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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.
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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
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Gallego-Parrilla JJ, Severi E, Chandra G, Palmer T. Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001431. [PMID: 38363712 PMCID: PMC10924467 DOI: 10.1099/mic.0.001431] [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: 11/08/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The twin-arginine protein transport (Tat) system exports folded proteins across the cytoplasmic membranes of prokaryotes and the energy transducing-membranes of plant thylakoids and mitochondria. Proteins are targeted to the Tat machinery by N-terminal signal peptides with a conserved twin-arginine motif, and some substrates are exported as heterodimers where the signal peptide is present on one of the partner proteins. A subset of Tat substrates is found in the membrane. Tat-dependent membrane proteins usually have large globular domains and a single transmembrane helix present at the N- or C-terminus. Five Tat substrates that have C-terminal transmembrane helices have previously been characterized in the model bacterium Escherichia coli. Each of these is an iron-sulfur cluster-containing protein involved in electron transfer from hydrogen or formate. Here we have undertaken a bioinformatic search to identify further tail-anchored Tat substrates encoded in bacterial genomes. Our analysis has revealed additional tail-anchored iron-sulfur proteins associated in modules with either a b-type cytochrome or a quinol oxidase. We also identified further candidate tail-anchored Tat substrates, particularly among members of the actinobacterial phylum, that are not predicted to contain cofactors. Using reporter assays, we show experimentally that six of these have both N-terminal Tat signal peptides and C-terminal transmembrane helices. The newly identified proteins include a carboxypeptidase and a predicted protease, and four sortase substrates for which membrane integration is a prerequisite for covalent attachment to the cell wall.
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Affiliation(s)
- José Jesús Gallego-Parrilla
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Emmanuele Severi
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Govind Chandra
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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3
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Liu B, Wei Q, Yang M, Shi L, Zhang K, Ge B. Effect of toyF on wuyiencin and toyocamycin production by Streptomyces albulus CK-15. World J Microbiol Biotechnol 2022; 38:65. [PMID: 35229201 DOI: 10.1007/s11274-022-03234-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022]
Abstract
Streptomyces albulus CK-15 produces various secondary metabolites, including the antibiotics wuyiencin and toyocamycin, which can reportedly control a broad range of plant fungal diseases. The production of these nucleoside antibiotics in CK-15 is regulated by two biosynthesis gene clusters. To investigate the potential effect of toyocamycin biosynthesis on wuyiencin production, we herein generated S. albulus strains in which a key gene in the toyocamycin biosynthesis gene cluster, namely toyF, was either deleted or overexpressed. The toyF deletion mutant ∆toyF did not produce toyocamycin, while the production of wuyiencin increased by 23.06% in comparison with that in the wild-type (WT) strain. In addition, ΔtoyF reached the highest production level of wuyiencin 4 h faster than the WT strain (60 h vs. and 64 h). Further, toyocamycin production by the toyF overexpression strain was two-fold higher than by the WT strain, while wuyiencin production was reduced by 29.10%. qRT-PCR showed that most genes in the toyocamycin biosynthesis gene cluster were expressed at lower levels in ∆toyF as compared with those in the WT strain, while the expression levels of genes in the wuyiencin biosynthesis gene cluster were upregulated. Finally, the growth rate of ∆toyF was much faster than that of the WT strain when cultured on solid or liquid medium. Based on our findings, we report that in industrial fermentation processes, ∆toyF has the potential to increase the production of wuyiencin and reduce the timeframe of fermentation.
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Affiliation(s)
- Binghua Liu
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Qiuhe Wei
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaoling Yang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liming Shi
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kecheng Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Beibei Ge
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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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.
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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
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Mannose- and Mannobiose-Specific Responses of the Insect-Associated Cellulolytic Bacterium Streptomyces sp. Strain SirexAA-E. Appl Environ Microbiol 2021; 87:e0271920. [PMID: 33990299 DOI: 10.1128/aem.02719-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The cellulolytic insect symbiont bacterium Streptomyces sp. strain SirexAA-E secretes a suite of carbohydrate-active enzymes (CAZymes), which are involved in the degradation of various polysaccharides in the plant cell wall, in response to the available carbon sources. Here, we examined a poorly understood response of this bacterium to mannan, one of the major plant cell wall components. SirexAA-E grew well on mannose, carboxymethyl cellulose (CMC), and locust bean gum (LBG) as sole carbon sources in the culture medium. The secreted proteins from each culture supernatant were tested for their polysaccharide-degrading ability, and the composition of secreted CAZymes in each sample was determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results indicated that mannose, LBG, and CMC induced the secretion of mannan and cellulose-degrading enzymes. Interestingly, two α-1,2-mannosidases were abundantly secreted during growth on mannose and LBG. Using genomic analysis, we found a unique 12-bp palindromic sequence motif at 4 locations in the SirexAA-E genome, two of which were found upstream of the above-mentioned α-1,2-mannosidase genes, along with a newly identified mannose and mannobiose-responsive transcriptional regulator, SsManR. Furthermore, the previously reported cellobiose-responsive repressor, SsCebR, was determined to also use mannobiose as an effector ligand. To test whether mannobiose induces the sets of genes under the control of the two regulators, SirexAA-E was grown on mannobiose, and the secretome composition was analyzed. As hypothesized, the composition of the mannobiose secretome combined sets of CAZymes found in both LBG and CMC secretomes, and thus they are likely under the regulation of both SsManR and SsCebR. IMPORTANCE Streptomyces sp. SirexAA-E, a microbial symbiont of biomass-harvesting insects, secretes a suite of polysaccharide-degrading enzymes dependent on the available carbon sources. However, the response of this bacterium to mannan has not been documented. In this study, we investigated the response of this bacterium to mannose, mannobiose, and galactomannan (LBG). By combining biochemical, proteomic, and genomic approaches, we discovered a novel mannose and mannobiose responsive transcriptional regulator, SsManR, which selectively regulates three α-1,2-mannosidase-coding genes. We also demonstrated that the previously described cellobiose responsive regulator, SsCebR, could use mannobiose as an effector ligand. Overall, our findings suggest that the Streptomyces sp. SirexAA-E responds to mannose and mannooligosaccharides through two different transcriptional repressors that regulate the secretion of the plant cell wall-degrading enzymes to extract carbon sources in the host environment.
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Susmitha A, Bajaj H, Madhavan Nampoothiri K. The divergent roles of sortase in the biology of Gram-positive bacteria. ACTA ACUST UNITED AC 2021; 7:100055. [PMID: 34195501 PMCID: PMC8225981 DOI: 10.1016/j.tcsw.2021.100055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/16/2022]
Abstract
The bacterial cell wall contains numerous surface-exposed proteins, which are covalently anchored and assembled by a sortase family of transpeptidase enzymes. The sortase are cysteine transpeptidases that catalyzes the covalent attachment of surface protein to the cell wall peptidoglycan. Among the reported six classes of sortases, each distinct class of sortase plays a unique biological role in anchoring a variety of surface proteins to the peptidoglycan of both pathogenic and non-pathogenic Gram-positive bacteria. Sortases not only exhibit virulence and pathogenesis properties to host cells, but also possess a significant role in gut retention and immunomodulation in probiotic microbes. The two main distinct functions are to attach proteins directly to the cell wall or assemble pili on the microbial surface. This review provides a compendium of the distribution of different classes of sortases present in both pathogenic and non-pathogenic Gram-positive bacteria and also the noteworthy role played by them in bacterial cell wall assembly which enables each microbe to effectively interact with its environment.
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Affiliation(s)
- Aliyath Susmitha
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Harsha Bajaj
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
| | - Kesavan Madhavan Nampoothiri
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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7
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Multifunctional Amyloids in the Biology of Gram-Positive Bacteria. Microorganisms 2020; 8:microorganisms8122020. [PMID: 33348645 PMCID: PMC7766987 DOI: 10.3390/microorganisms8122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/18/2023] Open
Abstract
Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.
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8
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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.
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Anderl A, Kolmar H, Fuchsbauer HL. The metal-binding properties of the long chaplin from Streptomyces mobaraensis: A bioinformatic and biochemical approach. J Inorg Biochem 2019; 202:110878. [PMID: 31698184 DOI: 10.1016/j.jinorgbio.2019.110878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
Chaplins are amphiphilic proteins coating the surface of aerial hyphae under formation of amyloid-like rodlet layers in streptomycetes. The long chaplin from Streptomyces mobaraensis, Sm-Chp1, harbors extended histidine-rich stretches allowing protein attachment to metal affinity resins. A comprehensive BLASTP search revealed similarity with many putative metal-binding proteins but the deduced sequence motifs were not shared by histidine-rich domains of well-studied proteins. Biochemical analyses showed affinity of Sm-Chp1 for Ni2+, Cu2+ and Zn2+, a binding capacity of 7-8 metal ions, and dissociation constants in a double digit micromolar range. The occurrence of genes for membrane-bound metal transporters and several intra- and extracellular metalloenzymes in the genome of S. mobaraensis suggests that Sm-Chp1 may be a novel type of translocase shifting metals across the rodlet layer from the environment into the cell wall.
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Affiliation(s)
- Anita Anderl
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany; Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany.
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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.
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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
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11
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A comprehensive in silico analysis of sortase superfamily. J Microbiol 2019; 57:431-443. [DOI: 10.1007/s12275-019-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/22/2022]
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12
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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.
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Van Gerven N, Van der Verren SE, Reiter DM, Remaut H. The Role of Functional Amyloids in Bacterial Virulence. J Mol Biol 2018; 430:3657-3684. [PMID: 30009771 PMCID: PMC6173799 DOI: 10.1016/j.jmb.2018.07.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 12/14/2022]
Abstract
Amyloid fibrils are best known as a product of human and animal protein misfolding disorders, where amyloid formation is associated with cytotoxicity and disease. It is now evident that for some proteins, the amyloid state constitutes the native structure and serves a functional role. These functional amyloids are proving widespread in bacteria and fungi, fulfilling diverse functions as structural components in biofilms or spore coats, as toxins and surface-active fibers, as epigenetic material, peptide reservoirs or adhesins mediating binding to and internalization into host cells. In this review, we will focus on the role of functional amyloids in bacterial pathogenesis. The role of functional amyloids as virulence factor is diverse but mostly indirect. Nevertheless, functional amyloid pathways deserve consideration for the acute and long-term effects of the infectious disease process and may form valid antimicrobial targets. Functional amyloids are widespread in bacteria, pathogenic and non-pathogenic. Bacterial biofilms most commonly function as structural support in the extracellular matrix of biofilms or spore coats, and in cell–cell and cell-surface adherence. The amyloid state can be the sole structured and functional state, or can be facultative, as a secondary state to folded monomeric subunits. Bacterial amyloids can enhance virulence by increasing persistence, cell adherence and invasion, intracellular survival, and pathogen spread by increased environmental survival. Bacterial amyloids may indirectly inflict disease by triggering inflammation, contact phase activation and possibly induce or aggravate human pathological aggregation disorders.
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Affiliation(s)
- Nani Van Gerven
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sander E Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Dirk M Reiter
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
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14
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Howlett R, Read N, Varghese A, Kershaw C, Hancock Y, Smith MCM. Streptomyces coelicolor strains lacking polyprenol phosphate mannose synthase and protein O-mannosyl transferase are hyper-susceptible to multiple antibiotics. MICROBIOLOGY-SGM 2018; 164:369-382. [PMID: 29458553 PMCID: PMC5882110 DOI: 10.1099/mic.0.000605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Polyprenol phosphate mannose (PPM) is a lipid-linked sugar donor used by extra-cytoplasmic glycosyl tranferases in bacteria. PPM is synthesized by polyprenol phosphate mannose synthase, Ppm1, and in most Actinobacteria is used as the sugar donor for protein O-mannosyl transferase, Pmt, in protein glycosylation. Ppm1 and Pmt have homologues in yeasts and humans, where they are required for protein O-mannosylation. Actinobacteria also use PPM for lipoglycan biosynthesis. Here we show that ppm1 mutants of Streptomyces coelicolor have increased susceptibility to a number of antibiotics that target cell wall biosynthesis. The pmt mutants also have mildly increased antibiotic susceptibilities, in particular to β-lactams and vancomycin. Despite normal induction of the vancomycin gene cluster, vanSRJKHAX, the pmt and ppm1 mutants remained highly vancomycin sensitive indicating that the mechanism of resistance is blocked post-transcriptionally. Differential RNA expression analysis indicated that catabolic pathways were downregulated and anabolic ones upregulated in the ppm1 mutant compared to the parent or complemented strains. Of note was the increase in expression of fatty acid biosynthetic genes in the ppm1- mutant. A change in lipid composition was confirmed using Raman spectroscopy, which showed that the ppm1- mutant had a greater relative proportion of unsaturated fatty acids compared to the parent or the complemented mutant. Taken together, these data suggest that an inability to synthesize PPM (ppm1) and loss of the glycoproteome (pmt- mutant) can detrimentally affect membrane or cell envelope functions leading to loss of intrinsic and, in the case of vancomycin, acquired antibiotic resistance.
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Affiliation(s)
| | | | - Anpu Varghese
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Y Hancock
- Department of Physics, University of York, York, UK.,York Centre for Complex Systems Analysis, University of York, York, UK
| | - Margaret C M Smith
- Department of Biology, University of York, York, UK.,Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
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15
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Nikghalb KD, Horvath NM, Prelesnik JL, Banks OGB, Filipov PA, Row RD, Roark TJ, Antos JM. Expanding the Scope of Sortase-Mediated Ligations by Using Sortase Homologues. Chembiochem 2017; 19:185-195. [PMID: 29124839 DOI: 10.1002/cbic.201700517] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 02/04/2023]
Abstract
Sortase-catalyzed transacylation reactions are widely used for the construction of non-natural protein derivatives. However, the most commonly used enzyme for these strategies (sortase A from Staphylococcus aureus) is limited by its narrow substrate scope. To expand the range of substrates compatible with sortase-mediated reactions, we characterized the in vitro substrate preferences of eight sortase A homologues. From these studies, we identified sortase A enzymes that recognize multiple substrates that are unreactive toward sortase A from S. aureus. We further exploited the ability of sortase A from Streptococcus pneumoniae to recognize an LPATS substrate to perform a site-specific modification of the N-terminal serine residue in the naturally occurring antimicrobial peptide DCD-1L. Finally, we unexpectedly observed that certain substrates (LPATXG, X=Nle, Leu, Phe, Tyr) were susceptible to transacylation at alternative sites within the substrate motif, and sortase A from S. pneumoniae was capable of forming oligomers. Overall, this work provides a foundation for the further development of sortase enzymes for use in protein modification.
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Affiliation(s)
- Keyvan D Nikghalb
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Nicholas M Horvath
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Jesse L Prelesnik
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Orion G B Banks
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Pavel A Filipov
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - R David Row
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Travis J Roark
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - John M Antos
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
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16
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Som Chaudhury S, Das Mukhopadhyay C. Functional amyloids: interrelationship with other amyloids and therapeutic assessment to treat neurodegenerative diseases. Int J Neurosci 2017; 128:449-463. [PMID: 29076790 DOI: 10.1080/00207454.2017.1398153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sutapa Som Chaudhury
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, West Bengal, India
| | - Chitrangada Das Mukhopadhyay
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, West Bengal, India
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17
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Zhang P, Wu L, Zhu Y, Liu M, Wang Y, Cao G, Chen XL, Tao M, Pang X. Deletion of MtrA Inhibits Cellular Development of Streptomyces coelicolor and Alters Expression of Developmental Regulatory Genes. Front Microbiol 2017; 8:2013. [PMID: 29085353 PMCID: PMC5650626 DOI: 10.3389/fmicb.2017.02013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 09/29/2017] [Indexed: 11/18/2022] Open
Abstract
The developmental life cycle of Streptomyces species includes aerial hyphae formation and spore maturation, two distinct developmental processes that are controlled, respectively, by two families of developmental regulatory genes, bld and whi. In this study, we show that the response regulator MtrA (SCO3013) is critical for normal development of aerial hyphae in S. coelicolor and related species. ΔmtrA, a deletion mutant of the response regulator gene mtrA, exhibited the bald phenotype typical of bld mutants defective in aerial mycelium formation, with formation either much delayed or absent depending on the culture medium. Transcriptional analysis indicated that MtrA activates multiple genes involved in formation of aerial mycelium, including chp, rdl, and ram genes, as well as developmental regulatory genes of the bld and whi families. However, the major regulatory gene bldD showed enhanced expression in ΔmtrA, suggesting it is repressed by MtrA. electrophoretic mobility shift assays indicated that MtrA binds upstream of several genes with altered expression in ΔmtrA, including bldD and whiI, and sequences similar to the consensus binding sequence for MtrA of another actinomycete, Mycobacterium tuberculosis, were found in the bound sites. A loosely conserved recognition sequence containing two short, direct repeats was identified for MtrA of S. coelicolor and was validated using mutational analysis. MtrA homologs are widely distributed among Streptomyces species, and as with S. coelicolor, deletion of the mtrA homologs sve_2757 from S. venezuelae and sli_3357 from S. lividans resulted in conditional bald morphology. Our study suggests a critical and conserved role for MtrA in Streptomyces development.
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Affiliation(s)
- Peipei Zhang
- The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Lili Wu
- The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Yanping Zhu
- The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Meng Liu
- The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Yemin Wang
- The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Guangxiang Cao
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
| | - Xiu-Lan Chen
- The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Meifeng Tao
- The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
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18
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Dragoš A, Kovács ÁT, Claessen D. The Role of Functional Amyloids in Multicellular Growth and Development of Gram-Positive Bacteria. Biomolecules 2017; 7:biom7030060. [PMID: 28783117 PMCID: PMC5618241 DOI: 10.3390/biom7030060] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 01/15/2023] Open
Abstract
Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils in the two distant Gram-positive bacteria, Streptomyces coelicolor and Bacillus subtilis. We describe how amyloid fibrils contribute to a multitude of developmental processes in each of these systems, including multicellular growth and community development. Despite this variety of tasks, we know surprisingly little about how their assembly is organized to fulfill all these roles.
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Affiliation(s)
- Anna Dragoš
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Dennis Claessen
- Institute of Biology, Leiden University, 2333BE Leiden, The Netherlands.
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19
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Jacobitz AW, Kattke MD, Wereszczynski J, Clubb RT. Sortase Transpeptidases: Structural Biology and Catalytic Mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:223-264. [PMID: 28683919 DOI: 10.1016/bs.apcsb.2017.04.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent because of its ability to ligate biomolecules together in vitro via a covalent peptide bond. Here we review what is known about the structures and catalytic mechanism of sortase enzymes. Based on their primary sequences, most sortase homologs can be classified into six distinct subfamilies, called class A-F enzymes. Atomic structures reveal unique, class-specific variations that support alternate substrate specificities, while structures of sortase enzymes bound to sorting signal mimics shed light onto the molecular basis of substrate recognition. The results of computational studies are reviewed that provide insight into how key reaction intermediates are stabilized during catalysis, as well as the mechanism and dynamics of substrate recognition. Lastly, the reported in vitro activities of sortases are compared, revealing that the transpeptidation activity of SaSrtA is at least 20-fold faster than other sortases that have thus far been characterized. Together, the results of the structural, computational, and biochemical studies discussed in this review begin to reveal how sortases decorate the microbial surface with proteins and pili, and may facilitate ongoing efforts to discover therapeutically useful small molecule inhibitors.
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Affiliation(s)
- Alex W Jacobitz
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Michele D Kattke
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Jeff Wereszczynski
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - Robert T Clubb
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States.
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20
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Puorger C, Di Girolamo S, Lipps G. Elucidation of the Recognition Sequence of Sortase B from Bacillus anthracis by Using a Newly Developed Liquid Chromatography–Mass Spectrometry-Based Method. Biochemistry 2017; 56:2641-2650. [DOI: 10.1021/acs.biochem.7b00108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chasper Puorger
- Institute for Chemistry and
Bioanalytics, University of Applied Sciences and Arts, Gründenstrasse
40, 4132 Muttenz, Switzerland
| | - Salvatore Di Girolamo
- Institute for Chemistry and
Bioanalytics, University of Applied Sciences and Arts, Gründenstrasse
40, 4132 Muttenz, Switzerland
| | - Georg Lipps
- Institute for Chemistry and
Bioanalytics, University of Applied Sciences and Arts, Gründenstrasse
40, 4132 Muttenz, Switzerland
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21
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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.
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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
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22
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Kattke MD, Chan AH, Duong A, Sexton DL, Sawaya MR, Cascio D, Elliot MA, Clubb RT. Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal. PLoS One 2016; 11:e0167763. [PMID: 27936128 PMCID: PMC5148588 DOI: 10.1371/journal.pone.0167763] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/18/2016] [Indexed: 01/17/2023] Open
Abstract
Many species of Gram-positive bacteria use sortase transpeptidases to covalently affix proteins to their cell wall or to assemble pili. Sortase-displayed proteins perform critical and diverse functions for cell survival, including cell adhesion, nutrient acquisition, and morphological development, among others. Based on their amino acid sequences, there are at least six types of sortases (class A to F enzymes); however, class E enzymes have not been extensively studied. Class E sortases are used by soil and freshwater-dwelling Actinobacteria to display proteins that contain a non-canonical LAXTG sorting signal, which differs from 90% of known sorting signals by substitution of alanine for proline. Here we report the first crystal structure of a class E sortase, the 1.93 Å resolution structure of the SrtE1 enzyme from Streptomyces coelicolor. The active site is bound to a tripeptide, providing insight into the mechanism of substrate binding. SrtE1 possesses β3/β4 and β6/β7 active site loops that contact the LAXTG substrate and are structurally distinct from other classes. We propose that SrtE1 and other class E sortases employ a conserved tyrosine residue within their β3/β4 loop to recognize the amide nitrogen of alanine at position P3 of the sorting signal through a hydrogen bond, as seen here. Incapability of hydrogen-bonding with canonical proline-containing sorting signals likely contributes to class E substrate specificity. Furthermore, we demonstrate that surface anchoring of proteins involved in aerial hyphae formation requires an N-terminal segment in SrtE1 that is presumably positioned within the cytoplasm. Combined, our results reveal unique features within class E enzymes that enable them to recognize distinct sorting signals, and could facilitate the development of substrate-based inhibitors of this important enzyme family.
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Affiliation(s)
- Michele D. Kattke
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Albert H. Chan
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Andrew Duong
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Danielle L. Sexton
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Michael R. Sawaya
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Duilio Cascio
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Marie A. Elliot
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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23
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Duong A, Koteva K, Sexton DL, Elliot MA. Liquid Chromatography-Tandem Mass Spectrometry to Define Sortase Cleavage Products. Methods Mol Biol 2016; 1440:99-108. [PMID: 27311667 DOI: 10.1007/978-1-4939-3676-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sortase enzymes have specific endopeptidase activity, cleaving within a defined pentapeptide sequence at the C-terminal end of their protein substrates. Here, we describe how monitoring sortase cleavage activity can be achieved using peptide substrates. Peptide cleavage can be readily analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS), which allows for the precise definition of cleavage sites. This technique could be used to analyze the peptidase activity of any enzyme, and identify sites of cleavage within any peptide.
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Affiliation(s)
- Andrew Duong
- Department of Biology, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Kalinka Koteva
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Danielle L Sexton
- Department of Biology, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Life Science Building, RM 329, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
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24
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Suryadinata R, Seabrook SA, Adams TE, Nuttall SD, Peat TS. Structural and biochemical analyses of a Clostridium perfringens sortase D transpeptidase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1505-13. [PMID: 26143922 PMCID: PMC4498605 DOI: 10.1107/s1399004715009219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/14/2015] [Indexed: 01/08/2023]
Abstract
The assembly and anchorage of various pathogenic proteins on the surface of Gram-positive bacteria is mediated by the sortase family of enzymes. These cysteine transpeptidases catalyze a unique sorting signal motif located at the C-terminus of their target substrate and promote the covalent attachment of these proteins onto an amino nucleophile located on another protein or on the bacterial cell wall. Each of the six distinct classes of sortases displays a unique biological role, with sequential activation of multiple sortases often observed in many Gram-positive bacteria to decorate their peptidoglycans. Less is known about the members of the class D family of sortases (SrtD), but they have a suggested role in spore formation in an oxygen-limiting environment. Here, the crystal structure of the SrtD enzyme from Clostridium perfringens was determined at 1.99 Å resolution. Comparative analysis of the C. perfringens SrtD structure reveals the typical eight-stranded β-barrel fold observed in all other known sortases, along with the conserved catalytic triad consisting of cysteine, histidine and arginine residues. Biochemical approaches further reveal the specifics of the SrtD catalytic activity in vitro, with a significant preference for the LPQTGS sorting motif. Additionally, the catalytic activity of SrtD is most efficient at 316 K and can be further improved in the presence of magnesium cations. Since C. perfringens spores are heat-resistant and lead to foodborne illnesses, characterization of the spore-promoting sortase SrtD may lead to the development of new antimicrobial agents.
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Affiliation(s)
- Randy Suryadinata
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Shane A. Seabrook
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Timothy E. Adams
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Stewart D. Nuttall
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Thomas S. Peat
- Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria 3052, Australia
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25
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Heck T, Pham PH, Hammes F, Thöny-Meyer L, Richter M. Continuous Monitoring of Enzymatic Reactions on Surfaces by Real-Time Flow Cytometry: Sortase A Catalyzed Protein Immobilization as a Case Study. Bioconjug Chem 2014; 25:1492-500. [DOI: 10.1021/bc500230r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tobias Heck
- Laboratory
for Bioactive Materials, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Phu-Huy Pham
- Laboratory
for Bioactive Materials, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Frederik Hammes
- Department
of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Linda Thöny-Meyer
- Laboratory
for Bioactive Materials, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Michael Richter
- Laboratory
for Bioactive Materials, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
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26
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Petrus MLC, Claessen D. Pivotal roles for Streptomyces cell surface polymers in morphological differentiation, attachment and mycelial architecture. Antonie van Leeuwenhoek 2014; 106:127-39. [PMID: 24682579 DOI: 10.1007/s10482-014-0157-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/12/2014] [Indexed: 01/07/2023]
Abstract
Cells that are part of a multicellular structure are typically embedded in an extracellular matrix, which is produced by the community members. These matrices, the composition of which is highly diverse between different species, are typically composed of large amounts of extracellular polymeric substances, including polysaccharides, proteins, and nucleic acids. The functions of all these matrices are diverse: they provide protection, mechanical stability, mediate adhesion to surfaces, regulate motility, and form a cohesive network in which cells are transiently immobilized. In this review we discuss the role of matrix components produced by streptomycetes during growth, development and attachment. Compared to other bacteria it appears that streptomycetes can form morphologically and functionally distinct matrices using a core set of building blocks.
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Affiliation(s)
- Marloes L C Petrus
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Sylviusweg 72, 2300 RA, Leiden, The Netherlands
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27
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Functional analysis of the accessory protein TapA in Bacillus subtilis amyloid fiber assembly. J Bacteriol 2014; 196:1505-13. [PMID: 24488317 DOI: 10.1128/jb.01363-13] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis biofilm formation relies on the assembly of a fibrous scaffold formed by the protein TasA. TasA polymerizes into highly stable fibers with biochemical and morphological features of functional amyloids. Previously, we showed that assembly of TasA fibers requires the auxiliary protein TapA. In this study, we investigated the roles of TapA sequences from the C-terminal and N-terminal ends and TapA cysteine residues in its ability to promote the assembly of TasA amyloid-like fibers. We found that the cysteine residues are not essential for the formation of TasA fibers, as their replacement by alanine residues resulted in only minor defects in biofilm formation. Mutating sequences in the C-terminal half had no effect on biofilm formation. However, we identified a sequence of 8 amino acids in the N terminus that is key for TasA fiber formation. Strains expressing TapA lacking these 8 residues were completely defective in biofilm formation. In addition, this TapA mutant protein exhibited a dominant negative effect on TasA fiber formation. Even in the presence of wild-type TapA, the mutant protein inhibited fiber assembly in vitro and delayed biofilm formation in vivo. We propose that this 8-residue sequence is crucial for the formation of amyloid-like fibers on the cell surface, perhaps by mediating the interaction between TapA or TapA and TasA molecules.
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28
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Complex intra-operonic dynamics mediated by a small RNA in Streptomyces coelicolor. PLoS One 2014; 9:e85856. [PMID: 24465751 PMCID: PMC3896431 DOI: 10.1371/journal.pone.0085856] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/03/2013] [Indexed: 11/18/2022] Open
Abstract
Streptomyces are predominantly soil-dwelling bacteria that are best known for their multicellular life cycle and their prodigious metabolic capabilities. They are also renowned for their regulatory capacity and flexibility, with each species encoding >60 sigma factors, a multitude of transcription factors, and an increasing number of small regulatory RNAs. Here, we describe our characterization of a conserved small RNA (sRNA), scr4677. In the model species Streptomyces coelicolor, this sRNA is located in the intergenic region separating SCO4677 (an anti-sigma factor-encoding gene) and SCO4676 (a putative regulatory protein-encoding gene), close to the SCO4676 translation start site in an antisense orientation. There appears to be considerable genetic interplay between these different gene products, with wild type expression of scr4677 requiring function of the anti-sigma factor SCO4677, and scr4677 in turn influencing the abundance of SCO4676-associated transcripts. The scr4677-mediated effects were independent of RNase III (a double stranded RNA-specific nuclease), with RNase III having an unexpectedly positive influence on the level of SCO4676-associated transcripts. We have shown that both SCO4676 and SCO4677 affect the production of the blue-pigmented antibiotic actinorhodin under specific growth conditions, and that this activity appears to be independent of scr4677.
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Surface modification using interfacial assembly of the Streptomyces chaplin proteins. Appl Microbiol Biotechnol 2014; 98:4491-501. [DOI: 10.1007/s00253-013-5463-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/27/2013] [Accepted: 12/09/2013] [Indexed: 12/23/2022]
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Heck T, Pham PH, Yerlikaya A, Thöny-Meyer L, Richter M. Sortase A catalyzed reaction pathways: a comparative study with six SrtA variants. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00347k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Different enzyme variants of sortase A fromStaphylococcus aureuswere found to have distinct catalytic properties with regard to site-directed protein fusion and competing intermolecular crosslinking reactions.
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Affiliation(s)
- Tobias Heck
- Empa
- Swiss Federal Laboratories for Materials Science and Technology
- Laboratory for Bioactive Materials
- 9014 St. Gallen, Switzerland
| | - Phu-Huy Pham
- Empa
- Swiss Federal Laboratories for Materials Science and Technology
- Laboratory for Bioactive Materials
- 9014 St. Gallen, Switzerland
| | - Alpaslan Yerlikaya
- Empa
- Swiss Federal Laboratories for Materials Science and Technology
- Laboratory for Bioactive Materials
- 9014 St. Gallen, Switzerland
| | - Linda Thöny-Meyer
- Empa
- Swiss Federal Laboratories for Materials Science and Technology
- Laboratory for Bioactive Materials
- 9014 St. Gallen, Switzerland
| | - Michael Richter
- Empa
- Swiss Federal Laboratories for Materials Science and Technology
- Laboratory for Bioactive Materials
- 9014 St. Gallen, Switzerland
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Konovalova A, Søgaard-Andersen L, Kroos L. Regulated proteolysis in bacterial development. FEMS Microbiol Rev 2013; 38:493-522. [PMID: 24354618 DOI: 10.1111/1574-6976.12050] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/03/2013] [Accepted: 10/14/2013] [Indexed: 11/30/2022] Open
Abstract
Bacteria use proteases to control three types of events temporally and spatially during the processes of morphological development. These events are the destruction of regulatory proteins, activation of regulatory proteins, and production of signals. While some of these events are entirely cytoplasmic, others involve intramembrane proteolysis of a substrate, transmembrane signaling, or secretion. In some cases, multiple proteolytic events are organized into pathways, for example turnover of a regulatory protein activates a protease that generates a signal. We review well-studied and emerging examples and identify recurring themes and important questions for future research. We focus primarily on paradigms learned from studies of model organisms, but we note connections to regulated proteolytic events that govern bacterial adaptation, biofilm formation and disassembly, and pathogenesis.
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Affiliation(s)
- Anna Konovalova
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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Chaplins of Streptomyces coelicolor self-assemble into two distinct functional amyloids. J Struct Biol 2013; 184:301-9. [DOI: 10.1016/j.jsb.2013.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/23/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022]
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Swiercz JP, Nanji T, Gloyd M, Guarné A, Elliot MA. A novel nucleoid-associated protein specific to the actinobacteria. Nucleic Acids Res 2013; 41:4171-84. [PMID: 23427309 PMCID: PMC3627587 DOI: 10.1093/nar/gkt095] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Effective chromosome organization is central to the functioning of any cell. In bacteria, this organization is achieved through the concerted activity of multiple nucleoid-associated proteins. These proteins are not, however, universally conserved, and different groups of bacteria have distinct subsets that contribute to chromosome architecture. Here, we describe the characterization of a novel actinobacterial-specific protein in Streptomyces coelicolor. We show that sIHF (SCO1480) associates with the nucleoid and makes important contributions to chromosome condensation and chromosome segregation during Streptomyces sporulation. It also affects antibiotic production, suggesting an additional role in gene regulation. In vitro, sIHF binds DNA in a length-dependent but sequence-independent manner, without any obvious structural preferences. It does, however, impact the activity of topoisomerase, significantly altering DNA topology. The sIHF–DNA co-crystal structure reveals sIHF to be composed of two domains: a long N-terminal helix and a C-terminal helix-two turns-helix domain with two separate DNA interaction sites, suggesting a potential role in bridging DNA molecules.
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Affiliation(s)
- Julia P Swiercz
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
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DePas WH, Chapman MR. Microbial manipulation of the amyloid fold. Res Microbiol 2012; 163:592-606. [PMID: 23108148 PMCID: PMC3532741 DOI: 10.1016/j.resmic.2012.10.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/09/2012] [Indexed: 12/19/2022]
Abstract
Microbial biofilms are encased in a protein, DNA, and polysaccharide matrix that protects the community, promotes interactions with the environment, and helps cells adhere together. The protein component of these matrices is often a remarkably stable, β-sheet-rich polymer called amyloid. Amyloids form ordered, self-templating fibers that are highly aggregative, making them a valuable biofilm component. Some eukaryotic proteins inappropriately adopt the amyloid fold, and these misfolded protein aggregates disrupt normal cellular proteostasis, which can cause significant cytotoxicity. Indeed, until recently amyloids were considered solely the result of protein misfolding. However, research over the past decade has revealed how various organisms have capitalized on the amyloid fold by developing sophisticated biogenesis pathways that coordinate gene expression, protein folding, and secretion so that amyloid-related toxicities are minimized. How microbes manipulate amyloids, by augmenting their advantageous properties and by reducing their undesirable properties, will be the subject of this review.
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Affiliation(s)
- William H. DePas
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA
| | - Matthew R. Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan LSA, 830 North University Ave., Ann Arbor, MI, 48109, USA
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Bibb MJ, Domonkos A, Chandra G, Buttner MJ. Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σ(BldN) and a cognate anti-sigma factor, RsbN. Mol Microbiol 2012; 84:1033-49. [PMID: 22582857 DOI: 10.1111/j.1365-2958.2012.08070.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The chaplin and rodlin proteins together constitute the major components of the hydrophobic sheath that coats the aerial hyphae and spores in Streptomyces, and mutants lacking the chaplins are unable to erect aerial hyphae and differentiate on minimal media. We have gained insight into the developmental regulation of the chaplin (chp) and rodlin (rdl) genes by exploiting a new model species, Streptomyces venezuelae, which sporulates in liquid culture. Using microarrays, the chaplin and rodlin genes were found to be highly induced during submerged sporulation in a bldN-dependent manner. Using σ(BldN) ChIP-chip, we show that this dependence arises because the chaplin and rodlin genes are direct biochemical targets of σ(BldN) . sven3186 (here named rsbN for regulator of sigma BldN), the gene lying immediately downstream of bldN, was also identified as a target of σ(BldN) . Disruption of rsbN causes precocious sporulation and biochemical experiments demonstrate that RsbN functions as a σ(BldN) -specific anti-sigma factor.
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Affiliation(s)
- Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
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