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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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Mirza Agha M, Tavili E, Dabirmanesh B. Functional amyloids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:389-434. [PMID: 38811086 DOI: 10.1016/bs.pmbts.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
While amyloid has traditionally been viewed as a harmful formation, emerging evidence suggests that amyloids may also play a functional role in cell biology, contributing to normal physiological processes that have been conserved throughout evolution. Functional amyloids have been discovered in several creatures, spanning from bacteria to mammals. These amyloids serve a multitude of purposes, including but not limited to, forming biofilms, melanin synthesis, storage, information transfer, and memory. The functional role of amyloids has been consistently validated by the discovery of more functional amyloids, indicating a conceptual convergence. The biology of amyloids is well-represented by non-pathogenic amyloids, given the numerous ones already identified and the ongoing rate of new discoveries. In this chapter, functional amyloids in microorganisms, animals, and plants are described.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elaheh Tavili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Schlimpert S, Elliot MA. The Best of Both Worlds-Streptomyces coelicolor and Streptomyces venezuelae as Model Species for Studying Antibiotic Production and Bacterial Multicellular Development. J Bacteriol 2023; 205:e0015323. [PMID: 37347176 PMCID: PMC10367585 DOI: 10.1128/jb.00153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Streptomyces bacteria have been studied for more than 80 years thanks to their ability to produce an incredible array of antibiotics and other specialized metabolites and their unusual fungal-like development. Their antibiotic production capabilities have ensured continual interest from both academic and industrial sectors, while their developmental life cycle has provided investigators with unique opportunities to address fundamental questions relating to bacterial multicellular growth. Much of our understanding of the biology and metabolism of these fascinating bacteria, and many of the tools we use to manipulate these organisms, have stemmed from investigations using the model species Streptomyces coelicolor and Streptomyces venezuelae. Here, we explore the pioneering work in S. coelicolor that established foundational genetic principles relating to specialized metabolism and development, alongside the genomic and cell biology developments that led to the emergence of S. venezuelae as a new model system. We highlight key discoveries that have stemmed from studies of these two systems and discuss opportunities for future investigations that leverage the power and understanding provided by S. coelicolor and S. venezuelae.
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Affiliation(s)
- Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marie A. Elliot
- Department of Biology and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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Zanane C, Mitro S, Mazigh D, Lekchiri S, Hakim T, El Louali M, Latrache H, Zahir H. Characterization of Streptomyces Cell Surface by the Microbial Adhesion to Solvents Method. Int J Microbiol 2023; 2023:8841509. [PMID: 37214152 PMCID: PMC10195169 DOI: 10.1155/2023/8841509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
The cell surface physicochemical properties of Streptomyces should influencing the dispersal and adsorption of spores and hyphae in soil and should conditioning there interactions with organic or metal substances in the bioremediation of contaminated environment. These properties are concerning surface hydrophobicity, electron donor/acceptor, and charge surface. To date, only hydrophobicity of Streptomyces was studied by contact angle measurements and microbial adhesion to hydrocarbons (MATH). In this work, we studied the electron donor/acceptor character of the Streptomyces cell surface in two ionic strength 10-3 M and 10-1 M of KNO3. Thus, to facilitate the characterisation of the surfaces of microbial cells, we used a simple, rapid, and quantitative technique, the microbial adhesion method to solvents (MATS), which is based on the comparison of the affinity of microbial cells for a monopolar solvent with a polar solvent. The monopolar solvent can be acid (electron acceptor) or basic (electron donor), but both solvents should have a surface tension similar to that of the Kifshitz van der Waals components. At the significant ionic strength of the biological medium, the electron donor character is well expressed for all 14 Streptomyces strains with very significant differences among them ranging from 0% to 72.92%. When the cells were placed in a solution with a higher ionic strength, we were able to classify the donor character results into three categories. The first category is that the weak donor character of strains A53 and A58 became more expressed at 10-1 M KNO3 concentration. The second category is that three strains A30, A60, and A63 expressed a weaker character in a higher ionic strength. For the other strains, no expression of the donor trait was obtained at higher ionic strength. In a suspension with a concentration of 10-3 KNO3, only two strains expressed an electron acceptor character. This character is very important for strains A49, A57, A58, A60, A63, and A65 at 10-1M KNO3. This work has shown that these properties vary greatly depending on the Streptomyces strain. It is important to consider the change in physicochemical properties of surface cells with ionic strength when using Streptomyces in different bioprocesses.
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Affiliation(s)
- C. Zanane
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - S. Mitro
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - D. Mazigh
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - S. Lekchiri
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - T. Hakim
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - M. El Louali
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - H. Latrache
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - H. Zahir
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
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Bhowmick S, Shenouda ML, Tschowri N. Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces. MICROLIFE 2023; 4:uqad020. [PMID: 37223731 PMCID: PMC10117811 DOI: 10.1093/femsml/uqad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.
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Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mary L Shenouda
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Corresponding author. Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany. E-mail:
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Chen D, Nie M, Tang W, Zhang Y, Wang J, Lan Y, Chen Y, Du W. Whole lifecycle observation of single-spore germinated Streptomyces using a nanogap-stabilized microfluidic chip. MLIFE 2022; 1:341-349. [PMID: 38818224 PMCID: PMC10989842 DOI: 10.1002/mlf2.12039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/01/2022] [Accepted: 08/12/2022] [Indexed: 06/01/2024]
Abstract
Streptomyces is a model bacterium to study multicellular differentiation and the major reservoir for antibiotics discovery. However, the cellular-level lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools that can mimic their natural conditions. In this study, we developed a simple microfluidic chip for the cultivation and observation of the entire lifecycle of Streptomyces development from the single-cell perspective. The chip consists of channels for loading samples and supplying nutrients, microwell arrays for the seeding and growth of single spores, and air chambers beside the microwells that facilitate the development of aerial hyphae and spores. A unique feature of this chip is that each microwell is surrounded by a 1.5 µm nanogap connected to an air chamber, which provides a stabilized water-air interface. We used this chip to observe the lifecycle development of Streptomyces coelicolor and Streptomyces griseus germinated from single spores, which revealed differentiation of aerial hyphae with progeny spores at micron-scale water-air interfaces and air chambers. Finally, we demonstrated the applicability of this chip in phenotypic assays by showing that the microbial hormone A-Factor is involved in the regulatory pathways of aerial hyphae and spore formation. The microfluidic chip could become a robust tool for studying multicellular differentiation, single-spore heterogeneity, and secondary metabolism of single-spore germinated Streptomyces.
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Affiliation(s)
- Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Mengyue Nie
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wei Tang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of the Chinese Academy of SciencesBeijingChina
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7
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Seira Curto J, Surroca Lopez A, Casals Sanchez M, Tic I, Fernandez Gallegos MR, Sanchez de Groot N. Microbiome Impact on Amyloidogenesis. Front Mol Biosci 2022; 9:926702. [PMID: 35782871 PMCID: PMC9245625 DOI: 10.3389/fmolb.2022.926702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Our life is closely linked to microorganisms, either through a parasitic or symbiotic relationship. The microbiome contains more than 1,000 different bacterial species and outnumbers human genes by 150 times. Worryingly, during the last 10 years, it has been observed a relationship between alterations in microbiota and neurodegeneration. Several publications support the hypothesis that amyloid structures formed by microorganisms may trigger host proteins aggregation. In this review, we collect pieces of evidence supporting that the crosstalk between human and microbiota amyloid proteins could be feasible and, probably, a more common event than expected before. The combination of their outnumbers, the long periods of time that stay in our bodies, and the widespread presence of amyloid proteins in the bacteria Domain outline a worrying scenario. However, the identification of the exact microorganisms and the mechanisms through with they can influence human disease also opens the door to developing a new and diverse set of therapeutic strategies.
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Zhu Y, Wang X, Zhang J, Ni X, Zhang X, Tao M, Pang X. The regulatory gene wblA is a target of the orphan response regulator OrrA in Streptomyces coelicolor. Environ Microbiol 2022; 24:3081-3096. [PMID: 35384219 DOI: 10.1111/1462-2920.15992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
Our previous study using transposon mutagenesis indicated that disruption of the putative response regulator gene orrA impacted antibiotic production in Streptomyces coelicolor. In this study, the role of OrrA was further characterized by comparing the phenotypes and transcriptomic profiles of the wild-type S. coelicolor strain M145 and ΔorrA, a strain with an inactivated orrA gene. Chromatin immunoprecipitation using a strain expressing OrrA fused with FLAG showed that OrrA binds the promoter of wblA, whose expression was downregulated in ΔorrA. The interaction of OrrA with the wblA promoter was further validated by a pull-down assay. Similar to ΔorrA, the deletion mutant of wblA (ΔwblA) was defective in development, and developmental genes were expressed at similar levels in ΔorrA and ΔwblA. Although both OrrA and WblA downregulated actinorhodin and undecylprodigiosin, their roles in regulation of the calcium-dependent antibiotic and yellow-pigmented type I polyketide differed. sco1375, a gene of unknown function, was identified as another OrrA target, and overexpression of either sco1375 or wblA in ΔorrA partially restored the wild-type phenotype, indicating that these genes mediate some of the effects of OrrA. This study revealed targets of OrrA and provided more insights into the role of the orphan response regulator OrrA in Streptomyces. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yanping Zhu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.,Colleage of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xinyuan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jing Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xue Ni
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xia Zhang
- Qingdao Vland Biotech Group Inc, Qingdao, 266000, China
| | - Meifeng Tao
- The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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Zambri MP, Williams MA, Elliot MA. How Streptomyces thrive: Advancing our understanding of classical development and uncovering new behaviors. Adv Microb Physiol 2022; 80:203-236. [PMID: 35489792 DOI: 10.1016/bs.ampbs.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Streptomyces are soil- and marine-dwelling microbes that need to survive dramatic fluctuations in nutrient levels and environmental conditions. Here, we explore the advances made in understanding how Streptomyces bacteria can thrive in their natural environments. We examine their classical developmental cycle, and the intricate regulatory cascades that govern it. We discuss alternative growth strategies and behaviors, like the rapid expansion and colonization properties associated with exploratory growth, the release of membrane vesicles and S-cells from hyphal tips, and the acquisition of exogenous DNA along the lateral walls. We further investigate Streptomyces interactions with other organisms through the release of volatile compounds that impact nutrient levels, microbial growth, and insect behavior. Finally, we explore the increasingly diverse strategies employed by Streptomyces species in escaping and thwarting phage infections.
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Affiliation(s)
- Matthew P Zambri
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michelle A Williams
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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Hassan MN, Nabi F, Khan AN, Hussain M, Siddiqui WA, Uversky VN, Khan RH. The amyloid state of proteins: A boon or bane? Int J Biol Macromol 2022; 200:593-617. [PMID: 35074333 DOI: 10.1016/j.ijbiomac.2022.01.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend.
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Affiliation(s)
- Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Murtaza Hussain
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem A Siddiqui
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 10 Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy 11 of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College 13 of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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Amyloid Aggregation of Streptococcus mutans Cnm Influences Its Collagen-Binding Activity. Appl Environ Microbiol 2021; 87:e0114921. [PMID: 34406827 PMCID: PMC8516039 DOI: 10.1128/aem.01149-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The cnm gene, coding for the glycosylated collagen- and laminin-binding surface adhesin Cnm, is found in the genomes of approximately 20% of Streptococcus mutans clinical isolates and is associated with systemic infections and increased caries risk. Other surface-associated collagen-binding proteins of S. mutans, such as P1 and WapA, have been demonstrated to form an amyloid quaternary structure with functional implications within biofilms. In silico analysis predicted that the β-sheet-rich N-terminal collagen-binding domain (CBD) of Cnm has a propensity for amyloid aggregation, whereas the threonine-rich C-terminal domain was predicted to be disorganized. In this study, thioflavin-T fluorescence and electron microscopy were used to show that Cnm forms amyloids in either its native glycosylated or recombinant nonglycosylated form and that the CBD of Cnm is the main amyloidogenic unit of Cnm. We then performed a series of in vitro, ex vivo, and in vivo assays to characterize the amylogenic properties of Cnm. In addition, Congo red birefringence indicated that Cnm is a major amyloidogenic protein of S. mutans biofilms. Competitive binding assays using collagen-coated microtiter plates and dental roots, a substrate rich in collagen, revealed that Cnm monomers inhibit S. mutans binding to collagenous substrates, whereas Cnm amyloid aggregates lose this property. Thus, while Cnm contributes to recognition and initial binding of S. mutans to collagen-rich surfaces, amyloid formation by Cnm might act as a negative regulatory mechanism to modulate collagen-binding activity within S. mutans biofilms and warrants further investigation. IMPORTANCE Streptococcus mutans is a keystone pathogen that promotes caries by acidifying the dental biofilm milieu. The collagen- and laminin-binding glycoprotein Cnm is a virulence factor of S. mutans. Expression of Cnm by S. mutans is hypothesized to contribute to niche expansion, allowing colonization of multiple sites in the body, including collagen-rich surfaces such as dentin and heart valves. Here, we suggest that Cnm function might be modulated by its aggregation status. As a monomer, its primary function is to promote attachment to collagenous substrates via its collagen-binding domain (CBD). However, in later stages of biofilm maturation, the same CBD of Cnm could self-assemble into amyloid fibrils, losing the ability to bind to collagen and likely becoming a component of the biofilm matrix. Our findings shed light on the role of functional amyloids in S. mutans pathobiology and ecology.
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Influence of Consistency and Composition of Growth Medium on Surface Physicochemical Properties of Streptomyces. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Streptomyces are known for their ability to produce various secondary metabolites used in biotechnology, human medicine and agriculture. Understanding of surface properties is very interesting in the control of interfacial phenomena. The objective of this study was to investigate the effect of consistency and composition of growth medium on the physicochemical properties of the surface of Streptomyces strains. To achieve this objective, Six Streptomyces strains belonging to bioprocess and bio-interfaces laboratory are cultivated in two media Bennett (rich) and GBA (minimum). Both media are tested in solid (agar) and liquid (broth) mode. The wettability θw, electron donor character ˠ (-), electron acceptor character ˠ (+) and Surface free energy ΔGiwi are determined using contact angle measurements. On the two solid media Bennett and GBA, Streptomyces strains develop a hydrophobic surface (96.9° <θw<167.9°) with a weak electron donor character (0.3 mJm-2 < (ˠ (-)) <12.14 mJm-2) and a strong electron acceptor character (0.26 mJm-2 < ˠ (+) < 17.8 mJm-2) and a negative surface free energy ((- 11.8 mJm-2) < ΔGiwi < (-110 mJm-2)). Whereas on both Bennett and GBA liquid media, the surfaces of Streptomyces strains are generally hydrophilic (1.3° < θw < 9.33°) with a strong electron donor character (13.76 mJm-2 < ( ˠ (-)) < 70.06 mJm-2) and a positive surface free energy. By changing the composition of the culture medium, only a slight change in the degree of hydrophobicity and surface free energy of Streptomyces is observed. Regarding the effect of medium composition on the surface properties of Streptomyces, the degree of wettability and the values of surface free energy are no longer the same when the composition of the medium changes. These results could be applied in further studies interested in interfacial phenomena and microbial adhesion in biotechnological fields.
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Muok AR, Claessen D, Briegel A. Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria. THE ISME JOURNAL 2021; 15:2591-2600. [PMID: 33723381 PMCID: PMC8397704 DOI: 10.1038/s41396-021-00952-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 01/31/2023]
Abstract
Streptomycetes are sessile bacteria that produce metabolites that impact the behavior of microbial communities. Emerging studies have demonstrated that Streptomyces spores are distributed through various mechanisms, but it remains unclear how spores are transported to their preferred microenvironments, such as plant roots. Here, we show that Streptomyces spores are capable of utilizing the motility machinery of other soil bacteria. Motility assays and microscopy studies reveal that Streptomyces spores are transported to plant tissues by interacting directly with the flagella of both gram-positive and gram-negative bacteria. Genetics experiments demonstrate that this form of motility is facilitated by structural proteins on the spore coat. These results demonstrate that nonmotile bacteria are capable of utilizing the motility machinery of other microbes to complete necessary stages of their lifecycle.
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Affiliation(s)
- Alise R. Muok
- grid.5132.50000 0001 2312 1970Institute for Biology, Leiden University, Leiden, The Netherlands ,grid.5132.50000 0001 2312 1970Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- grid.5132.50000 0001 2312 1970Institute for Biology, Leiden University, Leiden, The Netherlands ,grid.5132.50000 0001 2312 1970Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Ariane Briegel
- grid.5132.50000 0001 2312 1970Institute for Biology, Leiden University, Leiden, The Netherlands ,grid.5132.50000 0001 2312 1970Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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Identification of the cognate response regulator of the orphan histidine kinase OhkA involved in both secondary metabolism and morphological differentiation in Streptomyces coelicolor. Appl Microbiol Biotechnol 2021; 105:5905-5914. [PMID: 34287659 DOI: 10.1007/s00253-021-11442-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 10/20/2022]
Abstract
In the model actinomycete strain, Streptomyces coelicolor, an orphan histidine kinase (HK) named OhkA (encoded by SCO1596), which belongs to bacterial two-component regulatory systems (TCSs), has been identified as being involved in the regulation of both antibiotic biosynthesis and morphological development. However, its cognate response regulator (RR) remains unknown due to its isolated genetic location on the genome, which impedes the elucidation of the mechanism underlying OhkA-mediated regulation. Here, we identified the orphan RR OrrA (encoded by SCO3008) as the cognate RR of OhkA according to mutant phenotypic changes, transcriptomics analysis, and bacterial two-hybrid experiment. Considering that the partner RR of the orphan HK is also orphan, a library of mutants with in-frame individual deletion of these functionally unknown orphan RR-encoding genes were generated. Through phenotypic analysis, it was found that the ∆orrA mutant exhibited similar phenotypic changes as that of the ∆ohkA mutant, showing increased production of actinorhodin (ACT) and undecylprodigiosin (RED), and pink colony surface. Further transcriptomics analysis showed these two mutants exhibited highly similar transcriptomics profiles. Finally, the direct interaction between OhkA and OrrA was revealed by bacterial two-hybrid system. The identification of the partner RR of OhkA lays a good foundation for an in-depth elucidation of the molecular mechanism underlying OhkA-mediated regulation of development and antibiotic biosynthesis in Streptomyces. KEY POINTS: • OrrA was identified as the partner RR of the orphan histidine kinase OhkA. • The ∆orrA and ∆ohkA mutants showed similar phenotype and transcriptomic profiling. • Specific interaction of OrrA and OhkA was revealed by bacterial two-hybrid system.
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15
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Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [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: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
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Gómez-Pérez D, Chaudhry V, Kemen A, Kemen E. Amyloid Proteins in Plant-Associated Microbial Communities. Microb Physiol 2021; 31:88-98. [PMID: 34107493 DOI: 10.1159/000516014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/17/2021] [Indexed: 11/19/2022]
Abstract
Amyloids have proven to be a widespread phenomenon rather than an exception. Many proteins presenting the hallmarks of this characteristic beta sheet-rich folding have been described to date. Particularly common are functional amyloids that play an important role in the promotion of survival and pathogenicity in prokaryotes. Here, we describe important developments in amyloid protein research that relate to microbe-microbe and microbe-host interactions in the plant microbiome. Starting with biofilms, which are a broad strategy for bacterial persistence that is extremely important for plant colonization. Microbes rely on amyloid-based mechanisms to adhere and create a protective coating that shelters them from external stresses and promotes cooperation. Another strategy generally carried out by amyloids is the formation of hydrophobic surface layers. Known as hydrophobins, these proteins coat the aerial hyphae and spores of plant pathogenic fungi, as well as certain bacterial biofilms. They contribute to plant virulence through promoting dissemination and infectivity. Furthermore, antimicrobial activity is an interesting outcome of the amyloid structure that has potential application in medicine and agriculture. There are many known antimicrobial amyloids released by animals and plants; however, those produced by bacteria or fungi remain still largely unknown. Finally, we discuss amyloid proteins with a more indirect mode of action in their host interactions. These include virulence-promoting harpins, signaling transduction that functions through amyloid templating, and root nodule bacteria proteins that promote plant-microbe symbiosis. In summary, amyloids are an interesting paradigm for their many functional mechanisms linked to bacterial survival in plant-associated microbial communities.
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Affiliation(s)
| | | | - Ariane Kemen
- ZMBP/IMIT, University of Tübingen, Tübingen, Germany
| | - Eric Kemen
- ZMBP/IMIT, University of Tübingen, Tübingen, Germany
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17
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Current Understanding on Adhesion and Biofilm Development in Actinobacteria. Int J Microbiol 2021; 2021:6637438. [PMID: 34122552 PMCID: PMC8166509 DOI: 10.1155/2021/6637438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 05/07/2021] [Indexed: 12/30/2022] Open
Abstract
Biofilm formation and microbial adhesion are two related and complex phenomena. These phenomena are known to play an important role in microbial life and various functions with positive and negative aspects. Actinobacteria have wide distribution in aquatic and terrestrial ecosystems. This phylum is very large and diverse and contains two important genera Streptomyces and Mycobacteria. The genus Streptomyces is the most biotechnologically important, while the genus Mycobacteria contains the pathogenic species of Mycobacteriaceae. According to the literature, the majority of studies carried out on actinomycetes are focused on the detection of new molecules. Despite the well-known diversity and metabolic activities, less attention has been paid to this phylum. Research on adhesion and biofilm formation is not well developed. In the present review, an attempt has been made to review the literature available on the different aspects on biofilm formation and adhesion of Actinobacteria. We focus especially on the genus Streptomyces. Furthermore, a brief overview about the molecules and structures involved in the adhesion phenomenon in the most relevant genus is summarized. We mention the mechanisms of quorum sensing and quorum quenching because of their direct association with biofilm formation.
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18
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Genetic Network Architecture and Environmental Cues Drive Spatial Organization of Phenotypic Division of Labor in Streptomyces coelicolor. mBio 2021; 12:mBio.00794-21. [PMID: 34006658 PMCID: PMC8262882 DOI: 10.1128/mbio.00794-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of bacteria are known to differentiate into cells with distinct phenotypic traits during processes such as biofilm formation or the development of reproductive structures. These cell types, by virtue of their specialized functions, embody a division of labor. However, how bacteria build spatial patterns of differentiated cells is not well understood. Here, we examine the factors that drive spatial patterns in divisions of labor in colonies of Streptomyces coelicolor, a multicellular bacterium capable of synthesizing an array of antibiotics and forming complex reproductive structures (e.g., aerial hyphae and spores). Using fluorescent reporters, we demonstrate that the pathways for antibiotic biosynthesis and aerial hypha formation are activated in distinct waves of gene expression that radiate outwards in S. coelicolor colonies. We also show that the spatiotemporal separation of these cell types depends on a key activator in the developmental pathway, AdpA. Importantly, when we manipulated local gradients by growing competing microbes nearby, or through physical disruption, expression in these pathways could be decoupled and/or disordered, respectively. Finally, the normal spatial organization of these cell types was partially restored with the addition of a siderophore, a public good made by these organisms, to the growth medium. Together, these results indicate that spatial divisions of labor in S. coelicolor colonies are determined by a combination of physiological gradients and regulatory network architecture, key factors that also drive patterns of cellular differentiation in multicellular eukaryotic organisms.
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19
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Dokouhaki M, Hung A, Kasapis S, Gras SL. Hydrophobins and chaplins: Novel bio-surfactants for food dispersions a review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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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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21
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Oliveira R, Bush MJ, Pires S, Chandra G, Casas-Pastor D, Fritz G, Mendes MV. The novel ECF56 SigG1-RsfG system modulates morphological differentiation and metal-ion homeostasis in Streptomyces tsukubaensis. Sci Rep 2020; 10:21728. [PMID: 33303917 PMCID: PMC7730460 DOI: 10.1038/s41598-020-78520-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Extracytoplasmic function (ECF) sigma factors are key transcriptional regulators that prokaryotes have evolved to respond to environmental challenges. Streptomyces tsukubaensis harbours 42 ECFs to reprogram stress-responsive gene expression. Among them, SigG1 features a minimal conserved ECF σ2-σ4 architecture and an additional C-terminal extension that encodes a SnoaL_2 domain, which is characteristic for ECF σ factors of group ECF56. Although proteins with such domain organisation are widely found among Actinobacteria, the functional role of ECFs with a fused SnoaL_2 domain remains unknown. Our results show that in addition to predicted self-regulatory intramolecular amino acid interactions between the SnoaL_2 domain and the ECF core, SigG1 activity is controlled by the cognate anti-sigma protein RsfG, encoded by a co-transcribed sigG1-neighbouring gene. Characterisation of ∆sigG1 and ∆rsfG strains combined with RNA-seq and ChIP-seq experiments, suggests the involvement of SigG1 in the morphological differentiation programme of S. tsukubaensis. SigG1 regulates the expression of alanine dehydrogenase, ald and the WhiB-like regulator, wblC required for differentiation, in addition to iron and copper trafficking systems. Overall, our work establishes a model in which the activity of a σ factor of group ECF56, regulates morphogenesis and metal-ions homeostasis during development to ensure the timely progression of multicellular differentiation.
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Affiliation(s)
- Rute Oliveira
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCBiology), ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sílvia Pires
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Delia Casas-Pastor
- Center for Synthetic Microbiology, Philipps-University Marburg, 35032, Marburg, Germany
| | - Georg Fritz
- School for Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| | - Marta V Mendes
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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22
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Tenconi E, Traxler M, Tellatin D, van Wezel GP, Rigali S. Prodiginines Postpone the Onset of Sporulation in Streptomyces coelicolor. Antibiotics (Basel) 2020; 9:E847. [PMID: 33256178 PMCID: PMC7760128 DOI: 10.3390/antibiotics9120847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 01/29/2023] Open
Abstract
Bioactive natural products are typically secreted by the producer strain. Besides that, this allows the targeting of competitors, also filling a protective role, reducing the chance of self-killing. Surprisingly, DNA-degrading and membrane damaging prodiginines (PdGs) are only produced intracellularly, and are required for the onset of the second round of programmed cell death (PCD) in Streptomyces coelicolor. In this work, we investigated the influence of PdGs on the timing of the morphological differentiation of S. coelicolor. The deletion of the transcriptional activator gene redD that activates the red cluster for PdGs or nutrient-mediated reduction of PdG synthesis both resulted in the precocious appearance of mature spore chains. Transcriptional analysis revealed an accelerated expression of key developmental genes in the redD null mutant, including bldN for the developmental σ factor BldN which is essential for aerial mycelium formation. In contrast, PdG overproduction due to the enhanced copy number of redD resulted in a delay or block in sporulation. In addition, confocal fluorescence microscopy revealed that the earliest aerial hyphae do not produce PdGs. This suggests that filaments that eventually differentiate into spore chains and are hence required for survival of the colony, are excluded from the second round of PCD induced by PdGs. We propose that one of the roles of PdGs would be to delay the entrance of S. coelicolor into the dormancy state (sporulation) by inducing the leakage of the intracellular content of dying filaments thereby providing nutrients for the survivors.
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Affiliation(s)
- Elodie Tenconi
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liège, Belgium; (E.T.); (D.T.)
- Hedera-22, Boulevard du rectorat 27b, B-4000 Liège, Belgium
| | - Matthew Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA;
| | - Déborah Tellatin
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liège, Belgium; (E.T.); (D.T.)
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands;
| | - Sébastien Rigali
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liège, Belgium; (E.T.); (D.T.)
- Hedera-22, Boulevard du rectorat 27b, B-4000 Liège, Belgium
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23
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Zhu Y, Lu T, Zhang J, Zhang P, Tao M, Pang X. A novel XRE family regulator that controls antibiotic production and development in Streptomyces coelicolor. Appl Microbiol Biotechnol 2020; 104:10075-10089. [PMID: 33057789 DOI: 10.1007/s00253-020-10950-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 10/23/2022]
Abstract
Although the genome of the Streptomyces model strain S. coelicolor was sequenced nearly two decades ago, the function of many annotated genes has not been verified, including that of gene sco1979, which was predicted to encode a transcriptional regulator of the xenobiotic response element (XRE) family. In this study, we showed that SCO1979 represses its own transcription and that deletion of sco1979 from S. coelicolor markedly enhanced production of three antibiotics, which are actinorhodin (ACT), undecylprodigiosin (RED), and calcium-dependent antibiotic (CDA), suggesting that SCO1979 represses their biosynthesis. We demonstrated that transcription of genes in the ACT, RED, and CDA pathways was generally increased in the mutant strain Δ1979 compared with levels in the wild-type strain M145. Additionally, purified recombinant SCO1979 interacted with DNA sequences upstream of sco1979 and actII-orf4, redZ, and cdaR, the pathway-specific regulators for the three pathways, implying that SCO1979 potentially regulates the ACT, RED, and CDA pathways via their specific regulators. In addition, disruption of sco1979 led to the notably delayed formation of aerial mycelium and spores, and consistent with this, transcription of genes associated with aerial hyphae and spore formation, such as chp and rdl, and ram, was reduced in Δ1979, implying the involvement of SCO1979 in cellular development control as well. In summary, our findings demonstrated that SCO1979 is a pleiotropic regulator with roles in both secondary metabolism and morphological development in S. coelicolor. KEY POINTS: • SCO1979 is a novel Streptomyces regulator of the XRE family. • SCO1979 regulates its own transcription. • SCO1979 regulates antibiotic production and cellular development.
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Affiliation(s)
- Yanping Zhu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ting Lu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jing Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peipei Zhang
- Colleage of Biomedical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Meifeng Tao
- The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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24
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Levkovich SA, Gazit E, Laor Bar-Yosef D. Two Decades of Studying Functional Amyloids in Microorganisms. Trends Microbiol 2020; 29:251-265. [PMID: 33041179 DOI: 10.1016/j.tim.2020.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
In the past two decades, amyloids, typically associated with human diseases, have been described to play various functional roles in nearly all life forms. The structural and functional diversity of microbial 'functional amyloids' has dramatically increased in recent years, expanding the canonical definition of these assembled molecules. Here, we provide a broad review of the current understanding of microbial functional amyloids and their diverse roles, putting the spotlight on recent discoveries in the field. We discuss their functions as structural scaffolds, surface-tension modulators, adhesion molecules, cell-cycle and gametogenesis regulators, toxins, and mediators of host-pathogen interactions. We outline how noncanonical amyloid morphologies and sophisticated regulatory mechanisms underlie their functional diversity and emphasize their therapeutic and biotechnological implications and applications.
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Affiliation(s)
- Shon A Levkovich
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel; Sagol Interdisciplinary School of Neurosciences, Tel Aviv University, Tel Aviv, Israel.
| | - Dana Laor Bar-Yosef
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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25
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Kosolapova AO, Antonets KS, Belousov MV, Nizhnikov AA. Biological Functions of Prokaryotic Amyloids in Interspecies Interactions: Facts and Assumptions. Int J Mol Sci 2020; 21:E7240. [PMID: 33008049 PMCID: PMC7582709 DOI: 10.3390/ijms21197240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Amyloids are fibrillar protein aggregates with an ordered spatial structure called "cross-β". While some amyloids are associated with development of approximately 50 incurable diseases of humans and animals, the others perform various crucial physiological functions. The greatest diversity of amyloids functions is identified within prokaryotic species where they, being the components of the biofilm matrix, function as adhesins, regulate the activity of toxins and virulence factors, and compose extracellular protein layers. Amyloid state is widely used by different pathogenic bacterial species in their interactions with eukaryotic organisms. These amyloids, being functional for bacteria that produce them, are associated with various bacterial infections in humans and animals. Thus, the repertoire of the disease-associated amyloids includes not only dozens of pathological amyloids of mammalian origin but also numerous microbial amyloids. Although the ability of symbiotic microorganisms to produce amyloids has recently been demonstrated, functional roles of prokaryotic amyloids in host-symbiont interactions as well as in the interspecies interactions within the prokaryotic communities remain poorly studied. Here, we summarize the current findings in the field of prokaryotic amyloids, classify different interspecies interactions where these amyloids are involved, and hypothesize about their real occurrence in nature as well as their roles in pathogenesis and symbiosis.
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Affiliation(s)
- Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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Sexton DL, Tocheva EI. Ultrastructure of Exospore Formation in Streptomyces Revealed by Cryo-Electron Tomography. Front Microbiol 2020; 11:581135. [PMID: 33072052 PMCID: PMC7541840 DOI: 10.3389/fmicb.2020.581135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/04/2020] [Indexed: 02/02/2023] Open
Abstract
Many bacteria form spores in response to adverse environmental conditions. Several sporulation pathways have evolved independently and occur through distinctive mechanisms. Here, using cryo-electron tomography (cryo-ET), we examine all stages of growth and exospore formation in the model organism Streptomyces albus. Our data reveal the native ultrastructure of vegetative hyphae, including the likely structures of the polarisome and cytoskeletal filaments. In addition, we observed septal junctions in vegetative septa, predicted to be involved in protein and DNA translocation between neighboring cells. During sporulation, the cell envelope undergoes dramatic remodeling, including the formation of a spore wall and two protective proteinaceous layers. Mature spores reveal the presence of a continuous spore coat and an irregular rodlet sheet. Together, these results provide an unprecedented examination of the ultrastructure in Streptomyces and further our understanding of the structural complexity of exospore formation.
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Affiliation(s)
- Danielle L Sexton
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Elitza I Tocheva
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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27
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Haist J, Neumann SA, Al-Bassam MM, Lindenberg S, Elliot MA, Tschowri N. Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development. Mol Microbiol 2020; 114:808-822. [PMID: 32797697 DOI: 10.1111/mmi.14581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/20/2020] [Indexed: 12/26/2022]
Abstract
The second messenger bis-3,5-cyclic di-guanosine monophosphate (c-di-GMP) determines when Streptomyces initiate sporulation. c-di-GMP signals are integrated into the genetic differentiation network by the regulator BldD and the sigma factor σWhiG . However, functions of the development-specific diguanylate cyclases (DGCs) CdgB and CdgC, and the c-di-GMP phosphodiesterases (PDEs) RmdA and RmdB, are poorly understood. Here, we provide biochemical evidence that the GGDEF-EAL domain protein RmdB from S. venezuelae is a monofunctional PDE that hydrolyzes c-di-GMP to 5'pGpG. Despite having an equivalent GGDEF-EAL domain arrangement, RmdA cleaves c-di-GMP to GMP and exhibits residual DGC activity. We show that an intact EAL motif is crucial for the in vivo function of both enzymes since strains expressing protein variants with an AAA motif instead of EAL are delayed in development, similar to null mutants. Transcriptome analysis of ∆cdgB, ∆cdgC, ∆rmdA, and ∆rmdB strains revealed that the c-di-GMP specified by these enzymes has a global regulatory role, with about 20% of all S. venezuelae genes being differentially expressed in the cdgC mutant. Our data suggest that the major c-di-GMP-controlled targets determining the timing and mode of sporulation are genes involved in cell division and the production of the hydrophobic sheath that covers Streptomyces aerial hyphae and spores.
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Affiliation(s)
- Julian Haist
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sara Alina Neumann
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Sandra Lindenberg
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marie A Elliot
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Natalia Tschowri
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
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Latoscha A, Wörmann ME, Tschowri N. Nucleotide second messengers in Streptomyces. MICROBIOLOGY-SGM 2020; 165:1153-1165. [PMID: 31535967 DOI: 10.1099/mic.0.000846] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibiotic producing Streptomyces sense and respond to environmental signals by using nucleotide second messengers, including (p)ppGpp, cAMP, c-di-GMP and c-di-AMP. As summarized in this review, these molecules are important message carriers that coordinate the complex Streptomyces morphological transition from filamentous growth to sporulation along with the secondary metabolite production. Here, we provide an overview of the enzymes that make and break these second messengers and suggest candidates for (p)ppGpp and cAMP enzymes to be studied. We highlight the target molecules that bind these signalling molecules and elaborate individual functions that they control in the context of Streptomyces development. Finally, we discuss open questions in the field, which may guide future studies in this exciting research area.
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Affiliation(s)
- Andreas Latoscha
- Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mirka E Wörmann
- Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Natalia Tschowri
- Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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29
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Dokouhaki M, Prime EL, Qiao GG, Kasapis S, Day L, Gras SL. Structural-rheological characteristics of Chaplin E peptide at the air/water interface; a comparison with β-lactoglobulin and β-casein. Int J Biol Macromol 2020; 144:742-750. [PMID: 31837361 DOI: 10.1016/j.ijbiomac.2019.12.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 11/27/2022]
Abstract
The Chaplin E peptide is a surface-active agent that can adsorb to the air/water interface and form interfacial films that display distinct interfacial properties as a function of pH. The ~2 nm thick homogeneous Chaplin E film formed under acidic conditions contains ordered structures that give a high dilatational elasticity. In contrast, the heterogeneous film formed under basic conditions contained fibrils resulting in a rough ~17 nm thick film with predominantly viscoelastic properties, probably due to the reduced intermolecular interactions. These fibrils were also susceptible to breakage, fragmenting into shorter fibrils, which gave a greater elasticity. The fibrils also lead to a greater shear viscosity compared to the ordered structures aligned within the Chaplin E film at pH 3.0. A higher stability was observed for the foam formed by the Chaplin E compared to the foam formed by β-lactoglobulin, consistent with the greater rheological properties observed for the Chaplin E film at the interface. Our findings suggest that Chaplin E has potential to provide long time stability to dispersions in food, consumer goods or pharmaceutical applications, forming films with greater rheological properties and at least similar thickness to those formed by other surface-active proteins such as β-casein and β-lactoglobulin.
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Affiliation(s)
- Mina Dokouhaki
- School of Science, RMIT University, Bundoora West Campus, VIC 3083, Australia.
| | - Emma L Prime
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Greg G Qiao
- The Department of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Stefan Kasapis
- School of Science, RMIT University, Bundoora West Campus, VIC 3083, Australia
| | - Li Day
- AgResearch Ltd., Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand
| | - Sally L Gras
- The Department of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia; The Bio21 Molecular Science and Biotechnology Institute and The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, Vic 3010, Australia.
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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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Kosolapova AO, Belousov MV, Sulatskaya AI, Belousova ME, Sulatsky MI, Antonets KS, Volkov KV, Lykholay AN, Shtark OY, Vasileva EN, Zhukov VA, Ivanova AN, Zykin PA, Kuznetsova IM, Turoverov KK, Tikhonovich IA, Nizhnikov AA. Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum. Biomolecules 2019; 9:biom9110694. [PMID: 31690032 PMCID: PMC6920782 DOI: 10.3390/biom9110694] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Amyloids represent protein fibrils with a highly ordered spatial structure, which not only cause dozens of incurable human and animal diseases but also play vital biological roles in Archaea, Bacteria, and Eukarya. Despite the fact that association of bacterial amyloids with microbial pathogenesis and infectious diseases is well known, there is a lack of information concerning the amyloids of symbiotic bacteria. In this study, using the previously developed proteomic method for screening and identification of amyloids (PSIA), we identified amyloidogenic proteins in the proteome of the root nodule bacterium Rhizobium leguminosarum. Among 54 proteins identified, we selected two proteins, RopA and RopB, which are predicted to have β-barrel structure and are likely to be involved in the control of plant-microbial symbiosis. We demonstrated that the full-length RopA and RopB form bona fide amyloid fibrils in vitro. In particular, these fibrils are β-sheet-rich, bind Thioflavin T (ThT), exhibit green birefringence upon staining with Congo Red (CR), and resist treatment with ionic detergents and proteases. The heterologously expressed RopA and RopB intracellularly aggregate in yeast and assemble into amyloid fibrils at the surface of Escherichia coli. The capsules of the R. leguminosarum cells bind CR, exhibit green birefringence, and contain fibrils of RopA and RopB in vivo.
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Affiliation(s)
- Anastasiia O Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Mikhail V Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Maria E Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Kirill S Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Kirill V Volkov
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Anna N Lykholay
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Oksana Y Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Ekaterina N Vasileva
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Vladimir A Zhukov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Alexandra N Ivanova
- Research Resource Center "Molecular and Cell Technologies", Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Komarov Botanical Institute RAS, 197376 Komarov Botanical Institute RAS, Russia.
| | - Pavel A Zykin
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Russia.
- Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia.
| | - Igor A Tikhonovich
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg, 196608, Russia.
| | - Anton A Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
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32
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Schumacher MA, Bush MJ, Bibb MJ, Ramos-León F, Chandra G, Zeng W, Buttner MJ. The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor. Nucleic Acids Res 2019; 46:7405-7417. [PMID: 29905823 PMCID: PMC6101532 DOI: 10.1093/nar/gky493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/24/2018] [Indexed: 11/13/2022] Open
Abstract
Streptomyces are filamentous bacteria with a complex developmental life cycle characterized by the formation of spore-forming aerial hyphae. Transcription of the chaplin and rodlin genes, which are essential for aerial hyphae production, is directed by the extracytoplasmic function (ECF) σ factor BldN, which is in turn controlled by an anti-σ factor, RsbN. RsbN shows no sequence similarity to known anti-σ factors and binds and inhibits BldN in an unknown manner. Here we describe the 2.23 Å structure of the RsbN–BldN complex. The structure shows that BldN harbors σ2 and σ4 domains that are individually similar to other ECF σ domains, which bind −10 and −35 promoter regions, respectively. The anti-σ RsbN consists of three helices, with α3 forming a long helix embraced between BldN σ2 and σ4 while RsbN α1–α2 dock against σ4 in a manner that would block −35 DNA binding. RsbN binding also freezes BldN in a conformation inactive for simultaneous −10 and −35 promoter interaction and RNAP binding. Strikingly, RsbN is structurally distinct from previously solved anti-σ proteins. Thus, these data characterize the molecular determinants controlling a central Streptomyces developmental switch and reveal RsbN to be the founding member of a new structural class of anti-σ factor.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Félix Ramos-León
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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33
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Nodwell JR. Microbe Profile: Streptomyces coelicolor: a burlesque of pigments and phenotypes. MICROBIOLOGY-SGM 2019; 165:953-955. [PMID: 31368887 PMCID: PMC7376255 DOI: 10.1099/mic.0.000821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The streptomycetes are soil-dwelling bacteria that are found in soil everywhere on Earth: the molecule geosmin, which they produce as part of their life cycle, is what gives soil its familiar ‘earthy’ smell. The species is best known for the production of biologically active small molecules called ‘natural products’. These molecules are the source of most of our antibiotics and anti-fungals, as well as many other drugs. The streptomycetes have a filamentous form rather than the more familiar rod-shaped spirochete and coccoid forms. They exhibit a complex life cycle and sporulation mechanism involving several differentiated cell types, each having specific roles in the colony life history. Streptomyces coelicolor is an important model system for this genus – research on this bacterium has provided foundational information for all of these fascinating processes.
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Affiliation(s)
- Justin R Nodwell
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
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34
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Vollmer B, Steblau N, Ladwig N, Mayer C, Macek B, Mitousis L, Sigle S, Walter A, Wohlleben W, Muth G. Role of the Streptomyces spore wall synthesizing complex SSSC in differentiation of Streptomyces coelicolor A3(2). Int J Med Microbiol 2019; 309:151327. [PMID: 31324525 DOI: 10.1016/j.ijmm.2019.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 10/26/2022] Open
Abstract
A crucial stage of the Streptomyces life cycle is the sporulation septation, a process were dozens of cross walls are synchronously formed in the aerial hyphae in a highly coordinated manner. This process includes the remodeling of the spore envelopes to make Streptomyces spores resistant to detrimental environmental conditions. Sporulation septation and the synthesis of the thickened spore envelope in S. coelicolor A3(2) involves the Streptomyces spore wall synthesizing complex SSSC. The SSSC is a multi-protein complex including proteins directing peptidoglycan synthesis (MreBCD, PBP2, Sfr, RodZ) and cell wall glycopolymer synthesis (PdtA). It also includes two eukaryotic like serin/threonine protein kinases (eSTPK), PkaI and PkaH, which were shown to phosphorylate MreC. Since unbalancing phosphorylation activity by either deleting eSTPK genes or by expressing a second copy of an eSTPK gene affected proper sporulation, a model was developed, in which the activity of the SSSC is controlled by protein phosphorylation.
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Affiliation(s)
- B Vollmer
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - N Steblau
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - N Ladwig
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - C Mayer
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - B Macek
- Proteome Center Tuebingen, Interfakultaeres Institut für Zellbiologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - L Mitousis
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - S Sigle
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - A Walter
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - W Wohlleben
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - G Muth
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany.
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35
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Lonetto MA, Donohue TJ, Gross CA, Buttner MJ. Discovery of the extracytoplasmic function σ factors. Mol Microbiol 2019; 112:348-355. [PMID: 31115926 DOI: 10.1111/mmi.14307] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2019] [Indexed: 12/14/2022]
Abstract
This special issue of Molecular Microbiology marks the 25th anniversary of the discovery of the extracytoplasmic function (ECF) σ factors, proteins that subsequently emerged as the largest group of alternative σ factors and one of the three major pillars of signal transduction in bacteria, alongside one- and two-component systems. A single bacterial genome can encode > 100 ECF σ factors, and combined with their cognate anti-σ factors, they represent a modular design that primarily functions in transmembrane signal transduction. Here, we first describe the immediate events that led to the 1994 publication in the Proceeding of the National Academy of Sciences USA, and then set them in the broader context of key events in the history of σ biology research.
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Affiliation(s)
- Michael A Lonetto
- Department of Informatics, Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Timothy J Donohue
- Department of Bacteriology, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53706, USA
| | - Carol A Gross
- Department of Microbiology and Immunology and Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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36
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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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Thoma L, Vollmer B, Oesterhelt F, Muth G. Live-cell imaging of Streptomyces conjugation. Int J Med Microbiol 2019; 309:338-343. [PMID: 31175019 DOI: 10.1016/j.ijmm.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/06/2019] [Accepted: 05/26/2019] [Indexed: 11/19/2022] Open
Abstract
Time-lapse imaging of conjugative plasmid transfer in Streptomyces revealed intriguing insights into the unique two-step conjugation process of this Gram+ mycelial soil bacterium. Differentially labelling of donor and recipient strains with distinct fluorescent proteins allowed the visualization of plasmid transfer in living mycelium. In nearly all observed matings, plasmid transfer occurred when donor and recipient hyphae made intimate contact at the lateral walls. Plasmid transfer does not involve a complete fusion of donor and recipient hyphae, but depends on a pore formed by the FtsK-like DNA translocase TraB. Following the initial transfer at the contact site of donor and recipient, the plasmids spread within the recipient mycelium by invading neighboring compartments, separated by cross walls. Intra-mycelial plasmid spreading depends on a septal cross wall localized multi-protein DNA translocation apparatus consisting of TraB and several Spd proteins and is abolished in a spd mutant. The ability to spread within the recipient mycelium is a crucial adaptation to the mycelial life style of Streptomyces, potentiating the efficiency of plasmid transfer.
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Affiliation(s)
- L Thoma
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - B Vollmer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - F Oesterhelt
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen IMIT, Mikrobielle Wirkstoffe, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - G Muth
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany.
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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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Growth and differentiation properties of pikromycin-producing Streptomyces venezuelae ATCC15439. J Microbiol 2019; 57:388-395. [PMID: 30721456 DOI: 10.1007/s12275-019-8539-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
Abstract
Streptomycetes naturally produce a variety of secondary metabolites, in the process of physiological differentiation. Streptomyces venezuelae differentiates into spores in liquid media, serving as a good model system for differentiation and a host for exogenous gene expression. Here, we report the growth and differentiation properties of S. venezuelae ATCC-15439 in liquid medium, which produces pikromycin, along with genome-wide gene expression profile. Comparison of growth properties on two media (SPA, MYM) revealed that the stationary phase cell viability rapidly decreased in SPA. Submerged spores showed partial resistance to lysozyme and heat, similar to what has been observed for better-characterized S. venezuelae ATCC10712, a chloramphenicol producer. TEM revealed that the differentiated cells in the submerged culture showed larger cell size, thinner cell wall than the aerial spores. We analyzed transcriptome profiles of cells grown in liquid MYM at various growth phases. During transition and/or stationary phases, many differentiationrelated genes were well expressed as judged by RNA level, except some genes forming hydrophobic coats in aerial mycelium. Since submerged spores showed thin cell wall and partial resistance to stresses, we examined cellular expression of MreB protein, an actin-like protein known to be required for spore wall synthesis in Streptomycetes. In contrast to aerial spores where MreB was localized in septa and spore cell wall, submerged spores showed no detectable signal. Therefore, even though the mreB transcripts are abundant in liquid medium, its protein level and/or its interaction with spore wall synthetic complex appear impaired, causing thinner- walled and less sturdy spores in liquid culture.
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Bacterial Amyloids: Biogenesis and Biomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:113-159. [DOI: 10.1007/978-981-13-9791-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Daniels W, Bouvin J, Busche T, Rückert C, Simoens K, Karamanou S, Van Mellaert L, Friðjónsson ÓH, Nicolai B, Economou A, Kalinowski J, Anné J, Bernaerts K. Transcriptomic and fluxomic changes in Streptomyces lividans producing heterologous protein. Microb Cell Fact 2018; 17:198. [PMID: 30577858 PMCID: PMC6302529 DOI: 10.1186/s12934-018-1040-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/26/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Gram-positive Streptomyces lividans TK24 is an attractive host for heterologous protein production because of its high capability to secrete proteins-which favors correct folding and facilitates downstream processing-as well as its acceptance of methylated DNA and its low endogeneous protease activity. However, current inconsistencies in protein yields urge for a deeper understanding of the burden of heterologous protein production on the cell. In the current study, transcriptomics and [Formula: see text]-based fluxomics were exploited to uncover gene expression and metabolic flux changes associated with heterologous protein production. The Rhodothermus marinus thermostable cellulase A (CelA)-previously shown to be successfully overexpressed in S. lividans-was taken as an example protein. RESULTS RNA-seq and [Formula: see text]-based metabolic flux analysis were performed on a CelA-producing and an empty-plasmid strain under the same conditions. Differential gene expression, followed by cluster analysis based on co-expression and co-localization, identified transcriptomic responses related to secretion-induced stress and DNA damage. Furthermore, the OsdR regulon (previously associated with hypoxia, oxidative stress, intercellular signaling, and morphological development) was consistently upregulated in the CelA-producing strain and exhibited co-expression with isoenzymes from the pentose phosphate pathway linked to secondary metabolism. Increased expression of these isoenzymes matches to increased fluxes in the pentose phosphate pathway. Additionally, flux maps of the central carbon metabolism show increased flux through the tricarboxylic acid cycle in the CelA-producing strain. Redirection of fluxes in the CelA-producing strain leads to higher production of NADPH, which can only partly be attributed to increased secretion. CONCLUSIONS Transcriptomic and fluxomic changes uncover potential new leads for targeted strain improvement strategies which may ease the secretion stress and metabolic burden associated with heterologous protein synthesis and secretion, and may help create a more consistently performing S. lividans strain. Yet, links to secondary metabolism and redox balancing should be further investigated to fully understand the S. lividans metabolome under heterologous protein production.
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Affiliation(s)
- Wouter Daniels
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Jeroen Bouvin
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Kenneth Simoens
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Lieve Van Mellaert
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | | | - Bart Nicolai
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium.
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Erskine E, MacPhee CE, Stanley-Wall NR. Functional Amyloid and Other Protein Fibers in the Biofilm Matrix. J Mol Biol 2018; 430:3642-3656. [PMID: 30098341 PMCID: PMC6173796 DOI: 10.1016/j.jmb.2018.07.026] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 02/06/2023]
Abstract
Biofilms are ubiquitous in the natural and man-made environment. They are defined as microbes that are encapsulated in an extracellular, self-produced, biofilm matrix. Growing evidence from the genetic and biochemical analysis of single species biofilms has linked the presence of fibrous proteins to a functional biofilm matrix. Some of these fibers have been described as functional amyloid or amyloid-like fibers. Here we provide an overview of the biophysical and biological data for a wide range of protein fibers found in the biofilm matrix of Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Elliot Erskine
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Cait E MacPhee
- James Clerk Maxwell Building, School of Physics, University of Edinburgh, The Kings Buildings, Mayfield Road, Edinburgh, EH9 3JZ, UK.
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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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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Lu T, Zhu Y, Zhang P, Sheng D, Cao G, Pang X. SCO5351 is a pleiotropic factor that impacts secondary metabolism and morphological development in Streptomyces coelicolor. FEMS Microbiol Lett 2018; 365:5040222. [DOI: 10.1093/femsle/fny150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/16/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Ting Lu
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Yanping Zhu
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Peipei Zhang
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Duohong Sheng
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
| | - Guangxiang Cao
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, China
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
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45
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Upadhyay A, Mishra A. Amyloids of multiple species: are they helpful in survival? Biol Rev Camb Philos Soc 2018; 93:1363-1386. [DOI: 10.1111/brv.12399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 01/13/2018] [Accepted: 01/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Arun Upadhyay
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan 342011 India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan 342011 India
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Abstract
Many bacteria can assemble functional amyloid fibers on their cell surface. Most bacterial amyloids contribute to biofilm or other community behaviors where cells interact with a surface or with other cells. Bacterial amyloids, like all functional amyloids, share structural and biochemical properties with disease-associated eukaryotic amyloids. The general ability of amyloids to bind specific dyes, like Congo red and Thioflavin T, and their resistance to denaturation have provided useful tools for scoring and quantifying bacterial amyloid formation. Here, we present basic approaches to study bacterial amyloids by focusing on the well-studied curli amyloid fibers expressed by Enterobacteriaceae. These methods exploit the specific tinctorial and biophysical properties of amyloids. The methods described here are straightforward and can be easily applied by any modern molecular biology lab for the study of other bacterial amyloids.
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Affiliation(s)
- Margery L Evans
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth Gichana
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yizhou Zhou
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew R Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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Dokouhaki M, Hung A, Prime EL, Qiao GG, Day L, Gras SL. pH-Induced interfacial properties of Chaplin E from Streptomyces coelicolor. Colloids Surf B Biointerfaces 2017; 160:589-597. [PMID: 29028607 DOI: 10.1016/j.colsurfb.2017.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/14/2017] [Accepted: 10/03/2017] [Indexed: 10/18/2022]
Abstract
Chaplin E, or Chp E, is a surface active peptide secreted by Streptomyces coelicolor that adopts different structures depending on solution pH but the effect of these structures on the interfacial properties of Chp E is not known. In experiments paired with simulations, Chp E was found to display pH-dependent interfacial assembly and surface activity. At pH 3.0, Chp E formed an ordered non-amyloidal interfacial film with high surface activity; while at pH 10.0, Chp E self-assembled into a heterogeneous film containing randomly arranged fibrils at the interface that was less surface active compared to the film formed at pH 3.0. In simulations at pH 10.0, Chp E molecules showed a higher propensity for dimerization within the solution phase, lower rate of adsorption to the interface and tighter inter-molecular associations at the interface, consistent with the lower surface activity and smaller interfacial area coverage per molecule measured at this pH compared to at pH 3.0. A model is presented for the role of Chp E in the developmental differentiation of Streptomyces coelicolor, where Chp E contributes to changes in surface tension at low pH and the formation of fibrils on the surface of aerial hyphae at high pH. Our data also suggest Chp E could be a promising surface active agent with functional activity that can be controlled by pH.
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Affiliation(s)
- Mina Dokouhaki
- The Melbourne School of Engineering and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew Hung
- School of Science, RMIT University, VIC 3001, Australia
| | - Emma L Prime
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia; Polymer Science Group, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Greg G Qiao
- Polymer Science Group, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Li Day
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand
| | - Sally L Gras
- The Melbourne School of Engineering and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, VIC 3010, Australia.
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48
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Bobek J, Šmídová K, Čihák M. A Waking Review: Old and Novel Insights into the Spore Germination in Streptomyces. Front Microbiol 2017; 8:2205. [PMID: 29180988 PMCID: PMC5693915 DOI: 10.3389/fmicb.2017.02205] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/26/2017] [Indexed: 01/02/2023] Open
Abstract
The complex development undergone by Streptomyces encompasses transitions from vegetative mycelial forms to reproductive aerial hyphae that differentiate into chains of single-celled spores. Whereas their mycelial life – connected with spore formation and antibiotic production – is deeply investigated, spore germination as the counterpoint in their life cycle has received much less attention. Still, germination represents a system of transformation from metabolic zero point to a new living lap. There are several aspects of germination that may attract our attention: (1) Dormant spores are strikingly well-prepared for the future metabolic restart; they possess stable transcriptome, hydrolytic enzymes, chaperones, and other required macromolecules stabilized in a trehalose milieu; (2) Germination itself is a specific sequence of events leading to a complete morphological remodeling that include spore swelling, cell wall reconstruction, and eventually germ tube emergences; (3) Still not fully unveiled are the strategies that enable the process, including a single cell’s signal transduction and gene expression control, as well as intercellular communication and the probability of germination across the whole population. This review summarizes our current knowledge about the germination process in Streptomyces, while focusing on the aforementioned points.
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Affiliation(s)
- Jan Bobek
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czechia.,Chemistry Department, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Ústí nad Labem, Czechia.,Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Klára Šmídová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czechia.,Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Matouš Čihák
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czechia
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49
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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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50
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Jones SE, Elliot MA. 'Exploring' the regulation of Streptomyces growth and development. Curr Opin Microbiol 2017; 42:25-30. [PMID: 29024914 DOI: 10.1016/j.mib.2017.09.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/06/2017] [Accepted: 09/14/2017] [Indexed: 12/14/2022]
Abstract
The Streptomyces life cycle encompasses three well-established developmental stages: vegetative hyphae, aerial hyphae and spores. Many regulators governing the transitions between these life cycle stages have been identified, and recent work is shedding light on their specific functions. A new discovery has shown Streptomyces can deviate from this classic life cycle through a process termed 'exploration', where cells rapidly traverse solid surfaces. Exploration does not require any of the traditional developmental regulators, and therefore provides an exciting new context in which to uncover novel developmental pathways. Here, we summarize our understanding of how Streptomyces exploration is controlled, and we speculate on how insight into classical regulation and stress response systems can inform future research into the regulation of exploratory growth.
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Affiliation(s)
- Stephanie E Jones
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Marie A Elliot
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1.
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