm
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432, As, Norway
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Differentially conserved staphylococcal SH3b_5 cell wall binding domains confer increased staphylolytic and streptolytic activity to a streptococcal prophage endolysin domain. Gene 2009; 443:32-41. [DOI: 10.1016/j.gene.2009.04.023] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/16/2009] [Accepted: 04/24/2009] [Indexed: 11/19/2022]
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