1
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Wang Q. The role of forkhead-associated (FHA)-domain proteins in plant biology. PLANT MOLECULAR BIOLOGY 2023; 111:455-472. [PMID: 36849846 DOI: 10.1007/s11103-023-01338-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
The forkhead-associated (FHA) domain, a well-characterized small protein module that mediates protein-protein interactions by targeting motifs containing phosphothreonine, is present in many regulatory molecules like protein kinase, phosphatases, transcription factors, and other functional proteins. FHA-domain containing proteins in yeast and human are involved in a large variety of cellular processes such as DNA repair, cell cycle arrest, or pre-mRNA processing. Since the first FHA-domain protein, kinase-associated protein phosphatase (KAPP) was found in plants, the interest in plant FHA-containing proteins has increased dramatically, mainly due to the important role of FHA domain-containing proteins in plant growth and development. In this review, we provide a comprehensive overview of the fundamental properties of FHA domain-containing proteins in plants, and systematically summarized and analyzed the research progress of proteins containing the FHA domain in plants. We also emphasized that AT5G47790 and its homologs may play an important role as the regulatory subunit of protein phosphatase 1 (PP1) in plants.
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Affiliation(s)
- Qiuling Wang
- Institute of Future Agriculture, State Key Laboratory of Crop Stress Biology for Arid Areas, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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2
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Gao Z, Zhang W, Chang R, Zhang S, Yang G, Zhao G. Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells. Front Microbiol 2021; 12:751880. [PMID: 34759902 PMCID: PMC8573418 DOI: 10.3389/fmicb.2021.751880] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS.
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Affiliation(s)
| | | | | | | | - Guiwen Yang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guoyan Zhao
- College of Life Science, Shandong Normal University, Jinan, China
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3
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Rastogi S, Ellinwood S, Augenstreich J, Mayer-Barber KD, Briken V. Mycobacterium tuberculosis inhibits the NLRP3 inflammasome activation via its phosphokinase PknF. PLoS Pathog 2021; 17:e1009712. [PMID: 34324582 PMCID: PMC8321130 DOI: 10.1371/journal.ppat.1009712] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved to evade host innate immunity by interfering with macrophage functions. Interleukin-1β (IL-1β) is secreted by macrophages after the activation of the inflammasome complex and is crucial for host defense against Mtb infections. We have previously shown that Mtb is able to inhibit activation of the AIM2 inflammasome and subsequent pyroptosis. Here we show that Mtb is also able to inhibit host cell NLRP3 inflammasome activation and pyroptosis. We identified the serine/threonine kinase PknF as one protein of Mtb involved in the NLRP3 inflammasome inhibition, since the pknF deletion mutant of Mtb induces increased production of IL-1β in bone marrow-derived macrophages (BMDMs). The increased production of IL-1β was dependent on NLRP3, the adaptor protein ASC and the protease caspase-1, as revealed by studies performed in gene-deficient BMDMs. Additionally, infection of BMDMs with the pknF deletion mutant resulted in increased pyroptosis, while the IL-6 production remained unchanged compared to Mtb-infected cells, suggesting that the mutant did not affect the priming step of inflammasome activation. In contrast, the activation step was affected since potassium efflux, chloride efflux and the generation of reactive oxygen species played a significant role in inflammasome activation and subsequent pyroptosis mediated by the Mtb pknF mutant strain. In conclusion, we reveal here that the serine/threonine kinase PknF of Mtb plays an important role in innate immune evasion through inhibition of the NLRP3 inflammasome. Mycobacterium tuberculosis (Mtb) infections are causing millions of deaths per year and the pathogen is highly adapted to its human host. Host cell phagocytes take up Mtb but the bacterium is capable of manipulating the host cell to enhance its own survival. In the current study we discover a novel pathway of host cell manipulation and innate immune evasion by Mtb. We show that the activation of a host cell defense complex, the inflammasome, is limited after Mtb infection. Most importantly, we identify a bacterial protein, PknF, that is involved in inflammasome inhibition.
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Affiliation(s)
- Shivangi Rastogi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Sarah Ellinwood
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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4
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Cabarca S, Frazão de Souza M, Albert de Oliveira A, Vignoli Muniz GS, Lamy MT, Vinicius Dos Reis C, Takarada J, Effer B, Souza LS, Iriarte de la Torre L, Couñago R, Pinto Oliveira CL, Balan A. Structure of the Mycobacterium tuberculosis cPknF and conformational changes induced in forkhead-associated regulatory domains. Curr Res Struct Biol 2021; 3:165-178. [PMID: 34382010 PMCID: PMC8339232 DOI: 10.1016/j.crstbi.2021.07.001] [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: 04/09/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has 11 Serine-Threonine Protein Kinases (STPK) that control numerous physiological processes, including cell growth, cell division, metabolic flow, and transcription. PknF is one of the 11 Mtb STPKs that has, among other substrates, two FHA domains (FHA-1 and FHA-2) of the ATP-Binding Cassette (ABC) transporter Rv1747. Phosphorylation in T152 and T210 located in a non-structured linker that connects Rv1747 FHA domains is considerate to be the regulatory mechanism of the transporter. In this work, we resolved the three-dimensional structure of the PknF catalytic domain (cPknF) in complex with the human kinase inhibitor IKK16. cPknF is conserved when compared to other STPKs but shows specific residues in the binding site where the inhibitor is positioned. In addition, using Small Angle X-Ray Scattering analysis we monitored the behavior of the wild type and three FHA-phosphomimetic mutants in solution, and measured the cPknF affinity for these domains. The kinase showed higher affinity for the non-phosphorylated wild type domain and preference for phosphorylation of T152 inducing the rapprochement of the domains and significant structural changes. The results shed some light on the process of regulating the transporter's activity by phosphorylation and arises important questions about evolution and importance of this mechanism for the bacillus. Rv1747 is an ABC transporter which activity is regulated by PknF. cPknF is a typical Serine/Threonine Protein Kinase that can be explored as drug target. The higher affinity of cPknF for FHA-2 is important for further conformational changes. Rv1747 activation model reveals a concatenated activity essential for the system.
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Affiliation(s)
- Sindy Cabarca
- Programa de Pós-graduação em Genética, Universidade Estadual de Campinas, Campinas, 13083-862, SP, Brazil.,Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.,Grupo Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, 700001, Sucre, Colombia
| | - Maximilia Frazão de Souza
- Grupo de Fluidos Complexos, Departamento de Física Experimental, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, SP, Brazil
| | - Andrew Albert de Oliveira
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14049-900, SP, Brazil
| | - Gabriel S Vignoli Muniz
- Departamento de Física Geral, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - M Teresa Lamy
- Departamento de Física Geral, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - Caio Vinicius Dos Reis
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, 13083-886, São Paulo, Brazil
| | - Jessica Takarada
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, 13083-886, São Paulo, Brazil
| | - Brian Effer
- Center of Excellence in Traslational Medicine (CEMT) and Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de la Frontera, Temuco, 01145, Chile
| | - Lucas Santos Souza
- Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Lilia Iriarte de la Torre
- Programa de Pós-graduação em Genética, Universidade Estadual de Campinas, Campinas, 13083-862, SP, Brazil.,Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.,Grupo Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, 700001, Sucre, Colombia
| | - Rafael Couñago
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, 13083-886, São Paulo, Brazil
| | - Cristiano Luis Pinto Oliveira
- Grupo de Fluidos Complexos, Departamento de Física Experimental, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, SP, Brazil
| | - Andrea Balan
- Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
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5
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Jackson M, Stevens CM, Zhang L, Zgurskaya HI, Niederweis M. Transporters Involved in the Biogenesis and Functionalization of the Mycobacterial Cell Envelope. Chem Rev 2021; 121:5124-5157. [PMID: 33170669 PMCID: PMC8107195 DOI: 10.1021/acs.chemrev.0c00869] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The biology of mycobacteria is dominated by a complex cell envelope of unique composition and structure and of exceptionally low permeability. This cell envelope is the basis of many of the pathogenic features of mycobacteria and the site of susceptibility and resistance to many antibiotics and host defense mechanisms. This review is focused on the transporters that assemble and functionalize this complex structure. It highlights both the progress and the limits of our understanding of how (lipo)polysaccharides, (glyco)lipids, and other bacterial secretion products are translocated across the different layers of the cell envelope to their final extra-cytoplasmic location. It further describes some of the unique strategies evolved by mycobacteria to import nutrients and other products through this highly impermeable barrier.
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Affiliation(s)
- Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Casey M. Stevens
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
| | - Helen I. Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
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6
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Azaldegui CA, Vecchiarelli AG, Biteen JS. The emergence of phase separation as an organizing principle in bacteria. Biophys J 2021; 120:1123-1138. [PMID: 33186556 PMCID: PMC8059088 DOI: 10.1016/j.bpj.2020.09.023] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Recent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This article assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPS in vivo in bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria.
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Affiliation(s)
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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7
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The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics. BIOLOGY 2020; 9:biology9120443. [PMID: 33291531 PMCID: PMC7761784 DOI: 10.3390/biology9120443] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022]
Abstract
Simple Summary Mycobacterium tuberculosis is a bacterium of great medical importance because it causes tuberculosis, a disease that affects millions of people worldwide. Two important features are related to this bacterium: its ability to infect and survive inside the host, minimizing the immune response, and the burden of clinical isolates that are highly resistant to antibiotics treatment. These two phenomena are directly affected by cell envelope proteins, such as proteins from the ATP-Binding Cassette (ABC transporters) superfamily. In this review, we have compiled information on all the M. tuberculosis ABC transporters described so far, both from a functional and structural point of view, and show their relevance for the bacillus and the potential targets for studies aiming to control the microorganism and structural features. Abstract Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its cellular envelope plasticity, which can be modulated to adapt to an unfriendly host environment; to manipulate the host immune response; and to resist therapeutic treatment, increasing in this way the drug resistance of TB. The superfamily of ATP-Binding Cassette (ABC) transporters are integral membrane proteins that include both importers and exporters. Both types share a similar structural organization, yet only importers have a periplasmic substrate-binding domain, which is essential for substrate uptake and transport. ABC transporter-type importers play an important role in the bacillus physiology through the transport of several substrates that will interfere with nutrition, pathogenesis, and virulence. Equally relevant, exporters have been involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, largely affecting the survival and development of multiple drug-resistant strains. Here, we review known ABC transporters from M. tuberculosis, with particular focus on the diversity of their structural features and relevance in infection and drug resistance.
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8
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Abstract
Understanding how Mycobacterium tuberculosis survives during antibiotic treatment is necessary to rationally devise more effective tuberculosis (TB) chemotherapy regimens. Using genome-wide mutant fitness profiling and the mouse model of TB, we identified genes that alter antibiotic efficacy specifically in the infection environment and associated several of these genes with natural genetic variants found in drug-resistant clinical isolates. These data suggest strategies for synergistic therapies that accelerate bacterial clearance, and they identify mechanisms of adaptation to drug exposure that could influence treatment outcome. Effective tuberculosis treatment requires at least 6 months of combination therapy. Alterations in the physiological state of the bacterium during infection are thought to reduce drug efficacy and prolong the necessary treatment period, but the nature of these adaptations remain incompletely defined. To identify specific bacterial functions that limit drug effects during infection, we employed a comprehensive genetic screening approach to identify mutants with altered susceptibility to the first-line antibiotics in the mouse model. We identified many mutations that increase the rate of bacterial clearance, suggesting new strategies for accelerating therapy. In addition, the drug-specific effects of these mutations suggested that different antibiotics are limited by distinct factors. Rifampin efficacy is inferred to be limited by cellular permeability, whereas isoniazid is preferentially affected by replication rate. Many mutations that altered bacterial clearance in the mouse model did not have an obvious effect on drug susceptibility using in vitro assays, indicating that these chemical-genetic interactions tend to be specific to the in vivo environment. This observation suggested that a wide variety of natural genetic variants could influence drug efficacy in vivo without altering behavior in standard drug-susceptibility tests. Indeed, mutations in a number of the genes identified in our study are enriched in drug-resistant clinical isolates, identifying genetic variants that may influence treatment outcome. Together, these observations suggest new avenues for improving therapy, as well as the mechanisms of genetic adaptations that limit it. IMPORTANCE Understanding how Mycobacterium tuberculosis survives during antibiotic treatment is necessary to rationally devise more effective tuberculosis (TB) chemotherapy regimens. Using genome-wide mutant fitness profiling and the mouse model of TB, we identified genes that alter antibiotic efficacy specifically in the infection environment and associated several of these genes with natural genetic variants found in drug-resistant clinical isolates. These data suggest strategies for synergistic therapies that accelerate bacterial clearance, and they identify mechanisms of adaptation to drug exposure that could influence treatment outcome.
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9
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Chen J, Tan W, Wang W, Hou S, Chen G, Xia L, Lu Y. Identification of common antigens of three pathogenic Nocardia species and development of DNA vaccine against fish nocardiosis. FISH & SHELLFISH IMMUNOLOGY 2019; 95:357-367. [PMID: 31678532 DOI: 10.1016/j.fsi.2019.09.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/06/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Fish nocardiosis is a chronic granulomatous bacterial disease and three pathogens have been reported so far, including Nocardia asteroids, N. seriolae and N. salmonicida. However, the absence of antigen markers is a bottleneck for developing effective vaccines against fish nocardiosis. In this study, the antigenicity of whole-cell protein of these three pathogenic Nocardia species were profiled by immunoproteomic analysis and 7 common immunogenic proteins were identified as follows: molecular chaperone DnaK (DnaK), molecular chaperone GroEL (GroEL), 30 S ribosomal protein S1 (RpsA), TerD family protein (TerD), FHA domain-containing protein (FHA), 50 S ribosomal protein L7/L12 (RplL) and PspA/IM30 family protein (PspA). Furthermore, the DNA vaccine encoding FHA gene against fish nocardiosis was developed and its efficacy was investigated in hybrid snakehead. The results suggested that it needed at least 7 d to transport pcDNA-FHA DNA vaccine from injected muscle to head kidney, spleen and liver and stimulate host's immune system for later protection. In addition, non-specific immunity paraments (serum lysozyme (LYZ), peroxidase (POD), acid phosphatase (ACP), alkaline phosphatase (AKP) and superoxide dismutase (SOD) activities), specific antibody (IgM) titers production and immune-related genes (MHCIα, MHCIIα, CD4, CD8α, IL-1β and TNFα) were used to evaluate the immune response induced in pcDNA-FHA vaccinated hybrid snakehead, it proved that all these mentioned immune activities were significantly enhanced after immunization. The results also showed hybrid snakehead vaccinated with pcDNA-FHA had higher survival rate (79.33%) compared with the controls after challenge with N. seriolae, indicating that the pcDNA-FHA DNA vaccine can supply immune protection against N. seriolae infection. Taken together, this study may warrant further development of these common immunogenic proteins as the antigens for vaccine or diagnosis and facilitate the prevention and treatment of fish nocardiosis.
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Affiliation(s)
- Jianlin Chen
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, Guangdong, China
| | - Wanchun Tan
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, China
| | - Wenji Wang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, Guangdong, China
| | - Suying Hou
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, Guangdong, China
| | - Guoquan Chen
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, Guangdong, China
| | - Liqun Xia
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, China; Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, Guangdong, China.
| | - Yishan Lu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, Guangdong, China; Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, Guangdong, China.
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10
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Buhl M, Kästle C, Geyer A, Autenrieth IB, Peter S, Willmann M. Molecular Evolution of Extensively Drug-Resistant (XDR) Pseudomonas aeruginosa Strains From Patients and Hospital Environment in a Prolonged Outbreak. Front Microbiol 2019; 10:1742. [PMID: 31440214 PMCID: PMC6694792 DOI: 10.3389/fmicb.2019.01742] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/15/2019] [Indexed: 11/24/2022] Open
Abstract
In this study, we aimed to elucidate a prolonged outbreak of extensively drug-resistant (XDR) Pseudomonas aeruginosa, at two adjacent hospitals over a time course of 4 years. Since all strains exhibited a similar antibiotic susceptibility pattern and carried the carbapenemase gene blaVIM, a monoclonal outbreak was assumed. To shed light on the intra-hospital evolution of these strains over time, whole genome sequence (WGS) analysis of 100 clinical and environmental outbreak strains was employed. Phylogenetic analysis of the core genome revealed the outbreak to be polyclonal, rather than monoclonal as initially suggested. The vast majority of strains fell into one of two major clusters, composed of 27 and 59 strains, and their accessory genome each revealed over 400 and 600 accessory genes, respectively, thus indicating an unexpectedly high structural diversity among phylogenetically clustered strains. Further analyses focused on the cluster with 59 strains, representing the hospital from which both clinical and environmental strains were available. Our investigation clearly shows both accumulation and loss of genes occur very frequently over time, as reflected by analysis of protein enrichment as well as functional enrichment. In addition, we investigated adaptation through single nucleotide polymorphisms (SNPs). Among the genes affected by SNPs, there are a multidrug efflux pump (mexZ) and a mercury detoxification operon (merR) with deleterious mutations, potentially leading to loss of repression with resistance against antibiotics and disinfectants. Our results not only confirm WGS to be a powerful tool for epidemiologic analyses, but also provide insights into molecular evolution during an XDR P. aeruginosa hospital outbreak. Genome mutation unveiled a striking genetic plasticity on an unexpectedly high level, mostly driven by horizontal gene transfer. Our study adds valuable information to the molecular understanding of “real-world” Intra-hospital P. aeruginosa evolution and is a step forward toward more personalized medicine in infection control.
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Affiliation(s)
- Michael Buhl
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Christina Kästle
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - André Geyer
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
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11
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Phase separation and clustering of an ABC transporter in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2019; 116:16326-16331. [PMID: 31366629 DOI: 10.1073/pnas.1820683116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Phase separation drives numerous cellular processes, ranging from the formation of membrane-less organelles to the cooperative assembly of signaling proteins. Features such as multivalency and intrinsic disorder that enable condensate formation are found not only in cytosolic and nuclear proteins, but also in membrane-associated proteins. The ABC transporter Rv1747, which is important for Mycobacterium tuberculosis (Mtb) growth in infected hosts, has a cytoplasmic regulatory module consisting of 2 phosphothreonine-binding Forkhead-associated domains joined by an intrinsically disordered linker with multiple phospho-acceptor threonines. Here we demonstrate that the regulatory modules of Rv1747 and its homolog in Mycobacterium smegmatis form liquid-like condensates as a function of concentration and phosphorylation. The serine/threonine kinases and sole phosphatase of Mtb tune phosphorylation-enhanced phase separation and differentially colocalize with the resulting condensates. The Rv1747 regulatory module also phase-separates on supported lipid bilayers and forms dynamic foci when expressed heterologously in live yeast and M. smegmatis cells. Consistent with these observations, single-molecule localization microscopy reveals that the endogenous Mtb transporter forms higher-order clusters within the Mycobacterium membrane. Collectively, these data suggest a key role for phase separation in the function of these mycobacterial ABC transporters and their regulation via intracellular signaling.
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12
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Hoffmann L, Anders K, Bischof LF, Ye X, Reimann J, Khadouma S, Pham TK, van der Does C, Wright PC, Essen LO, Albers SV. Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius. J Biol Chem 2019; 294:7460-7471. [PMID: 30902813 PMCID: PMC6509490 DOI: 10.1074/jbc.ra119.007709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/20/2019] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation-dependent interactions play crucial regulatory roles in all domains of life. Forkhead-associated (FHA) and von Willebrand type A (vWA) domains are involved in several phosphorylation-dependent processes of multiprotein complex assemblies. Although well-studied in eukaryotes and bacteria, the structural and functional contexts of these domains are not yet understood in Archaea. Here, we report the structural base for such an interacting pair of FHA and vWA domain-containing proteins, ArnA and ArnB, in the thermoacidophilic archaeon Sulfolobus acidocaldarius, where they act synergistically and negatively modulate motility. The structure of the FHA domain of ArnA at 1.75 Å resolution revealed that it belongs to the subclass of FHA domains, which recognizes double-pSer/pThr motifs. We also solved the 1.5 Å resolution crystal structure of the ArnB paralog vWA2, disclosing a complex topology comprising the vWA domain, a β-sandwich fold, and a C-terminal helix bundle. We further show that ArnA binds to the C terminus of ArnB, which harbors all the phosphorylation sites identified to date and is important for the function of ArnB in archaellum regulation. We also observed that expression levels of the archaellum components in response to changes in nutrient conditions are independent of changes in ArnA and ArnB levels and that a strong interaction between ArnA and ArnB observed during growth on rich medium sequentially diminishes after nutrient limitation. In summary, our findings unravel the structural features in ArnA and ArnB important for their interaction and functional archaellum expression and reveal how nutrient conditions affect this interaction.
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Affiliation(s)
- Lena Hoffmann
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Katrin Anders
- the Philipps University, Department of Chemistry, 35032 Marburg, Germany
| | - Lisa F Bischof
- From the Institute for Biology II, Molecular Biology of Archaea and
- the Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Xing Ye
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Julia Reimann
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Sunia Khadouma
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Trong K Pham
- the ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom, and
| | | | - Phillip C Wright
- the Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Lars-Oliver Essen
- the Philipps University, Department of Chemistry, 35032 Marburg, Germany,
- the LOEWE Center for Synthetic Microbiology, 35043 Marburg, Germany
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Chatterjee N, Ojha R, Khatoon N, Prajapati VK. Scrutinizing Mycobacterium tuberculosis membrane and secretory proteins to formulate multiepitope subunit vaccine against pulmonary tuberculosis by utilizing immunoinformatic approaches. Int J Biol Macromol 2018; 118:180-188. [DOI: 10.1016/j.ijbiomac.2018.06.080] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 11/17/2022]
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Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747. Structure 2018; 26:972-986.e6. [PMID: 29861345 DOI: 10.1016/j.str.2018.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 11/23/2022]
Abstract
The Mycobacterium tuberculosis ATP-binding cassette transporter Rv1747 is a putative exporter of cell wall biosynthesis intermediates. Rv1747 has a cytoplasmic regulatory module consisting of two pThr-interacting Forkhead-associated (FHA) domains connected by a conformationally disordered linker with two phospho-acceptor threonines (pThr). The structures of FHA-1 and FHA-2 were determined by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, respectively. Relative to the canonical 11-strand β-sandwich FHA domain fold of FHA-1, FHA-2 is circularly permuted and lacking one β-strand. Nevertheless, the two share a conserved pThr-binding cleft. FHA-2 is less stable and more dynamic than FHA-1, yet binds model pThr peptides with moderately higher affinity (∼50 μM versus 500 μM equilibrium dissociation constants). Based on NMR relaxation and chemical shift perturbation measurements, when joined within a polypeptide chain, either FHA domain can bind either linker pThr to form intra- and intermolecular complexes. We hypothesize that this enables tunable phosphorylation-dependent multimerization to regulate Rv1747 transporter activity.
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15
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Smith LJ, Bochkareva A, Rolfe MD, Hunt DM, Kahramanoglou C, Braun Y, Rodgers A, Blockley A, Coade S, Lougheed KEA, Hafneh NA, Glenn SM, Crack JC, Le Brun NE, Saldanha JW, Makarov V, Nobeli I, Arnvig K, Mukamolova GV, Buxton RS, Green J. Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence. Nucleic Acids Res 2017; 45:6600-6612. [PMID: 28482027 PMCID: PMC5499769 DOI: 10.1093/nar/gkx406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 04/28/2017] [Indexed: 12/05/2022] Open
Abstract
Mycobacterium tuberculosis (MTb) is the causative agent of pulmonary tuberculosis (TB). MTb colonizes the human lung, often entering a non-replicating state before progressing to life-threatening active infections. Transcriptional reprogramming is essential for TB pathogenesis. In vitro, Cmr (a member of the CRP/FNR super-family of transcription regulators) bound at a single DNA site to act as a dual regulator of cmr transcription and an activator of the divergent rv1676 gene. Transcriptional profiling and DNA-binding assays suggested that Cmr directly represses dosR expression. The DosR regulon is thought to be involved in establishing latent tuberculosis infections in response to hypoxia and nitric oxide. Accordingly, DNA-binding by Cmr was severely impaired by nitrosation. A cmr mutant was better able to survive a nitrosative stress challenge but was attenuated in a mouse aerosol infection model. The complemented mutant exhibited a ∼2-fold increase in cmr expression, which led to increased sensitivity to nitrosative stress. This, and the inability to restore wild-type behaviour in the infection model, suggests that precise regulation of the cmr locus, which is associated with Region of Difference 150 in hypervirulent Beijing strains of Mtb, is important for TB pathogenesis.
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Affiliation(s)
- Laura J Smith
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.,School of Pharmacy, De Montfort University, Leicester LE1 9BH, UK
| | | | - Matthew D Rolfe
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Debbie M Hunt
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Christina Kahramanoglou
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Yvonne Braun
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Angela Rodgers
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Alix Blockley
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Stephen Coade
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Kathryn E A Lougheed
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Nor Azian Hafneh
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK
| | - Sarah M Glenn
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
| | - José W Saldanha
- Division of Mathematical Biology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Vadim Makarov
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Kristine Arnvig
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Galina V Mukamolova
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK
| | - Roger S Buxton
- Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Jeffrey Green
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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16
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Almawi AW, Matthews LA, Guarné A. FHA domains: Phosphopeptide binding and beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:105-110. [DOI: 10.1016/j.pbiomolbio.2016.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/06/2016] [Indexed: 01/18/2023]
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Abstract
Reversible protein phosphorylation is the most common type of epigenetic posttranslational modification in living cells used as a major regulation mechanism of biological processes. The Mycobacterium tuberculosis genome encodes for 11 serine/threonine protein kinases that are responsible for sensing environmental signals to coordinate a cellular response to ensure the pathogen's infectivity, survival, and growth. To overcome killing mechanisms generated within the host during infection, M. tuberculosis enters a state of nonreplicating persistence that is characterized by arrested growth, limited metabolic activity, and phenotypic resistance to antimycobacterial drugs. In this article we focus our attention on the role of M. tuberculosis serine/threonine protein kinases in sensing the host environment to coordinate the bacilli's physiology, including growth, cell wall components, and central metabolism, to establish a persistent infection.
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18
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Glass LN, Swapna G, Chavadi SS, Tufariello JM, Mi K, Drumm JE, Lam TT, Zhu G, Zhan C, Vilchéze C, Arcos J, Chen Y, Bi L, Mehta S, Porcelli SA, Almo SC, Yeh SR, Jacobs WR, Torrelles JB, Chan J. Mycobacterium tuberculosis universal stress protein Rv2623 interacts with the putative ATP binding cassette (ABC) transporter Rv1747 to regulate mycobacterial growth. PLoS Pathog 2017; 13:e1006515. [PMID: 28753640 PMCID: PMC5549992 DOI: 10.1371/journal.ppat.1006515] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/09/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Abstract
We have previously shown that the Mycobacterium tuberculosis universal stress protein Rv2623 regulates mycobacterial growth and may be required for the establishment of tuberculous persistence. Here, yeast two-hybrid and affinity chromatography experiments have demonstrated that Rv2623 interacts with one of the two forkhead-associated domains (FHA I) of Rv1747, a putative ATP-binding cassette transporter annotated to export lipooligosaccharides. FHA domains are signaling protein modules that mediate protein-protein interactions to modulate a wide variety of biological processes via binding to conserved phosphorylated threonine (pT)-containing oligopeptides of the interactors. Biochemical, immunochemical and mass spectrometric studies have shown that Rv2623 harbors pT and specifically identified threonine 237 as a phosphorylated residue. Relative to wild-type Rv2623 (Rv2623WT), a mutant protein in which T237 has been replaced with a non-phosphorylatable alanine (Rv2623T237A) exhibits decreased interaction with the Rv1747 FHA I domain and diminished growth-regulatory capacity. Interestingly, compared to WT bacilli, an M. tuberculosis Rv2623 null mutant (ΔRv2623) displays enhanced expression of phosphatidyl-myo-inositol mannosides (PIMs), while the ΔRv1747 mutant expresses decreased levels of PIMs. Animal studies have previously shown that ΔRv2623 is hypervirulent, while ΔRv1747 is growth-attenuated. Collectively, these data have provided evidence that Rv2623 interacts with Rv1747 to regulate mycobacterial growth; and this interaction is mediated via the recognition of the conserved Rv2623 pT237-containing FHA-binding motif by the Rv1747 FHA I domain. The divergent aberrant PIM profiles and the opposing in vivo growth phenotypes of ΔRv2623 and ΔRv1747, together with the annotated lipooligosaccharide exporter function of Rv1747, suggest that Rv2623 interacts with Rv1747 to modulate mycobacterial growth by negatively regulating the activity of Rv1747; and that Rv1747 might function as a transporter of PIMs. Because these glycolipids are major mycobacterial cell envelope components that can impact on the immune response, our findings raise the possibility that Rv2623 may regulate bacterial growth, virulence, and entry into persistence, at least in part, by modulating the levels of bacillary PIM expression, perhaps through negatively regulating the Rv1747-dependent export of the immunomodulatory PIMs to alter host-pathogen interaction, thereby influencing the fate of M. tuberculosis in vivo.
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Affiliation(s)
- Lisa N. Glass
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Ganduri Swapna
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Sivagami Sundaram Chavadi
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - JoAnn M. Tufariello
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Kaixia Mi
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Joshua E. Drumm
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - TuKiet T. Lam
- MS & Proteomics Resource of the W.M. Keck Biotechnology Resource Laboratory, Yale University School Medicine, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Guofeng Zhu
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Chenyang Zhan
- Department of Biochemistry, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Catherine Vilchéze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Howard Hughes Medical Institute, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Jesus Arcos
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Yong Chen
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Lijun Bi
- Department of Medicine, School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Simren Mehta
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Steven A. Porcelli
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Steve C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Syun-Ru Yeh
- Departments of Physiology & Biophysics, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Howard Hughes Medical Institute, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Jordi B. Torrelles
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - John Chan
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
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Wan X, Koster K, Qian L, Desmond E, Brostrom R, Hou S, Douglas JT. Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis. PLoS One 2017; 12:e0175330. [PMID: 28394899 PMCID: PMC5386241 DOI: 10.1371/journal.pone.0175330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/25/2017] [Indexed: 02/05/2023] Open
Abstract
With its airborne transmission and prolonged latency period, Mycobacterium tuberculosis spreads worldwide as one of the most successful bacterial pathogens and continues to kill millions of people every year. M. tuberculosis lineage 1 is inferred to originate ancestrally based on the presence of the 52-bp TbD1 sequence and analysis of single nucleotide polymorphisms. Previously, we briefly reported the complete genome sequencing of M. tuberculosis strains 96121 and 96075, which belong to the ancient Manila family and modern Beijing family respectively. Here we present the comprehensive genomic analyses of the Manila family in lineage 1 compared to complete genomes in lineages 2-4. Principal component analysis of the presence and absence of CRISPR spacers suggests that Manila isolate 96121 is distinctly distant from lineages 2-4. We further identify a truncated whiB5 gene and a putative operon consisting of genes encoding a putative serine/threonine kinase PknH and a putative ABC transporter, which are only found in the genomes of Manila family isolates. Six single nucleotide polymorphisms are uniquely conserved in 38 Manila strains. Moreover, when compared to M. tuberculosis H37Rv, 59 proteins are under positive selection in Manila family isolate 96121 but not in Beijing family isolate 96075. The unique features further serve as biomarkers for Manila strains and may shed light on the limited transmission of this ancestral lineage outside of its Filipino host population.
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Affiliation(s)
- Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Kent Koster
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Lishi Qian
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Edward Desmond
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Richard Brostrom
- TB Control Program, Hawaii State Department of Health, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - James T. Douglas
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
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Bastos PAD, da Costa JP, Vitorino R. A glimpse into the modulation of post-translational modifications of human-colonizing bacteria. J Proteomics 2016; 152:254-275. [PMID: 27888141 DOI: 10.1016/j.jprot.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/22/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.
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Affiliation(s)
- Paulo André Dias Bastos
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Chemistry, University of Aveiro, Portugal
| | | | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
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Abstract
The Mycobacterium tuberculosis genome encodes 11 serine/threonine protein kinases (STPKs). A similar number of two-component systems are also present, indicating that these two signal transduction mechanisms are both important in the adaptation of this bacterial pathogen to its environment. The M. tuberculosis phosphoproteome includes hundreds of Ser- and Thr-phosphorylated proteins that participate in all aspects of M. tuberculosis biology, supporting a critical role for the STPKs in regulating M. tuberculosis physiology. Nine of the STPKs are receptor type kinases, with an extracytoplasmic sensor domain and an intracellular kinase domain, indicating that these kinases transduce external signals. Two other STPKs are cytoplasmic and have regulatory domains that sense changes within the cell. Structural analysis of some of the STPKs has led to advances in our understanding of the mechanisms by which these STPKs are activated and regulated. Functional analysis has provided insights into the effects of phosphorylation on the activity of several proteins, but for most phosphoproteins the role of phosphorylation in regulating function is unknown. Major future challenges include characterizing the functional effects of phosphorylation for this large number of phosphoproteins, identifying the cognate STPKs for these phosphoproteins, and determining the signals that the STPKs sense. Ultimately, combining these STPK-regulated processes into larger, integrated regulatory networks will provide deeper insight into M. tuberculosis adaptive mechanisms that contribute to tuberculosis pathogenesis. Finally, the STPKs offer attractive targets for inhibitor development that may lead to new therapies for drug-susceptible and drug-resistant tuberculosis.
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22
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Linares D, Jean N, Van Overtvelt P, Ouidir T, Hardouin J, Blache Y, Molmeret M. The marine bacteria Shewanella frigidimarina NCIMB400 upregulates the type VI secretion system during early biofilm formation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:110-121. [PMID: 26617163 DOI: 10.1111/1758-2229.12358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/19/2015] [Indexed: 06/05/2023]
Abstract
Shewanella sp. are facultative anaerobic Gram-negative bacteria, extensively studied for their electron transfer ability. Shewanella frigidimarina has been detected and isolated from marine environments, and in particular, from biofilms. However, its ability to adhere to surfaces and form a biofilm is poorly understood. In this study, we show that the ability to adhere and to form a biofilm of S. frigidimarina NCIMB400 is significantly higher than that of Shewanella oneidensis in our conditions. We also show that this strain forms a biofilm in artificial seawater, whereas in Luria-Bertani, this capacity is reduced. To identify proteins involved in early biofilm formation, a proteomic analysis of sessile versus planktonic membrane-enriched fractions allowed the identification of several components of the same type VI secretion system gene cluster: putative Hcp1 and ImpB proteins as well as a forkhead-associated domain-containing protein. The upregulation of Hcp1 a marker of active translocation has been confirmed using quantitative reverse transcription polymerase chain reaction. Our data demonstrated the presence of a single and complete type VI secretion system in S. frigidimarina NCIMB400 genome, upregulated in sessile compared with planktonic conditions. The fact that three proteins including the secreted protein Hcp1 have been identified may suggest that this type VI secretion system is functional.
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Affiliation(s)
- Denis Linares
- Université de Toulon, MAPIEM, EA4323, 83957, La Garde, France
| | | | | | - Tassadit Ouidir
- UMR 6270 CNRS, Laboratoire Polymères, Biopolymères, Surfaces, Université de Rouen, Mont-Saint-Aignan, F-76820, France
| | - Julie Hardouin
- UMR 6270 CNRS, Laboratoire Polymères, Biopolymères, Surfaces, Université de Rouen, Mont-Saint-Aignan, F-76820, France
| | - Yves Blache
- Université de Toulon, MAPIEM, EA4323, 83957, La Garde, France
| | - Maëlle Molmeret
- Université de Toulon, MAPIEM, EA4323, 83957, La Garde, France
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23
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Richard-Greenblatt M, Bach H, Adamson J, Peña-Diaz S, Li W, Steyn AJC, Av-Gay Y. Regulation of Ergothioneine Biosynthesis and Its Effect on Mycobacterium tuberculosis Growth and Infectivity. J Biol Chem 2015; 290:23064-76. [PMID: 26229105 DOI: 10.1074/jbc.m115.648642] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/06/2022] Open
Abstract
Ergothioneine (EGT) is synthesized in mycobacteria, but limited knowledge exists regarding its synthesis, physiological role, and regulation. We have identified Rv3701c from Mycobacterium tuberculosis to encode for EgtD, a required histidine methyltransferase that catalyzes first biosynthesis step in EGT biosynthesis. EgtD was found to be phosphorylated by the serine/threonine protein kinase PknD. PknD phosphorylates EgtD both in vitro and in a cell-based system on Thr(213). The phosphomimetic (T213E) but not the phosphoablative (T213A) mutant of EgtD failed to restore EGT synthesis in a ΔegtD mutant. The findings together with observed elevated levels of EGT in a pknD transposon mutant during in vitro growth suggests that EgtD phosphorylation by PknD negatively regulates EGT biosynthesis. We further showed that EGT is required in a nutrient-starved model of persistence and is needed for long term infection of murine macrophages.
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Affiliation(s)
| | - Horacio Bach
- From the Division of Infectious Diseases, Department of Medicine and
| | - John Adamson
- Kwazulu-Natal Research Institute for Tuberculosis and HIV, Durban, South Africa 4001
| | - Sandra Peña-Diaz
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Wu Li
- Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China, and
| | - Adrie J C Steyn
- Kwazulu-Natal Research Institute for Tuberculosis and HIV, Durban, South Africa 4001, Department of Microbiology and Centers for AIDS Research and Free Radical Biology, University of Alabama, Birmingham, Alabama 35233
| | - Yossef Av-Gay
- From the Division of Infectious Diseases, Department of Medicine and
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Cui T, He ZG. Improved understanding of pathogenesis from protein interactions inMycobacteriumtuberculosis. Expert Rev Proteomics 2014; 11:745-55. [DOI: 10.1586/14789450.2014.971762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Spivey VL, Whalan RH, Hirst EMA, Smerdon SJ, Buxton RS. An attenuated mutant of the Rv1747 ATP-binding cassette transporter of Mycobacterium tuberculosis and a mutant of its cognate kinase, PknF, show increased expression of the efflux pump-related iniBAC operon. FEMS Microbiol Lett 2013; 347:107-15. [PMID: 23915284 PMCID: PMC3908365 DOI: 10.1111/1574-6968.12230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 11/30/2022] Open
Abstract
The ATP-binding cassette transporter Rv1747 is required for the growth of Mycobacterium tuberculosis in mice and in macrophages. Its structure suggests it is an exporter. Rv1747 forms a two-gene operon with pknF coding for the serine/threonine protein kinase PknF, which positively modulates the function of the transporter. We show that deletion of Rv1747 or pknF results in a number of transcriptional changes which could be complemented by the wild type allele, most significantly up-regulation of the iniBAC genes. This operon is inducible by isoniazid and ethambutol and by a broad range of inhibitors of cell wall biosynthesis and is required for efflux pump functioning. However, neither the Rv1747 or pknF mutant showed increased susceptibility to a range of drugs and cell wall stress reagents including isoniazid and ethambutol, cell wall structure and cell division appear normal by electron microscopy, and no differences in lipoarabinomannan were found. Transcription from the pknF promoter was not induced by a range of stress reagents. We conclude that the loss of Rv1747 affects cell wall biosynthesis leading to the production of intermediates that cause induction of iniBAC transcription and implicates it in exporting a component of the cell wall, which is necessary for virulence.
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Affiliation(s)
- Vicky L Spivey
- Division of Mycobacterial Research, MRC National Institute for Medical Research, London, UK
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Gaudion A, Dawson L, Davis E, Smollett K. Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: its operon and regulon. Tuberculosis (Edinb) 2013; 93:482-91. [PMID: 23871545 PMCID: PMC3776920 DOI: 10.1016/j.tube.2013.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/15/2013] [Accepted: 05/19/2013] [Indexed: 01/21/2023]
Abstract
A major step in the pathogenesis of Mycobacterium tuberculosis is the ability to survive inside macrophages, where it is exposed to a number of DNA damaging agents. The alternative sigma factor SigG has been shown to be upregulated by DNA damaging agents and by macrophage infection, but not to regulate genes of the DNA repair pathway. Here we show that SigG is expressed from at least two promoters, the most dominant of these being the DNA damage inducible RecA_Ndp promoter. This promoter is located within the annotated coding region of SigG and so the correct translational start site was determined experimentally and found to be 114 bp downstream of the annotated start site. Examining the gene expression profile of a SigG over-expression strain found a small number of genes to up-regulated, two of these encoded proteins containing glyoxylase-like domains.
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Affiliation(s)
- Alison Gaudion
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Weiling H, Xiaowen Y, Chunmei L, Jianping X. Function and evolution of ubiquitous bacterial signaling adapter phosphopeptide recognition domain FHA. Cell Signal 2013. [DOI: 10.1016/j.cellsig.2012.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Szumowski JD, Adams KN, Edelstein PH, Ramakrishnan L. Antimicrobial efflux pumps and Mycobacterium tuberculosis drug tolerance: evolutionary considerations. Curr Top Microbiol Immunol 2013; 374:81-108. [PMID: 23242857 PMCID: PMC3859842 DOI: 10.1007/82_2012_300] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The need for lengthy treatment to cure tuberculosis stems from phenotypic drug resistance, also known as drug tolerance, which has been previously attributed to slowed bacterial growth in vivo. We discuss recent findings that challenge this model and instead implicate macrophage-induced mycobacterial efflux pumps in antimicrobial tolerance. Although mycobacterial efflux pumps may have originally served to protect against environmental toxins, in the pathogenic mycobacteria, they appear to have been repurposed for intracellular growth. In this light, we discuss the potential of efflux pump inhibitors such as verapamil to shorten tuberculosis treatment by their dual inhibition of tolerance and growth.
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Affiliation(s)
- John D Szumowski
- Department of Medicine (Division of Infectious Diseases), University of Washington, Seattle, WA, USA,
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Fivian-Hughes AS, Houghton J, Davis EO. Mycobacterium tuberculosis thymidylate synthase gene thyX is essential and potentially bifunctional, while thyA deletion confers resistance to p-aminosalicylic acid. MICROBIOLOGY-SGM 2011; 158:308-318. [PMID: 22034487 PMCID: PMC3352284 DOI: 10.1099/mic.0.053983-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Thymidylate synthase (TS) enzymes catalyse the biosynthesis of deoxythymidine monophosphate (dTMP or thymidylate), and so are important for DNA replication and repair. Two different types of TS proteins have been described (ThyA and ThyX), which have different enzymic mechanisms and unrelated structures. Mycobacteria are unusual as they encode both thyA and thyX, and the biological significance of this is not yet understood. Mycobacterium tuberculosis ThyX is thought to be essential and a potential drug target. We therefore analysed M. tuberculosis thyA and thyX expression levels, their essentiality and roles in pathogenesis. We show that both thyA and thyX are expressed in vitro, and that this expression significantly increased within murine macrophages. Under all conditions tested, thyA expression exceeded that of thyX. Mutational studies show that M. tuberculosis thyX is essential, confirming that the enzyme is a plausible drug target. The requirement for M. tuberculosis thyX in the presence of thyA implies that the essential function of ThyX is something other than dTM synthesis [corrected].We successfully deleted thyA from the M. tuberculosis genome, and this deletion conferred an in vitro growth defect that was not observed in vivo. Presumably ThyX performs TS activity within M. tuberculosis ΔthyA at a sufficient rate in vivo for normal growth, but the rate in vitro is less than optimal. We also demonstrate that thyA deletion confers M. tuberculosis p-aminosalicylic acid resistance, and show by complementation studies that ThyA T202A and V261G appear to be functional and non-functional, respectively.
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Affiliation(s)
- Amanda S Fivian-Hughes
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Joanna Houghton
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Elaine O Davis
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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