1
|
Sivaramalingam SS, Jothivel D, Govindarajan DK, Kadirvelu L, Sivaramakrishnan M, Chithiraiselvan DD, Kandaswamy K. Structural and functional insights of sortases and their interactions with antivirulence compounds. Curr Res Struct Biol 2024; 8:100152. [PMID: 38989133 PMCID: PMC11231552 DOI: 10.1016/j.crstbi.2024.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 05/18/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Sortase proteins play a crucial role as integral membrane proteins in anchoring bacterial surface proteins by recognizing them through a Cell-Wall Sorting (CWS) motif and cleaving them at specific sites before initiating pilus assembly. Both sortases and their substrate proteins are major virulence factors in numerous Gram-positive pathogens, making them attractive targets for antimicrobial intervention. Recognizing the significance of virulence proteins, a comprehensive exploration of their structural and functional characteristics is essential to enhance our understanding of pilus assembly in diverse Gram-positive bacteria. Therefore, this review article discusses the structural features of different classes of sortases and pilin proteins, primarily serving as substrates for sortase-assembled pili. Moreover, it thoroughly examines the molecular-level interactions between sortases and their inhibitors, providing insights from both structural and functional perspectives. In essence, this review article will provide a contemporary and complete understanding of both sortase pathways and various strategies to target them effectively to counteract the virulence.
Collapse
Affiliation(s)
- Sowmiya Sri Sivaramalingam
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Deepsikha Jothivel
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Deenadayalan Karaiyagowder Govindarajan
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore
| | - Lohita Kadirvelu
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Muthusaravanan Sivaramakrishnan
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
- Department of Biotechnology, Mepco Schlenk Engineering College, Tamil Nadu, India
| | - Dhivia Dharshika Chithiraiselvan
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Kumaravel Kandaswamy
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| |
Collapse
|
2
|
Votvik AK, Røhr ÅK, Bissaro B, Stepnov AA, Sørlie M, Eijsink VGH, Forsberg Z. Structural and functional characterization of the catalytic domain of a cell-wall anchored bacterial lytic polysaccharide monooxygenase from Streptomyces coelicolor. Sci Rep 2023; 13:5345. [PMID: 37005446 PMCID: PMC10067821 DOI: 10.1038/s41598-023-32263-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/24/2023] [Indexed: 04/04/2023] Open
Abstract
Bacterial lytic polysaccharide monooxygenases (LPMOs) are known to oxidize the most abundant and recalcitrant polymers in Nature, namely cellulose and chitin. The genome of the model actinomycete Streptomyces coelicolor A3(2) encodes seven putative LPMOs, of which, upon phylogenetic analysis, four group with typical chitin-oxidizing LPMOs, two with typical cellulose-active LPMOs, and one which stands out by being part of a subclade of non-characterized enzymes. The latter enzyme, called ScLPMO10D, and most of the enzymes found in this subclade are unique, not only because of variation in the catalytic domain, but also as their C-terminus contains a cell wall sorting signal (CWSS), which flags the LPMO for covalent anchoring to the cell wall. Here, we have produced a truncated version of ScLPMO10D without the CWSS and determined its crystal structure, EPR spectrum, and various functional properties. While showing several structural and functional features typical for bacterial cellulose active LPMOs, ScLPMO10D is only active on chitin. Comparison with two known chitin-oxidizing LPMOs of different taxa revealed interesting functional differences related to copper reactivity. This study contributes to our understanding of the biological roles of LPMOs and provides a foundation for structural and functional comparison of phylogenetically distant LPMOs with similar substrate specificities.
Collapse
Affiliation(s)
- Amanda K Votvik
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
- INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway.
| |
Collapse
|
3
|
Malik A, Subramaniyam S, Kim CB, Manavalan B. SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information. Comput Struct Biotechnol J 2021; 20:165-174. [PMID: 34976319 PMCID: PMC8703055 DOI: 10.1016/j.csbj.2021.12.014] [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] [Received: 09/01/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Sortase enzymes are cysteine transpeptidases that embellish the surface of Gram-positive bacteria with various proteins thereby allowing these microorganisms to interact with their neighboring environment. It is known that several of their substrates can cause pathological implications, so researchers have focused on the development of sortase inhibitors. Currently, six different classes of sortases (A-F) are recognized. However, with the extensive application of bacterial genome sequencing projects, the number of potential sortases in the public databases has exploded, presenting considerable challenges in annotating these sequences. It is very laborious and time-consuming to characterize these sortase classes experimentally. Therefore, this study developed the first machine-learning-based two-layer predictor called SortPred, where the first layer predicts the sortase from the given sequence and the second layer predicts their class from the predicted sortase. To develop SortPred, we constructed an original benchmarking dataset and investigated 31 feature descriptors, primarily on five feature encoding algorithms. Afterward, each of these descriptors were trained using a random forest classifier and their robustness was evaluated with an independent dataset. Finally, we selected the final model independently for both layers depending on the performance consistency between cross-validation and independent evaluation. SortPred is expected to be an effective tool for identifying bacterial sortases, which in turn may aid in designing sortase inhibitors and exploring their functions. The SortPred webserver and a standalone version are freely accessible at: https://procarb.org/sortpred.
Collapse
Affiliation(s)
- Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul 03016, Republic of Korea
| | | | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea
| | | |
Collapse
|
4
|
Ishikawa E, Yamada T, Yamaji K, Serata M, Fujii D, Umesaki Y, Tsuji H, Nomoto K, Ito M, Okada N, Nagaoka M, Gomi A. Critical roles of a housekeeping sortase of probiotic Bifidobacterium bifidum in bacterium-host cell crosstalk. iScience 2021; 24:103363. [PMID: 34825137 PMCID: PMC8603203 DOI: 10.1016/j.isci.2021.103363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/09/2021] [Accepted: 10/25/2021] [Indexed: 10/30/2022] Open
Abstract
Bifidobacterium bifidum YIT 10347 (BF-1) is adhesive in vitro. Here we studied the molecular aspects of the BF-1 adhesion process. We identified and characterized non-adhesive mutants and found that a class E housekeeping sortase was critical for the adhesion to mucin. These mutants were significantly less adhesive to GCIY cells than was the wild type (WT), which protected GCIY cells against acid treatment more than did a non-adhesive mutant. The non-adhesive mutants aberrantly accumulated precursors of putative sortase-dependent proteins (SDPs). Recombinant SDPs bound to mucin. Disruption of the housekeeping sortase influenced expression of SDPs and pilus components. Mutants defective in a pilin or in an SDP showed the same adhesion properties as WT. Therefore, multiple SDPs and pili seem to work cooperatively to achieve adhesion, and the housekeeping sortase is responsible for cell wall anchoring of its substrates to ensure their proper biological function.
Collapse
Affiliation(s)
- Eiji Ishikawa
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Tetsuya Yamada
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Kazuaki Yamaji
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Masaki Serata
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Daichi Fujii
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Yoshinori Umesaki
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Hirokazu Tsuji
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Koji Nomoto
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan.,Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masahiro Ito
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Masato Nagaoka
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Atsushi Gomi
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| |
Collapse
|
5
|
Nitulescu G, Margina D, Zanfirescu A, Olaru OT, Nitulescu GM. Targeting Bacterial Sortases in Search of Anti-Virulence Therapies with Low Risk of Resistance Development. Pharmaceuticals (Basel) 2021; 14:ph14050415. [PMID: 33946434 PMCID: PMC8147154 DOI: 10.3390/ph14050415] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/29/2022] Open
Abstract
Increasingly ineffective antibiotics and rapid spread of multi- and pan-resistant bacteria represent a global health threat; hence, the need of developing new antimicrobial medicines. A first step in this direction is identifying new molecular targets, such as virulence factors. Sortase A represents a virulence factor essential for the pathogenesis of Gram-positive pathogens, some of which have a high risk for human health. We present here an exhaustive collection of sortases inhibitors grouped by relevant chemical features: vinyl sulfones, 3-aryl acrylic acids and derivatives, flavonoids, naphtoquinones, anthraquinones, indoles, pyrrolomycins, isoquinoline derivatives, aryl β-aminoethyl ketones, pyrazolethiones, pyridazinones, benzisothiazolinones, 2-phenyl-benzoxazole and 2-phenyl-benzofuran derivatives, thiadiazoles, triazolothiadiazoles, 2-(2-phenylhydrazinylidene)alkanoic acids, and 1,2,4-thiadiazolidine-3,5-dione. This review focuses on highlighting their structure–activity relationships, using the half maximal inhibitory concentration (IC50), when available, as an indicator of each compound effect on a specific sortase. The information herein is useful for acquiring knowledge on diverse natural and synthetic sortases inhibitors scaffolds and for understanding the way their structural variations impact IC50. It will hopefully be the inspiration for designing novel effective and safe sortase inhibitors in order to create new anti-infective compounds and to help overcoming the current worldwide antibiotic shortage.
Collapse
|
6
|
Anchoring surface proteins to the bacterial cell wall by sortase enzymes: how it started and what we know now. Curr Opin Microbiol 2021; 60:73-79. [PMID: 33611145 DOI: 10.1016/j.mib.2021.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 11/20/2022]
Abstract
In Gram-positive bacteria, the peptidoglycan serves as a placeholder for surface display of a unique class of monomeric and polymeric proteins, or pili - the precursors of which harbor a cell wall sorting signal with LPXTG motif that is recognized by a conserved transpeptidase enzyme called sortase. Since this original discovery over two decades ago, extensive genetic, biochemical and structural studies have illuminated the basic mechanisms of sortase-mediated cell wall anchoring of surface proteins and pili. We now know how LPXTG-containing surface proteins are folded post-translocationally, how sortase enzymes recognize substrates, and how a remnant of the cell wall sorting signal modulates intramembrane signaling. In this review, we will highlight new findings from a few model experimental paradigms and present future prospects for the field.
Collapse
|
7
|
Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum. Biochem J 2020; 476:3835-3847. [PMID: 31815278 DOI: 10.1042/bcj20190812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022]
Abstract
Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A-F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.
Collapse
|
8
|
Ramirez NA, Das A, Ton-That H. New Paradigms of Pilus Assembly Mechanisms in Gram-Positive Actinobacteria. Trends Microbiol 2020; 28:999-1009. [PMID: 32499101 DOI: 10.1016/j.tim.2020.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023]
Abstract
Adhesive pili in Gram-positive bacteria represent a variety of extracellular multiprotein polymers that mediate bacterial colonization of specific host tissues and associated pathogenesis. Pili are assembled in two distinct but coupled steps, an orderly crosslinking of pilin monomers and subsequent anchoring of the polymer to peptidoglycan, catalyzed by two transpeptidase enzymes - the pilus-specific sortase and the housekeeping sortase. Here, we review this biphasic assembly mechanism based on studies of two prototypical models, the heterotrimeric pili in Corynebacterium diphtheriae and the heterodimeric pili in Actinomyces oris, highlighting some newly emerged basic paradigms. The disparate mechanisms of protein ligation mediated by the pilus-specific sortase and the spatial positioning of adhesive pili on the cell surface modulated by the housekeeping sortase are among the notable highlights.
Collapse
Affiliation(s)
- Nicholas A Ramirez
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, CT, USA
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, CA, USA; Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, CA, USA.
| |
Collapse
|
9
|
Chang C, Wu C, Osipiuk J, Siegel SD, Zhu S, Liu X, Joachimiak A, Clubb RT, Das A, Ton-That H. Cell-to-cell interaction requires optimal positioning of a pilus tip adhesin modulated by gram-positive transpeptidase enzymes. Proc Natl Acad Sci U S A 2019; 116:18041-18049. [PMID: 31427528 PMCID: PMC6731673 DOI: 10.1073/pnas.1907733116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Assembly of pili on the gram-positive bacterial cell wall involves 2 conserved transpeptidase enzymes named sortases: One for polymerization of pilin subunits and another for anchoring pili to peptidoglycan. How this machine controls pilus length and whether pilus length is critical for cell-to-cell interactions remain unknown. We report here in Actinomyces oris, a key colonizer in the development of oral biofilms, that genetic disruption of its housekeeping sortase SrtA generates exceedingly long pili, catalyzed by its pilus-specific sortase SrtC2 that possesses both pilus polymerization and cell wall anchoring functions. Remarkably, the srtA-deficient mutant fails to mediate interspecies interactions, or coaggregation, even though the coaggregation factor CafA is present at the pilus tip. Increasing ectopic expression of srtA in the mutant progressively shortens pilus length and restores coaggregation accordingly, while elevated levels of shaft pilins and SrtC2 produce long pili and block coaggregation by SrtA+ bacteria. With structural studies, we uncovered 2 key structural elements in SrtA that partake in recognition of pilin substrates and regulate pilus length by inducing the capture and transfer of pilus polymers to the cell wall. Evidently, coaggregation requires proper positioning of the tip adhesin CafA via modulation of pilus length by the housekeeping sortase SrtA.
Collapse
Affiliation(s)
- Chungyu Chang
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, CA 90095;
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030
| | - Jerzy Osipiuk
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439
| | - Sara D Siegel
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030
| | - Shiwei Zhu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510
| | - Xiangan Liu
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, CT 06030
| | - Hung Ton-That
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, CA 90095;
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
| |
Collapse
|
10
|
Anderl A, Ferlemann C, Muth M, Henkel-Gupalo A, Ebenig A, Brenner-Weiß G, Kolmar H, Fuchsbauer HL. Biochemical study of sortase E2 from Streptomyces mobaraensis and determination of transglutaminase cross-linking sites. FEBS Lett 2019; 593:1944-1956. [PMID: 31155711 DOI: 10.1002/1873-3468.13466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 12/15/2022]
Abstract
Distinct streptomycetes such as Streptomyces mobaraensis produce the protein cross-linking enzyme transglutaminase. Bioinformatic analysis predicted the occurrence of seven sortases exerting transpeptidation reactions similarly to transglutaminase. Here, we report the production and characterization of sortase E2 (Sm-SrtE2) solubilized by removal of its membrane anchor domain. Sm-SrtE2 activity was measured using pentapeptides predicted to be cell wall sorting signals of putative sortase substrate proteins. Preferred linkage to Gly3 by Sm-SrtE2 was in the order LAETG>>LAHTG>>LAQTG~LANTG>LARTG. Chaplin 1 from S. mobaraensis was further demonstrated to be an excellent substrate of both the intrinsic Sm-SrtE2 and transglutaminase. The unexpected discovery showing Gln-62 and Gln-65 of Δ1-50 -Sm-SrtE2 as transglutaminase cross-linking sites suggests that low enzyme stability might be due to anchor domain truncation and a disordered N terminus.
Collapse
Affiliation(s)
- Anita Anderl
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany.,Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Cathrin Ferlemann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Marius Muth
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany.,Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany
| | - Antonina Henkel-Gupalo
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Aileen Ebenig
- Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Gerald Brenner-Weiß
- Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| |
Collapse
|
11
|
A comprehensive in silico analysis of sortase superfamily. J Microbiol 2019; 57:431-443. [DOI: 10.1007/s12275-019-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/22/2022]
|
12
|
Characterization of the housekeeping sortase from the human pathogen Propionibacterium acnes: first investigation of a class F sortase. Biochem J 2019; 476:665-682. [PMID: 30670573 DOI: 10.1042/bcj20180885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/17/2022]
Abstract
Sortase enzymes play an important role in Gram-positive bacteria. They are responsible for the covalent attachment of proteins to the surface of the bacteria and perform this task via a highly sequence-specific transpeptidation reaction. Since these immobilized proteins are often involved in pathogenicity of Gram-positive bacteria, characterization of this type of enzyme is also of medical relevance. Different classes of sortases (A-F) have been found, which recognize characteristic recognition sequences present in substrate proteins. Up to date, sortase A from Staphylococcus aureus, a housekeeping class A sortase, is the most thoroughly studied representative of the sortase family of enzymes. Here we report the in-depth characterization of the class F sortase from Propionibacterium acnes, a class of sortases that has not been investigated before. As Sortase F is the only transpeptidase found in the P. acnes genome, it is the housekeeping sortase of this organism. Sortase F from P. acnes shows a behavior similar to sortases from class A in terms of pH dependence, recognition sequence and catalytic activity; furthermore, its activity is independent of bivalent ions, which contrasts to sortase A from S. aureus We demonstrate that sortase F is useful for protein engineering applications, by producing a site-specifically conjugated homogenous antibody-drug conjugate with a potency similar to that of a conjugate prepared with sortase A. Thus, the detailed characterization presented here will not only enable the development of anti-virulence agents targeting P. acnes but also provides a powerful alternative to sortase A for protein engineering applications.
Collapse
|
13
|
Stanborough T, Suryadinata R, Fegan N, Powell SM, Tamplin M, Nuttall SD, Chandry PS. Characterisation of the Brochothrix thermosphacta sortase A enzyme. FEMS Microbiol Lett 2018; 365:5056718. [PMID: 30052925 DOI: 10.1093/femsle/fny184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/18/2018] [Indexed: 12/11/2022] Open
Abstract
Gram-positive bacteria utilise class A sortases to coat the surface of their cells with a diversity of proteins that facilitate interactions with their environment and play fundamental roles in cell physiology and virulence. A putative sortase A gene was identified in the genome of the poorly studied meat spoilage bacterium Brochothrix thermosphacta. To understand how this bacterium mediates interactions with its environment, an N-terminal truncated, His-tagged variant of this protein (His6-BtSrtA) was expressed and purified. Catalytic activity of recombinant His6-BtSrtA was investigated, including sorting motif recognition of target proteins and bioconjugation activity. Further, the B. thermosphacta genome was examined for the presence of sortase A (SrtA) protein substrates. His6-BtSrtA readily formed intermediate complexes with LPXTG-tagged proteins. Although the reaction was inefficient, nucleophilic attack of the resultant thioacyl intermediates by tri-glycine was observed. Genome examination identified 11 potential SrtA substrates, two of which contained protein domains associated with adherence of pathogens to host extracellular matrix proteins and cells, suggesting the B. thermosphacta SrtA may be indirectly involved in its attachment to meat surfaces. Thus, further work in this area could provide crucial insight into molecular mechanisms involved in the colonisation of meat by B. thermosphacta.
Collapse
Affiliation(s)
- Tamsyn Stanborough
- CSIRO Agriculture and Food, Werribee, VIC 3030, Australia.,CSIRO Manufacturing, Parkville, VIC 3030, Australia
| | | | - Narelle Fegan
- CSIRO Agriculture and Food, Werribee, VIC 3030, Australia
| | - Shane M Powell
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| | - Mark Tamplin
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| | | | | |
Collapse
|
14
|
Tsolis KC, Tsare EP, Orfanoudaki G, Busche T, Kanaki K, Ramakrishnan R, Rousseau F, Schymkowitz J, Rückert C, Kalinowski J, Anné J, Karamanou S, Klapa MI, Economou A. Comprehensive subcellular topologies of polypeptides in Streptomyces. Microb Cell Fact 2018; 17:43. [PMID: 29544487 PMCID: PMC5853079 DOI: 10.1186/s12934-018-0892-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. Results Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible. We first introduced a uniform, improved nomenclature that re-annotated the names of ~ 4000 proteins based on functional and structural information. Then protein localization was assigned de novo using prediction tools and edited by manual curation for 7494 proteins, including information for 183 proteins that resulted from a recent genome re-annotation and are not available in current databases. The S. lividans proteome was also linked with those of other model bacterial strains including Streptomyces coelicolor A3(2) and Escherichia coli K-12, based on protein homology, and can be accessed through an open web interface. Finally, experimental data derived from proteomics experiments have been incorporated and provide validation for protein existence or topology for 579 proteins. Proteomics also reveals proteins released from vesicles that bleb off the membrane. All export systems known in S. lividans are also presented and exported proteins assigned export routes, where known. Conclusions SToPSdb provides an updated and comprehensive protein localization annotation resource for S. lividans and other streptomycetes. It forms the basis for future linking to databases containing experimental data of proteomics, genomics and metabolomics studies for this organism. Electronic supplementary material The online version of this article (10.1186/s12934-018-0892-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Konstantinos C Tsolis
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Evridiki-Pandora Tsare
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece.,Department of General Biology, School of Medicine, University of Patras, Patras, Greece
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology-FoRTH, P.O. Box 1385, Iraklio, Crete, Greece
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Katerina Kanaki
- Institute of Molecular Biology and Biotechnology-FoRTH, P.O. Box 1385, Iraklio, Crete, Greece
| | - Reshmi Ramakrishnan
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain & Disease Research and VIB Switch Laboratory, Department for Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, 33594, Bielefeld, Germany
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Spyridoula Karamanou
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Maria I Klapa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Dpt. of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| |
Collapse
|
15
|
Jacobitz AW, Kattke MD, Wereszczynski J, Clubb RT. Sortase Transpeptidases: Structural Biology and Catalytic Mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:223-264. [PMID: 28683919 DOI: 10.1016/bs.apcsb.2017.04.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent because of its ability to ligate biomolecules together in vitro via a covalent peptide bond. Here we review what is known about the structures and catalytic mechanism of sortase enzymes. Based on their primary sequences, most sortase homologs can be classified into six distinct subfamilies, called class A-F enzymes. Atomic structures reveal unique, class-specific variations that support alternate substrate specificities, while structures of sortase enzymes bound to sorting signal mimics shed light onto the molecular basis of substrate recognition. The results of computational studies are reviewed that provide insight into how key reaction intermediates are stabilized during catalysis, as well as the mechanism and dynamics of substrate recognition. Lastly, the reported in vitro activities of sortases are compared, revealing that the transpeptidation activity of SaSrtA is at least 20-fold faster than other sortases that have thus far been characterized. Together, the results of the structural, computational, and biochemical studies discussed in this review begin to reveal how sortases decorate the microbial surface with proteins and pili, and may facilitate ongoing efforts to discover therapeutically useful small molecule inhibitors.
Collapse
Affiliation(s)
- Alex W Jacobitz
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Michele D Kattke
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Jeff Wereszczynski
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - Robert T Clubb
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States.
| |
Collapse
|
16
|
Khare B, V L Narayana S. Pilus biogenesis of Gram-positive bacteria: Roles of sortases and implications for assembly. Protein Sci 2017; 26:1458-1473. [PMID: 28493331 DOI: 10.1002/pro.3191] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/26/2022]
Abstract
Successful adherence, colonization, and survival of Gram-positive bacteria require surface proteins, and multiprotein assemblies called pili. These surface appendages are attractive pharmacotherapeutic targets and understanding their assembly mechanisms is essential for identifying a new class of 'anti-infectives' that do not elicit microbial resistance. Molecular details of the Gram-negative pilus assembly are available indepth, but the Gram-positive pilus biogenesis is still an emerging field and investigations continue to reveal novel insights into this process. Pilus biogenesis in Gram-positive bacteria is a biphasic process that requires enzymes called pilus-sortases for assembly and a housekeeping sortase for covalent attachment of the assembled pilus to the peptidoglycan cell wall. Emerging structural and functional data indicate that there are at least two groups of Gram-positive pili, which require either the Class C sortase or Class B sortase in conjunction with LepA/SipA protein for major pilin polymerization. This observation suggests two distinct modes of sortase-mediated pilus biogenesis in Gram-positive bacteria. Here we review the structural and functional biology of the pilus-sortases from select streptococcal pilus systems and their role in Gram-positive pilus assembly.
Collapse
Affiliation(s)
- Baldeep Khare
- Center for Structural Biology, School of Optometry, University of Alabama at Birmingham, Birmingham, USA
| | - Sthanam V L Narayana
- Center for Structural Biology, School of Optometry, University of Alabama at Birmingham, Birmingham, USA
| |
Collapse
|
17
|
Das S, Pawale VS, Dadireddy V, Singh AK, Ramakumar S, Roy RP. Structure and specificity of a new class of Ca 2+-independent housekeeping sortase from Streptomyces avermitilis provide insights into its non-canonical substrate preference. J Biol Chem 2017; 292:7244-7257. [PMID: 28270507 DOI: 10.1074/jbc.m117.782037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/06/2017] [Indexed: 11/06/2022] Open
Abstract
Surface proteins in Gram-positive bacteria are incorporated into the cell wall through a peptide ligation reaction catalyzed by transpeptidase sortase. Six main classes (A-F) of sortase have been identified of which class A sortase is meant for housekeeping functions. The prototypic housekeeping sortase A (SaSrtA) from Staphylococcus aureus cleaves LPXTG-containing proteins at the scissile T-G peptide bond and ligates protein-LPXT to the terminal Gly residue of the nascent cross-bridge of peptidoglycan lipid II precursor. Sortase-mediated ligation ("sortagging") of LPXTG-containing substrates and Gly-terminated nucleophiles occurs in vitro as well as in cellulo in the presence of Ca2+ and has been applied extensively for protein conjugations. Although the majority of applications emanate from SaSrtA, low catalytic efficiency, LPXTG specificity restriction, and Ca2+ requirement (particularly for in cellulo applications) remain a drawback. Given that Gram-positive bacteria genomes encode a variety of sortases, natural sortase mining can be a viable complementary approach akin to engineering of wild-type SaSrtA. Here, we describe the structure and specificity of a new class E sortase (SavSrtE) annotated to perform housekeeping roles in Streptomyces avermitilis Biochemical experiments define the attributes of an optimum peptide substrate, demonstrate Ca2+-independent activity, and provide insights about contrasting functional characteristics of SavSrtE and SaSrtA. Crystal structure, substrate docking, and mutagenesis experiments have identified a critical residue that dictates the preference for a non-canonical LAXTG recognition motif over LPXTG. These results have implications for rational tailoring of substrate tolerance in sortases. Besides, Ca2+-independent orthogonal specificity of SavSrtE is likely to expand the sortagging toolkit.
Collapse
Affiliation(s)
- Sreetama Das
- From the Department of Physics, Indian Institute of Science, Bangalore 560012, and
| | | | | | | | | | - Rajendra P Roy
- the National Institute of Immunology, Delhi 110067, India
| |
Collapse
|