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Li X, Long X, Chen L, Guo X, Lu L, Hu L, He ZG. Mycobacterial phage TM4 requires a eukaryotic-like Ser/Thr protein kinase to silence and escape anti-phage immunity. Cell Host Microbe 2023; 31:1469-1480.e4. [PMID: 37567169 DOI: 10.1016/j.chom.2023.07.005] [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: 01/23/2023] [Revised: 05/15/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023]
Abstract
In eukaryotic cells, serine/threonine protein kinases (StpKs) play important roles in limiting viral infections. StpKs are commonly activated upon infections, inhibiting the expression of genes central for viral replication. Here, we report that a eukaryotic-like StpK7 encoded by MSMEG_1200 in M. smegmatis is required for mycobacteriophage TM4 to escape bacterial defense. stpK7 is located within a gene island, MSMEG_1191-MSMEG_1200, containing multiple anti-phage genes resembling the BREX (bacteriophage exclusion) phage-resistance system. StpK7 negatively regulates the expression of this gene island. Following phage TM4 infection, StpK7 is induced, directly phosphorylating the transcriptional regulator MSMEG_1198 and inhibiting its positive regulatory activity, thus reducing the expression of multiple downstream genes in the BREX-like gene island. Further analysis showed that genes within this anti-phage island critically regulate mycobacterial lipid hemostasis and phage adsorption. Collectively, this work characterizes a regulatory network driven by StpK7, which is utilized by phage TM4 to escape from the host defense against mycobacteria.
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Affiliation(s)
- Xiaohui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiating Long
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liu Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiao Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Lining Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zheng-Guo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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2
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Singha B, Behera D, Khan MZ, Singh NK, Sowpati DT, Gopal B, Nandicoori VK. The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein. J Biol Chem 2023; 299:102933. [PMID: 36690275 PMCID: PMC10011835 DOI: 10.1016/j.jbc.2023.102933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
SigA (σA) is an essential protein and the primary sigma factor in Mycobacterium tuberculosis (Mtb). However, due to the absence of genetic tools, our understanding of the role and regulation of σA activity and its molecular attributes that help modulate Mtb survival is scant. Here, we generated a conditional gene replacement of σA in Mtb and showed that its depletion results in a severe survival defect in vitro, ex vivo, and in vivo in a murine infection model. Our RNA-seq analysis suggests that σA either directly or indirectly regulates ∼57% of the Mtb transcriptome, including ∼28% of essential genes. Surprisingly, we note that despite having ∼64% similarity with σA, overexpression of the primary-like σ factor SigB (σB) fails to compensate for the absence of σA, suggesting minimal functional redundancy. RNA-seq analysis of the Mtb σB deletion mutant revealed that 433 genes are regulated by σB, of which 283 overlap with the σA transcriptome. Additionally, surface plasmon resonance, in vitro transcription, and functional complementation experiments reveal that σA residues between 132-179 that are disordered and missing from all experimentally determined σA-RNAP structural models are imperative for σA function. Moreover, phosphorylation of σA in the intrinsically disordered N-terminal region plays a regulatory role in modulating its activity. Collectively, these observations and analysis provide a rationale for the centrality of σA for the survival and pathogenicity of this bacillus.
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Affiliation(s)
- Biplab Singha
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Debashree Behera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | | | | | - Vinay Kumar Nandicoori
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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3
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Naz S, Singh Y, Nandicoori VK. Deletion of serine/threonine-protein kinase pknL from Mycobacterium tuberculosis reduces the efficacy of isoniazid and ethambutol. Tuberculosis (Edinb) 2021; 128:102066. [PMID: 33690080 DOI: 10.1016/j.tube.2021.102066] [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: 12/01/2020] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023]
Abstract
Serine/threonine-protein kinases in Mycobacterium tuberculosis (Mtb) form a preeminent regulatory system required to establish and maintain the infection in the host. Herein, we sought to decipher the biological role of PknL with the help of a gene replacement mutant RvΔpknL. Deletion of pknL results in the compromised growth under redox stress. The mutant showed significant survival defects in peritoneal macrophages, a significant decrease in the ability to establish infections and disseminate to the spleen in the murine model of infection. While the absence of pknL has no impact on either MIC or CFUs of ciprofloxacin and rifampicin treated bacilli, it increases the survival ~1.5-2.5 log fold upon isoniazid or ethambutol treatment. Collectively, data suggests that PknL aids in combating stress conditions in vitro, ex vivo, and in vivo and reduces the efficacy of isoniazid and ethambutol.
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Affiliation(s)
- Saba Naz
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
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4
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Regulation of Protein Post-Translational Modifications on Metabolism of Actinomycetes. Biomolecules 2020; 10:biom10081122. [PMID: 32751230 PMCID: PMC7464533 DOI: 10.3390/biom10081122] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
Protein post-translational modification (PTM) is a reversible process, which can dynamically regulate the metabolic state of cells through regulation of protein structure, activity, localization or protein–protein interactions. Actinomycetes are present in the soil, air and water, and their life cycle is strongly determined by environmental conditions. The complexity of variable environments urges Actinomycetes to respond quickly to external stimuli. In recent years, advances in identification and quantification of PTMs have led researchers to deepen their understanding of the functions of PTMs in physiology and metabolism, including vegetative growth, sporulation, metabolite synthesis and infectivity. On the other hand, most donor groups for PTMs come from various metabolites, suggesting a complex association network between metabolic states, PTMs and signaling pathways. Here, we review the mechanisms and functions of PTMs identified in Actinomycetes, focusing on phosphorylation, acylation and protein degradation in an attempt to summarize the recent progress of research on PTMs and their important role in bacterial cellular processes.
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5
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Cyanobacterial sigma factors: Current and future applications for biotechnological advances. Biotechnol Adv 2020; 40:107517. [DOI: 10.1016/j.biotechadv.2020.107517] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 11/15/2022]
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Mori M, Sammartino JC, Costantino L, Gelain A, Meneghetti F, Villa S, Chiarelli LR. An Overview on the Potential Antimycobacterial Agents Targeting Serine/Threonine Protein Kinases from Mycobacterium tuberculosis. Curr Top Med Chem 2019; 19:646-661. [PMID: 30827246 DOI: 10.2174/1568026619666190227182701] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/27/2018] [Accepted: 10/09/2018] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), still remains an urgent global health issue, mainly due to the emergence of multi-drug resistant strains. Therefore, there is a pressing need to develop novel and more efficient drugs to control the disease. In this context, targeting the pathogen virulence factors, and particularly signal mechanisms, seems to be a promising approach. An important transmembrane signaling system in Mtb is represented by receptor-type Serine/ Threonine protein kinases (STPKs). Mtb has 11 different STPKs, two of them, PknA and PknB, are essential. By contrast PknG and PknH are involved in Mtb virulence and adaptation, and are fundamental for the pathogen growth in infection models. Therefore, STPKs represent a very interesting group of pharmacological targets in M. tuberculosis. In this work, the principal inhibitors of the mycobacterial STPKs will be presented and discussed. In particular, medicinal chemistry efforts have been focused on discovering new antimycobacterial compounds, targeting three of these kinases, namely PknA, PknB and PknG. Generally, the inhibitory effect on these enzymes do not correlate with a significant antimycobacterial action in whole-cell assays. However, compounds with activity in the low micromolar range have been obtained, demonstrating that targeting Mtb STPKs could be a new promising strategy for the development of drugs to treat TB infections.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - José Camilla Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Luca Costantino
- Dipartimento Scienze della Vita, Universita degli Studi di Modena e Reggio Emilia, via Campi 103, 41121 Modena, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Laurent Roberto Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100 Pavia, Italy
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Tuning the Mycobacterium tuberculosis Alternative Sigma Factor SigF through the Multidomain Regulator Rv1364c and Osmosensory Kinase Protein Kinase D. J Bacteriol 2019; 201:JB.00725-18. [PMID: 30642988 DOI: 10.1128/jb.00725-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/02/2019] [Indexed: 12/20/2022] Open
Abstract
Bacterial alternative sigma factors are mostly regulated by a partner-switching mechanism. Regulation of the virulence-associated alternative sigma factor SigF of Mycobacterium tuberculosis has been an area of intrigue, with SigF having more predicted regulators than other sigma factors in this organism. Rv1364c is one such predicted regulator, the mechanism of which is confounded by the presence of both anti-sigma factor and anti-sigma factor antagonist functions in a single polypeptide. Using protein binding and phosphorylation assays, we demonstrate that the anti-sigma factor domain of Rv1364c mediates autophosphorylation of its antagonist domain and binds efficiently to SigF. Furthermore, we identified a direct role for the osmosensor serine/threonine kinase PknD in regulating the SigF-Rv1364c interaction, adding to the current understanding about the intersection of these discrete signaling networks. Phosphorylation of SigF also showed functional implications in its DNA binding ability, which may help in activation of the regulon. In M. tuberculosis, osmotic stress-dependent induction of espA, a SigF target involved in maintaining cell wall integrity, is curtailed upon overexpression of Rv1364c, showing its role as an anti-SigF factor. Overexpression of Rv1364c led to induction of another target, pks6, involved in lipid metabolism. This induction was, however, curtailed in the presence of osmotic stress conditions, suggesting modulation of SigF target gene expression via Rv1364c. These data provide evidence that Rv1364c acts an independent SigF regulator that is sensitive to the osmosensory signal, mediating the cross talk of PknD with the SigF regulon.IMPORTANCE Mycobacterium tuberculosis, capable of latently infecting the host and causing aggressive tissue damage during active tuberculosis, is endowed with a complex regulatory capacity built of several sigma factors, protein kinases, and phosphatases. These proteins regulate expression of genes that allow the bacteria to adapt to various host-derived stresses, like nutrient starvation, acidic pH, and hypoxia. The cross talk between these systems is not well understood. SigF is one such regulator of gene expression that helps M. tuberculosis to adapt to stresses and imparts virulence. This work provides evidence for its inhibition by the multidomain regulator Rv1364c and activation by the kinase PknD. The coexistence of negative and positive regulators of SigF in pathogenic bacteria reveals an underlying requirement for tight control of virulence factor expression.
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Caballero J, Morales-Bayuelo A, Navarro-Retamal C. Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. J Comput Aided Mol Des 2018; 32:1315-1336. [PMID: 30367309 DOI: 10.1007/s10822-018-0173-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/20/2018] [Indexed: 12/17/2022]
Abstract
In the last decades, human protein kinases (PKs) have been relevant as targets in the development of novel therapies against many diseases, but the study of Mycobacterium tuberculosis PKs (MTPKs) involved in tuberculosis pathogenesis began much later and has not yet reached an advanced stage of development. To increase knowledge of these enzymes, in this work we studied the structural features of MTPKs, with focus on their ATP-binding sites and their interactions with inhibitors. PknA, PknB, and PknG are the most studied MTPKs, which were previously crystallized; ATP-competitive inhibitors have been designed against them in the last decade. In the current work, reported PknA, PknB, and PknG inhibitors were extracted from literature and their orientations inside the ATP-binding site were proposed by using docking method. With this information, interaction fingerprints were elaborated, which reveal the more relevant residues for establishing chemical interactions with inhibitors. The non-crystallized MTPKs PknD, PknF, PknH, PknJ, PknK, and PknL were also studied; their three-dimensional structural models were developed by using homology modeling. The main characteristics of MTPK ATP-binding sites (the non-crystallized and crystallized MTPKs, including PknE and PknI) were accounted; schemes of the main polar and nonpolar groups inside their ATP-binding sites were constructed, which are suitable for a major understanding of these proteins as antituberculotic targets. These schemes could be used for establishing comparisons between MTPKs and human PKs in order to increase selectivity of MTPK inhibitors. As a key tool for guiding medicinal chemists interested in the design of novel MTPK inhibitors, our work provides a map of the structural elements relevant for the design of more selective ATP-competitive MTPK inhibitors.
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Affiliation(s)
- Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile.
| | - Alejandro Morales-Bayuelo
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
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9
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Chaurasiya SK. Tuberculosis: Smart manipulation of a lethal host. Microbiol Immunol 2018; 62:361-379. [PMID: 29687912 DOI: 10.1111/1348-0421.12593] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/21/2018] [Accepted: 04/16/2018] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis remains a global threat to human health. Development of drug resistance and co-infection with HIV has increased the morbidity and mortality caused by TB. Macrophages serve as primary defense against microbial infections, including TB. Upon recognition and uptake of mycobacteria, macrophages initiate a series of events designed to lead to generation of effective immune responses and clearance of infection. However, pathogenic mycobacteria utilize multiple mechanisms for manipulating macrophage responses to protect itself from being killed and to survive within these cells that are designed to kill them. The outcomes of mycobacterial infection are determined by several host- and pathogen-related factors. Significant advancements in understanding mycobacterial pathogenesis have been made in recent years. In this review, some of the important factors/mechanisms regulating mycobacterial survival inside macrophages are discussed.
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Affiliation(s)
- Shivendra K Chaurasiya
- Host-pathogen Interaction and Signal Transduction Laboratory, Department of Microbiology, School of Biological Sciences, Dr. Hari Singh Gour University, Sagar, MP-470003, India
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10
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Laqua K, Klemm M, Richard-Greenblatt M, Richter A, Liebe L, Huang T, Lin S, Guardia A, Pérez-Herran E, Ballell L, Av-Gay Y, Imming P. Synthesis, antimycobacterial activity and influence on mycobacterial InhA and PknB of 12-membered cyclodepsipeptides. Bioorg Med Chem 2018; 26:3166-3190. [PMID: 29706526 DOI: 10.1016/j.bmc.2018.04.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/16/2018] [Accepted: 04/20/2018] [Indexed: 11/26/2022]
Abstract
In recent years, several small natural cyclopeptides and cyclodepsipeptides were reported to have antimycobacterial activity. Following this lead, a synthetic pathway was developed for a small series of 12-membered ring compounds with one amide and two ester bonds (cyclotridepsipeptides). Within the series, the ring system proved to be necessary for growth inhibition of Mycobacterium smegmatis and Mycobacterium tuberculosis in the low micromolar range. Open-chain precursors and analogues were inactive. The compounds modulated autophosphorylation of the mycobacterial protein kinase B (PknB). PknB inhibitors were active at µM concentration against mycobacteria while inducers were inactive. PknB regulates the activity of the mycobacterial reductase InhA, the target of isoniazid. The activity of the series against Mycobacterium bovis BCG InhA overexpressing strains was indistinguishable from that of the parental strain suggesting that they do not inhibit InhA. All substances were not cytotoxic (HeLa > 5 µg/ml) and did not show any significant antiproliferative effect (HUVEC > 5 µg/ml; K-562 > 5 µg/ml). Within the scope of this study, the molecular target of this new type of small cyclodepsipeptide was not identified, but the data suggest interaction with PknB or other kinases may partly cause the activity.
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Affiliation(s)
- Katja Laqua
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany
| | - Marcel Klemm
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany
| | - Melissa Richard-Greenblatt
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany
| | - Linda Liebe
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Ana Guardia
- Diseases of the Developing World, Alternative Discovery & Development, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Esther Pérez-Herran
- Diseases of the Developing World, Alternative Discovery & Development, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluís Ballell
- Diseases of the Developing World, Alternative Discovery & Development, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Yossef Av-Gay
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle, Germany.
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Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. mBio 2018; 9:mBio.02333-17. [PMID: 29511081 PMCID: PMC5845002 DOI: 10.1128/mbio.02333-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis is the leading killer among infectious diseases worldwide. Increasing multidrug resistance has prompted new approaches for tuberculosis drug development, including targeted inhibition of virulence determinants and of signaling cascades that control many downstream pathways. We used a multisystem approach to determine the effects of a potent small-molecule inhibitor of the essential Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB. We observed differential levels of phosphorylation of many proteins and extensive changes in levels of gene expression, protein abundance, cell wall lipids, and intracellular metabolites. The patterns of these changes indicate regulation by PknA and PknB of several pathways required for cell growth, including ATP synthesis, DNA synthesis, and translation. These data also highlight effects on pathways for remodeling of the mycobacterial cell envelope via control of peptidoglycan turnover, lipid content, a SigE-mediated envelope stress response, transmembrane transport systems, and protein secretion systems. Integrated analysis of phosphoproteins, transcripts, proteins, and lipids identified an unexpected pathway whereby threonine phosphorylation of the essential response regulator MtrA decreases its DNA binding activity. Inhibition of this phosphorylation is linked to decreased expression of genes for peptidoglycan turnover, and of genes for mycolyl transferases, with concomitant changes in mycolates and glycolipids in the cell envelope. These findings reveal novel roles for PknA and PknB in regulating multiple essential cell functions and confirm that these kinases are potentially valuable targets for new antituberculosis drugs. In addition, the data from these linked multisystems provide a valuable resource for future targeted investigations into the pathways regulated by these kinases in the M. tuberculosis cell. Tuberculosis is the leading killer among infectious diseases worldwide. Increasing drug resistance threatens efforts to control this epidemic; thus, new antitubercular drugs are urgently needed. We performed an integrated, multisystem analysis of Mycobacterium tuberculosis responses to inhibition of its two essential serine/threonine protein kinases. These kinases allow the bacterium to adapt to its environment by phosphorylating cellular proteins in response to extracellular signals. We identified differentially phosphorylated proteins, downstream changes in levels of specific mRNA and protein abundance, and alterations in the metabolite and lipid content of the cell. These results include changes previously linked to growth arrest and also reveal new roles for these kinases in regulating essential processes, including growth, stress responses, transport of proteins and other molecules, and the structure of the mycobacterial cell envelope. Our multisystem data identify PknA and PknB as promising targets for drug development and provide a valuable resource for future investigation of their functions.
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12
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Zhou P, Wang X, Zhao Y, Yuan W, Xie J. Sigma factors mediated signaling in Mycobacterium tuberculosis. Future Microbiol 2018; 13:231-240. [DOI: 10.2217/fmb-2017-0127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Activation of signaling cascades is critical for Mycobacterium tuberculosis (Mtb) to adapt the macrophage lifestyle. Parallel to several signal systems, sigma factor systems, especially the extra-cytoplasmic function sigma factors, are crucial for Mtb signaling. Most sigma factors lack a signal sensory domain and often are activated by various proteins that perceive the environmental cues and relay the signals through variegated post-translational modifications via the activity of antisigma factor, protein kinase and related transcriptional regulators. Antisigma factors are further controlled by multiple mechanisms. SigK senses the environmental redox state directly. Phosphorylation and lysine acetylation added another dimension to the regulatory hierarchy. This review will provide insights into Mtb pathogenesis, and lay the foundation for the discovery of novel approaches for therapeutic interventions.
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Affiliation(s)
- Peifu Zhou
- Institute of Ethnic-Minority Medicine, School of Ethnic-Minority Medicine, Guizhou Minzu University, Guiyang 550025, PR China
| | - Xinpeng Wang
- School of Humanities & Sciences, Guizhou Minzu University, Guiyang 550025, PR China
| | - Yuzhong Zhao
- Institute of Ethnic-Minority Medicine, School of Ethnic-Minority Medicine, Guizhou Minzu University, Guiyang 550025, PR China
| | - Wei Yuan
- Institute of Tuberculosis Control & Prevention, Guizhou Provincial Center for Disease Control & Prevention, Guiyang 550004, PR China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, PR China
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13
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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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14
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Bigi MM, Blanco FC, Araújo FR, Thacker TC, Zumárraga MJ, Cataldi AA, Soria MA, Bigi F. Polymorphisms of 20 regulatory proteins between Mycobacterium tuberculosis and Mycobacterium bovis. Microbiol Immunol 2017; 60:552-60. [PMID: 27427512 DOI: 10.1111/1348-0421.12402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/21/2016] [Accepted: 07/13/2016] [Indexed: 12/21/2022]
Abstract
Mycobacterium tuberculosis and Mycobacterium bovis are responsible for tuberculosis in humans and animals, respectively. Both species are closely related and belong to the Mycobacterium tuberculosis complex (MTC). M. tuberculosis is the most ancient species from which M. bovis and other members of the MTC evolved. The genome of M. bovis is over >99.95% identical to that of M. tuberculosis but with seven deletions ranging in size from 1 to 12.7 kb. In addition, 1200 single nucleotide mutations in coding regions distinguish M. bovis from M. tuberculosis. In the present study, we assessed 75 M. tuberculosis genomes and 23 M. bovis genomes to identify non-synonymous mutations in 202 coding sequences of regulatory genes between both species. We identified species-specific variants in 20 regulatory proteins and confirmed differential expression of hypoxia-related genes between M. bovis and M. tuberculosis.
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Affiliation(s)
- María M Bigi
- School of Agronomy, UBA, Buenos Aires 1417, Argentina
| | - Federico Carlos Blanco
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | | | - Tyler C Thacker
- United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, 1920 Dayton Ave, Ames, Iowa 50010, USA
| | - Martín J Zumárraga
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | - Angel A Cataldi
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | | | - Fabiana Bigi
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
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15
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Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks. J Bacteriol 2016; 198:1360-73. [PMID: 26883824 DOI: 10.1128/jb.00935-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Regulating responses to stress is critical for all bacteria, whether they are environmental, commensal, or pathogenic species. For pathogenic bacteria, successful colonization and survival in the host are dependent on adaptation to diverse conditions imposed by the host tissue architecture and the immune response. Once the bacterium senses a hostile environment, it must enact a change in physiology that contributes to the organism's survival strategy. Inappropriate responses have consequences; hence, the execution of the appropriate response is essential for survival of the bacterium in its niche. Stress responses are most often regulated at the level of gene expression and, more specifically, transcription. This minireview focuses on mechanisms of regulating transcription initiation that are required by Mycobacterium tuberculosis to respond to the arsenal of defenses imposed by the host during infection. In particular, we highlight how certain features of M. tuberculosis physiology allow this pathogen to respond swiftly and effectively to host defenses. By enacting highly integrated and coordinated gene expression changes in response to stress,M. tuberculosis is prepared for battle against the host defense and able to persist within the human population.
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16
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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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17
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Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence. Microbiol Spectr 2015; 2:MGM2-0007-2013. [PMID: 26082107 DOI: 10.1128/microbiolspec.mgm2-0007-2013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid adaptation to changing environments is one of the keys to the success of microorganisms. Since infection is a dynamic process, it is possible to predict that Mycobacterium tuberculosis adaptation involves continuous modulation of its global transcriptional profile in response to the changing environment found in the human body. In the last 18 years several studies have stressed the role of sigma (σ) factors in this process. These are small interchangeable subunits of the RNA polymerase holoenzyme that are required for transcriptional initiation and that determine promoter specificity. The M. tuberculosis genome encodes 13 of these proteins, one of which--the principal σ factor σA--is essential. Of the other 12 σ factors, at least 6 are required for virulence. In this article we review our current knowledge of mycobacterial σ factors, their regulons, the complex mechanisms determining their regulation, and their roles in M. tuberculosis physiology and virulence.
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18
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Wright DP, Ulijasz AT. Regulation of transcription by eukaryotic-like serine-threonine kinases and phosphatases in Gram-positive bacterial pathogens. Virulence 2015; 5:863-85. [PMID: 25603430 PMCID: PMC4601284 DOI: 10.4161/21505594.2014.983404] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacterial eukaryotic-like serine threonine kinases (eSTKs) and serine threonine phosphatases (eSTPs) have emerged as important signaling elements that are indispensable for pathogenesis. Differing considerably from their histidine kinase counterparts, few eSTK genes are encoded within the average bacterial genome, and their targets are pleiotropic in nature instead of exclusive. The growing list of important eSTK/P substrates includes proteins involved in translation, cell division, peptidoglycan synthesis, antibiotic tolerance, resistance to innate immunity and control of virulence factors. Recently it has come to light that eSTK/Ps also directly modulate transcriptional machinery in many microbial pathogens. This novel form of regulation is now emerging as an additional means by which bacteria can alter their transcriptomes in response to host-specific environmental stimuli. Here we focus on the ability of eSTKs and eSTPs in Gram-positive bacterial pathogens to directly modulate transcription, the known mechanistic outcomes of these modifications, and their roles as an added layer of complexity in controlling targeted RNA synthesis to enhance virulence potential.
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Key Words
- OCS, one-component signaling
- PASTA, penicillin-binding protein and Ser/Thr kinase associated
- PPM, protein phosphatase metal binding
- PTM, posttranslational modification
- REC, receiver
- ROS, reactive oxygen species
- TCS, two-component signaling
- bacteria
- eSTK, eukaryotic-like serine-threonine kinase
- eSTP, eukaryotic-like serine-threonine phosphatase
- infection
- phosphorylation
- serine threonine kinase
- serine threonine phosphatase
- transcription
- wHTH, winged helix-turn-helix
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Affiliation(s)
- David P Wright
- a MRC Centre for Molecular Bacteriology and Infection (CMBI); Imperial College London ; London , UK
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19
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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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20
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Li X, Wu J, Han J, Hu Y, Mi K. Distinct Responses of Mycobacterium smegmatis to Exposure to Low and High Levels of Hydrogen Peroxide. PLoS One 2015. [PMID: 26225431 PMCID: PMC4520597 DOI: 10.1371/journal.pone.0134595] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Hydrogen peroxide (H2O2) is a natural oxidant produced by aerobic organisms and gives rise to oxidative damage, including DNA mutations, protein inactivation and lipid damage. The genus Mycobacterium utilizes redox sensors and H2O2 scavenging enzymes for the detoxification of H2O2. To date, the precise response to oxidative stress has not been fully elucidated. Here, we compared the effects of different levels of H2O2 on transcription in M. smegmatis using RNA-sequencing. A 0.2 mM H2O2 treatment had little effect on the growth and viability of M. smegmatis whereas 7 mM H2O2 was lethal. Analysis of global transcription showed that 0.2 mM H2O2 induced relatively few changes in gene expression, whereas a large proportion of the mycobacterial genome was found to be differentially expressed after treatment with 7 mM H2O2. Genes differentially expressed following treatment with 0.2 mM H2O2 included those coding for proteins involved in glycolysis-gluconeogenesis and fatty acid metabolism pathways, and expression of most genes encoding ribosomal proteins was lower following treatment with 7 mM H2O2. Our analysis shows that M. smegmatis utilizes the sigma factor MSMEG_5214 in response to 0.2 mM H2O2, and the RpoE1 sigma factors MSMEG_0573 and MSMEG_0574 in response to 7 mM H2O2. In addition, different transcriptional regulators responded to different levels of H2O2: MSMEG_1919 was induced by 0.2 mM H2O2, while high-level induction of DevR occurred in response to 7 mM H2O2. We detected the induction of different detoxifying enzymes, including genes encoding KatG, AhpD, TrxB and Trx, at different levels of H2O2 and the detoxifying enzymes were expressed at different levels of H2O2. In conclusion, our study reveals the changes in transcription that are induced in response to different levels of H2O2 in M. smegmatis.
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Affiliation(s)
- Xiaojing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing, 100101, China
- Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing 100101, Beijing, China
| | - Jun Wu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing, 100101, China
- Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing 100101, Beijing, China
| | - Jiao Han
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing, 100101, China
| | - Yongfei Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing, 100101, China
- Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing 100101, Beijing, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing, 100101, China
- Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing 100101, Beijing, China
- * E-mail:
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21
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Metri R, Hariharaputran S, Ramakrishnan G, Anand P, Raghavender US, Ochoa-Montaño B, Higueruelo AP, Sowdhamini R, Chandra NR, Blundell TL, Srinivasan N. SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav060. [PMID: 26130660 PMCID: PMC4485431 DOI: 10.1093/database/bav060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/26/2015] [Indexed: 11/20/2022]
Abstract
We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL:http://proline.biochem.iisc.ernet.in/sincre
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Affiliation(s)
- Rahul Metri
- Department of Biochemistry and Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore, India
| | - Sridhar Hariharaputran
- Department of Biochemistry and National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bellary Road, Bangalore, India
| | - Gayatri Ramakrishnan
- Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore, India, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India, and
| | | | | | | | - Alicia P Higueruelo
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bellary Road, Bangalore, India
| | | | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
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22
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Wang XM, Soetaert K, Peirs P, Kalai M, Fontaine V, Dehaye JP, Lefèvre P. Biochemical analysis of the NAD+-dependent malate dehydrogenase, a substrate of several serine/threonine protein kinases of Mycobacterium tuberculosis. PLoS One 2015; 10:e0123327. [PMID: 25860441 PMCID: PMC4393303 DOI: 10.1371/journal.pone.0123327] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 03/02/2015] [Indexed: 12/21/2022] Open
Abstract
PknD is one of the eleven eukaryotic-like serine/threonine protein kinases (STPKs) of Mycobacterium tuberculosis (Mtb). In vitro phosphorylation assays with the active recombinant PknD showed that the intracellular protein NAD+-dependent malate dehydrogenase (MDH) is a substrate of this kinase. MDH, an energy-supplying enzyme, catalyzes the interconversion of malate and oxaloacetate and plays crucial roles in several metabolic pathways including the citric acid cycle. The phosphorylation site was identified on threonine residues and the phosphorylation inhibited the MDH activity. In vitro, the recombinant MDH could also be phosphorylated by at least five other STPKs, PknA, PknE, PknH, PknJ, and PknG. Immunoprecipitation analysis revealed that MDH was hyperphosphorylated in the bacteria at the beginning of the stationary and under oxygen-limited conditions by STPKs other than PknD. On the contrary, when PknD-deficient mutant mycobacteria were grown in a phosphate-depleted medium, MDH was not detectably phosphorylated. These results suggest that although the MDH is a substrate of several mycobacterial STPKs, the activity of these kinases can depend on the environment, as we identified PknD as a key element in the MDH phosphorylation assay under phosphate-poor conditions.
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Affiliation(s)
- Xiao Ming Wang
- Scientific Institute of Public Health, Direction of Communicable and Infectious Diseases, Rue Engeland 642, 1180 Brussels, Belgium
| | - Karine Soetaert
- Scientific Institute of Public Health, Direction of Communicable and Infectious Diseases, Rue Engeland 642, 1180 Brussels, Belgium
| | - Priska Peirs
- Scientific Institute of Public Health, Direction of Communicable and Infectious Diseases, Rue Engeland 642, 1180 Brussels, Belgium
| | - Michaël Kalai
- Scientific Institute of Public Health, Direction of Communicable and Infectious Diseases, Rue Engeland 642, 1180 Brussels, Belgium
| | - Véronique Fontaine
- Unité de Microbiologie Pharmaceutique et Hygiène, Faculty of Pharmacy, Université Libre de Bruxelles, Boulevard du Triomphe, CP205/2, 1050 Brussels, Belgium
| | - Jean Paul Dehaye
- Unité de Microbiologie Pharmaceutique et Hygiène, Faculty of Pharmacy, Université Libre de Bruxelles, Boulevard du Triomphe, CP205/2, 1050 Brussels, Belgium
| | - Philippe Lefèvre
- Unité de Microbiologie Pharmaceutique et Hygiène, Faculty of Pharmacy, Université Libre de Bruxelles, Boulevard du Triomphe, CP205/2, 1050 Brussels, Belgium
- * E-mail:
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23
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Baer CE, Iavarone AT, Alber T, Sassetti CM. Biochemical and spatial coincidence in the provisional Ser/Thr protein kinase interaction network of Mycobacterium tuberculosis. J Biol Chem 2015; 289:20422-33. [PMID: 24928517 DOI: 10.1074/jbc.m114.559054] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many Gram-positive bacteria coordinate cellular processes by signaling through Ser/Thr protein kinases (STPKs), but the architecture of these phosphosignaling cascades is unknown. To investigate the network structure of a prokaryotic STPK system, we comprehensively explored the pattern of signal transduction in the Mycobacterium tuberculosis Ser/Thr kinome. Autophosphorylation is the dominant mode of STPK activation, but the 11 M. tuberculosis STPKs also show a specific pattern of efficient cross-phosphorylation in vitro. The biochemical specificity intrinsic to each kinase domain was used to map the provisional signaling network, revealing a three-layer architecture that includes master regulators, signal transducers, and terminal substrates. Fluorescence microscopy revealed that the STPKs are specifically localized in the cell. Master STPKs are concentrated at the same subcellular sites as their substrates, providing additional support for the biochemically defined network. Together, these studies imply a branched functional architecture of the M. tuberculosis Ser/Thr kinome that could enable horizontal signal spreading. This systems-level approach provides a biochemical and spatial framework for understanding Ser/Thr phospho-signaling in M. tuberculosis, which differs fundamentally from previously defined linear histidine kinase cascades.
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24
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Dey B, Bishai WR. Crosstalk between Mycobacterium tuberculosis and the host cell. Semin Immunol 2014; 26:486-96. [PMID: 25303934 DOI: 10.1016/j.smim.2014.09.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/02/2014] [Indexed: 11/15/2022]
Abstract
The successful establishment and maintenance of a bacterial infection depend on the pathogen's ability to subvert the host cell's defense response and successfully survive, proliferate, or persist within the infected cell. To circumvent host defense systems, bacterial pathogens produce a variety of virulence factors that potentiate bacterial adherence and invasion and usurp host cell signaling cascades that regulate intracellular microbial survival and trafficking. Mycobacterium tuberculosis, probably one of the most successful pathogens on earth, has coexisted with humanity for centuries, and this intimate and persistent connection between these two organisms suggests that the pathogen has evolved extensive mechanisms to evade the human immune system at multiple levels. While some of these mechanisms are mediated by factors released by M. tuberculosis, others rely on host components that are hijacked to prevent the generation of an effective immune response thus benefiting the survival of M. tuberculosis within the host cell. Here, we describe several of these mechanisms, with an emphasis on the cyclic nucleotide signaling and subversion of host responses that occur at the intracellular level when tubercle bacilli encounter macrophages, a cell that becomes a safe-house for M. tuberculosis although it is specialized to kill most microbes.
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Affiliation(s)
- Bappaditya Dey
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - William R Bishai
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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25
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Sherman DR, Grundner C. Agents of change - concepts in Mycobacterium tuberculosis Ser/Thr/Tyr phosphosignalling. Mol Microbiol 2014; 94:231-41. [PMID: 25099260 DOI: 10.1111/mmi.12747] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2014] [Indexed: 11/26/2022]
Abstract
The flow of information from the outside to the inside of bacterial cells is largely directed by protein kinases. In addition to histidine/aspartate phosphorelays of two-component response regulators, recent work in Mycobacterium tuberculosis (Mtb) reinforces the idea that phosphorylation on serine (Ser), threonine (Thr) and tyrosine (Tyr) is central to bacterial physiology and pathogenesis, and that the corresponding phosphosystems are highly similar to those in eukaryotes. In this way, eukaryotes are a useful guide to understanding Ser/Thr/Tyr phosphorylation (O-phosphorylation) in prokaryotes such as Mtb. However, as novel functions and components of bacterial O-phosphorylation are identified, distinct differences between pro- and eukaryotic phosphosignalling systems become apparent. The emerging picture of O-phosphorylation in Mtb is complicated, goes beyond the eukaryotic paradigms, and shows the limitations of viewing bacterial phosphosignalling within the confines of the 'eukaryotic-like' model. Here, we summarize recent findings about Ser/Thr and the recently discovered Tyr phosphorylation pathways in Mtb, highlight the similarities and differences between eukaryotic and prokaryotic O-phosphorylation, and pose additional questions about signalling components, pathway organization, and ultimately, the cellular roles of O-phosphorylation in Mtb physiology and pathogenesis.
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Affiliation(s)
- David R Sherman
- Seattle Biomedical Research Institute, Seattle, WA, 98109, USA; Department of Global Health, University of Washington, Seattle, WA, 98195, USA
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26
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Jayachandran R, BoseDasgupta S, Pieters J. Surviving the macrophage: tools and tricks employed by Mycobacterium tuberculosis. Curr Top Microbiol Immunol 2014; 374:189-209. [PMID: 23154833 DOI: 10.1007/82_2012_273] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Mycobacterium tuberculosis has evolved to withstand one of the most inhospitable cells within the human body, namely the macrophage, a cell that is normally geared toward the destruction of any invading microbe. How M. tuberculosis achieves this is still incompletely understood; however, a number of mechanisms are now known that provide advantages to M. tuberculosis for its survival and proliferation inside the macrophage. While some of these mechanisms are mediated by factors released by M. tuberculosis, others rely on host components that are being hijacked to benefit survival of M. tuberculosis within the macrophage as well to avoid the generation of an effective immune response. Here, we describe several of these mechanisms, also pointing out the potential usage of this knowledge toward the development of novel strategies to treat tuberculosis. Furthermore, we attempt to put the 'macrophage niche' into context with other intracellular pathogens and discuss some of the generalities as well as specializations that M. tuberculosis employs to survive.
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Affiliation(s)
- Rajesh Jayachandran
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
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27
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Hatzios SK, Baer CE, Rustad TR, Siegrist MS, Pang JM, Ortega C, Alber T, Grundner C, Sherman DR, Bertozzi CR. Osmosensory signaling in Mycobacterium tuberculosis mediated by a eukaryotic-like Ser/Thr protein kinase. Proc Natl Acad Sci U S A 2013; 110:E5069-77. [PMID: 24309377 PMCID: PMC3876250 DOI: 10.1073/pnas.1321205110] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Bacteria are able to adapt to dramatically different microenvironments, but in many organisms, the signaling pathways, transcriptional programs, and downstream physiological changes involved in adaptation are not well-understood. Here, we discovered that osmotic stress stimulates a signaling network in Mycobacterium tuberculosis regulated by the eukaryotic-like receptor Ser/Thr protein kinase PknD. Expression of the PknD substrate Rv0516c was highly induced by osmotic stress. Furthermore, Rv0516c disruption modified peptidoglycan thickness, enhanced antibiotic resistance, and activated genes in the regulon of the alternative σ-factor SigF. Phosphorylation of Rv0516c regulated the abundance of EspA, a virulence-associated substrate of the type VII ESX-1 secretion system. These findings identify an osmosensory pathway orchestrated by PknD, Rv0516c, and SigF that enables adaptation to osmotic stress through cell wall remodeling and virulence factor production. Given the widespread occurrence of eukaryotic-like Ser/Thr protein kinases in bacteria, these proteins may play a broad role in bacterial osmosensing.
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Affiliation(s)
| | - Christina E. Baer
- Molecular and Cell Biology, California Institute for Quantitative Biosciences (QB3), and
| | - Tige R. Rustad
- Seattle Biomedical Research Institute, Seattle, WA 98109; and
- Department of Global Health, University of Washington, Seattle, WA 98195
| | | | - Jennifer M. Pang
- Seattle Biomedical Research Institute, Seattle, WA 98109; and
- Department of Global Health, University of Washington, Seattle, WA 98195
| | - Corrie Ortega
- Seattle Biomedical Research Institute, Seattle, WA 98109; and
- Department of Global Health, University of Washington, Seattle, WA 98195
| | - Tom Alber
- Molecular and Cell Biology, California Institute for Quantitative Biosciences (QB3), and
| | - Christoph Grundner
- Seattle Biomedical Research Institute, Seattle, WA 98109; and
- Department of Global Health, University of Washington, Seattle, WA 98195
| | - David R. Sherman
- Seattle Biomedical Research Institute, Seattle, WA 98109; and
- Department of Global Health, University of Washington, Seattle, WA 98195
| | - Carolyn R. Bertozzi
- Departments of Chemistry and
- Molecular and Cell Biology, California Institute for Quantitative Biosciences (QB3), and
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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28
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Bowman J, Ghosh P. A complex regulatory network controlling intrinsic multidrug resistance in Mycobacterium smegmatis. Mol Microbiol 2013; 91:121-34. [PMID: 24176019 DOI: 10.1111/mmi.12448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2013] [Indexed: 01/27/2023]
Abstract
Mycobacteria are intrinsically resistant to a variety of stresses including many antibiotics. Although a number of pathways have been described to account for the observed resistances, the mechanisms that control the expression of genes required in these processes remain poorly defined. Here we report the role of a predicted anti-sigma factor, MSMEG_6129 and a predicted eukaryotic like serine/threonine protein kinase, MSMEG_5437, in the intrinsic resistance of Mycobacterium smegmatis to a variety of stresses including the genotoxic agent mitomycin C, hydrogen peroxide and at least four different antibiotics - isoniazid, chloramphenicol, erythromycin and tetracycline. We show that MSMEG_5437 influences the phosphorylation state of MSMEG_6129. Further, MSMEG_6129 controls the expression of a plethora of genes including efflux pumps, ABC transporters, catalases and transcription factors, either directly or via regulators like WhiB7, which account for the observed multi-drug resistance phenotypes. MSMEG_6129 in turn phosphorylates a contiguously located putative anti-anti-sigma factor, MSMEG_6127. We therefore propose that MSMEG_5437, MSMEG_6129 and MSMEG_6127 are components of a master regulatory network, upstream of whiB7, that controls the activity of one or more of the 28 sigma factors in M. smegmatis. Together, this network controls the expression of a regulon required for resistance to several unrelated antibiotics.
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Affiliation(s)
- Joshua Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2013; 20:123-33. [PMID: 23352146 DOI: 10.1016/j.chembiol.2012.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/30/2012] [Accepted: 11/20/2012] [Indexed: 01/03/2023]
Abstract
Computational prediction of protein function is frequently error-prone and incomplete. In Mycobacterium tuberculosis (Mtb), ~25% of all genes have no predicted function and are annotated as hypothetical proteins, severely limiting our understanding of Mtb pathogenicity. Here, we utilize a high-throughput quantitative activity-based protein profiling (ABPP) platform to probe, annotate, and validate ATP-binding proteins in Mtb. We experimentally validate prior in silico predictions of >240 proteins and identify 72 hypothetical proteins as ATP binders. ATP interacts with proteins with diverse and unrelated sequences, providing an expanded view of adenosine nucleotide binding in Mtb. Several hypothetical ATP binders are essential or taxonomically limited, suggesting specialized functions in mycobacterial physiology and pathogenicity.
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Abstract
SIGNIFICANCE The reactivity of the thiol in the side chain of cysteines is exploited by bacterial regulatory proteins that sense and respond to reactive oxygen and nitrogen species. RECENT ADVANCES Charged residues and helix dipoles diminish the pKa of redox active cysteines, resulting in a thiolate that is stabilized by neighboring polar amino acids. The reaction of peroxides with thiolates generates a sulfenic acid (-SOH) intermediate that often gives rise to a reversible disulfide bond. Peroxide-induced intramolecular and intermolecular disulfides and intermolecular mixed disulfides modulate the signaling activity of members of the LysR/OxyR, MarR/OhrR, and RsrA family of transcriptional regulators. Thiol-dependent regulators also help bacteria resist the nitrosative and nitroxidative stress. -SOHs, mixed disulfides, and S-nitrosothiols are some of the post-translational modifications induced by nitrogen oxides in the thiol groups of OxyR and SsrB bacterial regulatory proteins. Sulfenylation, disulfide bond formation, S-thiolation, and S-nitrosylation are reversible modifications amenable to feedback regulation by antioxidant and antinitrosative repair systems. The structural and functional changes engaged in the thiol-dependent sensing of reactive species have been adopted by several regulators to foster bacterial virulence during exposure to products of NADPH phagocyte oxidase and inducible nitric oxide synthase. CRITICAL ISSUES Investigations with LysR/OxyR, MarR/OhrR, and RsrA family members have helped in an understanding of the mechanisms by which thiols in regulatory proteins react with reactive species, thereby activating antioxidant and antinitrosative gene expression. FUTURE DIRECTIONS To define the determinants that provide selectivity of redox active thiolates for some reactive species but not others is an important challenge for future investigations.
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Affiliation(s)
- Andrés Vázquez-Torres
- Department of Microbiology, University of Colorado Denver School of Medicine, Aurora, Colorado, USA.
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Forrellad MA, Klepp LI, Gioffré A, Sabio y García J, Morbidoni HR, de la Paz Santangelo M, Cataldi AA, Bigi F. Virulence factors of the Mycobacterium tuberculosis complex. Virulence 2012; 4:3-66. [PMID: 23076359 PMCID: PMC3544749 DOI: 10.4161/viru.22329] [Citation(s) in RCA: 379] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) consists of closely related species that cause tuberculosis in both humans and animals. This illness, still today, remains to be one of the leading causes of morbidity and mortality throughout the world. The mycobacteria enter the host by air, and, once in the lungs, are phagocytated by macrophages. This may lead to the rapid elimination of the bacillus or to the triggering of an active tuberculosis infection. A large number of different virulence factors have evolved in MTBC members as a response to the host immune reaction. The aim of this review is to describe the bacterial genes/proteins that are essential for the virulence of MTBC species, and that have been demonstrated in an in vivo model of infection. Knowledge of MTBC virulence factors is essential for the development of new vaccines and drugs to help manage the disease toward an increasingly more tuberculosis-free world.
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Bhat SA, Singh N, Trivedi A, Kansal P, Gupta P, Kumar A. The mechanism of redox sensing in Mycobacterium tuberculosis. Free Radic Biol Med 2012; 53:1625-41. [PMID: 22921590 DOI: 10.1016/j.freeradbiomed.2012.08.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 08/03/2012] [Accepted: 08/03/2012] [Indexed: 12/25/2022]
Abstract
Tuberculosis epidemics have defied constraint despite the availability of effective treatment for the past half-century. Mycobacterium tuberculosis, the causative agent of TB, is continually exposed to a number of redox stressors during its pathogenic cycle. The mechanisms used by Mtb to sense redox stress and to maintain redox homeostasis are central to the success of Mtb as a pathogen. Careful analysis of the Mtb genome has revealed that Mtb lacks classical redox sensors such as FNR, FixL, and OxyR. Recent studies, however, have established that Mtb is equipped with various sophisticated redox sensors that can detect diverse types of redox stress, including hypoxia, nitric oxide, carbon monoxide, and the intracellular redox environment. Some of these sensors, such as heme-based DosS and DosT, are unique to mycobacteria, whereas others, such as the WhiB proteins and anti-σ factor RsrA, are unique to actinobacteria. This article provides a comprehensive review of the literature on these redox-sensory modules in the context of TB pathogenesis.
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Affiliation(s)
- Shabir Ahmad Bhat
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India
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Vashisht R, Mondal AK, Jain A, Shah A, Vishnoi P, Priyadarshini P, Bhattacharyya K, Rohira H, Bhat AG, Passi A, Mukherjee K, Choudhary KS, Kumar V, Arora A, Munusamy P, Subramanian A, Venkatachalam A, S G, Raj S, Chitra V, Verma K, Zaheer S, J B, Gurusamy M, Razeeth M, Raja I, Thandapani M, Mevada V, Soni R, Rana S, Ramanna GM, Raghavan S, Subramanya SN, Kholia T, Patel R, Bhavnani V, Chiranjeevi L, Sengupta S, Singh PK, Atray N, Gandhi S, Avasthi TS, Nisthar S, Anurag M, Sharma P, Hasija Y, Dash D, Sharma A, Scaria V, Thomas Z, Chandra N, Brahmachari SK, Bhardwaj A. Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis. PLoS One 2012; 7:e39808. [PMID: 22808064 PMCID: PMC3395720 DOI: 10.1371/journal.pone.0039808] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 05/30/2012] [Indexed: 11/18/2022] Open
Abstract
A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative 'Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed 'interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.
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Affiliation(s)
- Rohit Vashisht
- Council of Scientific and Industrial Research (CSIR), Delhi, India
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | | | - Akanksha Jain
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Anup Shah
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Priti Vishnoi
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | | | | | - Harsha Rohira
- Acharya Narendra Dev College, University of Delhi, India
| | - Ashwini G. Bhat
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Anurag Passi
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Keya Mukherjee
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | | | | | - Anshula Arora
- Acharya Narendra Dev College, University of Delhi, India
| | | | | | | | | | - Sweety Raj
- Acharya Narendra Dev College, University of Delhi, India
| | - Vijaya Chitra
- Sree Narayan Guru College, Coimbatore, Tamil Nadu, India
| | - Kaveri Verma
- Maharshi Dayanand University, Rohtak, Haryana, India
| | - Salman Zaheer
- Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, India
| | - Balaganesh J
- Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Mohammed Razeeth
- Bharathidasan University, Palkalaiperur, Tiruchirappall, Tamil Nadu, India
| | - Ilamathi Raja
- Bharathidasan University, Palkalaiperur, Tiruchirappall, Tamil Nadu, India
| | | | - Vishal Mevada
- Bitvirtual patan Node, Hem. North Gujarat University, Patan, Gujarat, India
| | - Raviraj Soni
- Bitvirtual patan Node, Hem. North Gujarat University, Patan, Gujarat, India
| | - Shruti Rana
- Bitvirtual patan Node, Hem. North Gujarat University, Patan, Gujarat, India
| | | | - Swetha Raghavan
- Business Intelligence Technologies India Pvt Ltd., Bangalore, Karnataka, India
| | - Sunil N. Subramanya
- Business Intelligence Technologies India Pvt Ltd., Bangalore, Karnataka, India
| | - Trupti Kholia
- Christ College, Vidya Niketan, Saurashtra University, Rajkot, Gujarat, India
| | - Rajesh Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Varsha Bhavnani
- Department of Biotechnology, University of Pune, Maharashtra State, India
| | | | - Soumi Sengupta
- Indian Statistical Institute, Kolkata, West Bengal, India
| | - Pankaj Kumar Singh
- Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, India
| | - Naresh Atray
- Shri Ram College of Pharmacy, Karnal, Haryana, India
| | - Swati Gandhi
- The Maharaj Sayajirao University of Baroda, Gujarat, India
| | - Tiruvayipati Suma Avasthi
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, Andhra Pradesh, India
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Meenakshi Anurag
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | | | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - Debasis Dash
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Arun Sharma
- Bioinformatics Centre, Institute of Microbial Technology, CSIR, Chandigarh, India
| | - Vinod Scaria
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Zakir Thomas
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - OSDD Consortium
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail: (SKB); (NC); (AB)
| | - Samir K. Brahmachari
- Council of Scientific and Industrial Research (CSIR), Delhi, India
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
- * E-mail: (SKB); (NC); (AB)
| | - Anshu Bhardwaj
- Council of Scientific and Industrial Research (CSIR), Delhi, India
- * E-mail: (SKB); (NC); (AB)
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Be NA, Bishai WR, Jain SK. Role of Mycobacterium tuberculosis pknD in the pathogenesis of central nervous system tuberculosis. BMC Microbiol 2012; 12:7. [PMID: 22243650 PMCID: PMC3322341 DOI: 10.1186/1471-2180-12-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Central nervous system disease is the most serious form of tuberculosis, and is associated with high mortality and severe neurological sequelae. Though recent clinical reports suggest an association of distinct Mycobacterium tuberculosis strains with central nervous system disease, the microbial virulence factors required have not been described previously. RESULTS We screened 398 unique M. tuberculosis mutants in guinea pigs to identify genes required for central nervous system tuberculosis. We found M. tuberculosis pknD (Rv0931c) to be required for central nervous system disease. These findings were central nervous system tissue-specific and were not observed in lung tissues. We demonstrated that pknD is required for invasion of brain endothelia (primary components of the blood-brain barrier protecting the central nervous system), but not macrophages, lung epithelia, or other endothelia. M. tuberculosis pknD encodes a "eukaryotic-like" serine-threonine protein kinase, with a predicted intracellular kinase and an extracellular (sensor) domain. Using confocal microscopy and flow cytometry we demonstrated that the M. tuberculosis PknD sensor is sufficient to trigger invasion of brain endothelia, a process which was neutralized by specific antiserum. CONCLUSIONS Our findings demonstrate a novel in vivo role for M. tuberculosis pknD and represent an important mechanism for bacterial invasion and virulence in central nervous system tuberculosis, a devastating and understudied disease primarily affecting young children.
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Affiliation(s)
- Nicholas A Be
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, 1550 Orleans Street, Baltimore, Maryland 21287, USA
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35
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Abstract
Genomic studies have revealed the presence of Ser/Thr kinases and phosphatases in many bacterial species, although their physiological roles have largely been unclear. Here we review bacterial Ser/Thr kinases (eSTKs) that show homology in their catalytic domains to eukaryotic Ser/Thr kinases and their partner phosphatases (eSTPs) that are homologous to eukaryotic phosphatases. We first discuss insights into the enzymatic mechanism of eSTK activation derived from structural studies on both the ligand-binding and catalytic domains. We then turn our attention to the identified substrates of eSTKs and eSTPs for a number of species and to the implications of these findings for understanding their physiological roles in these organisms.
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36
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Chakraborti PK, Matange N, Nandicoori VK, Singh Y, Tyagi JS, Visweswariah SS. Signalling mechanisms in Mycobacteria. Tuberculosis (Edinb) 2011; 91:432-40. [PMID: 21570916 DOI: 10.1016/j.tube.2011.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/28/2011] [Accepted: 04/10/2011] [Indexed: 11/18/2022]
Abstract
The importance of inter- and intracellular signal transduction in all forms of life cannot be underestimated. A large number of genes dedicated to cellular signalling are found in almost all sequenced genomes, and Mycobacteria are no exception. What appears to be interesting in Mycobacteria is that well characterized signalling mechanisms used by bacteria, such as the histidine-aspartate phosphorelay seen in two-component systems, are found alongside signalling components that closely mimic those seen in higher eukaryotes. This review will describe the important contribution made by researchers in India towards the identification and characterization of proteins involved in two-component signalling, protein phosphorylation and cyclic nucleotide metabolism.
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37
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Sajid A, Arora G, Gupta M, Upadhyay S, Nandicoori VK, Singh Y. Phosphorylation of Mycobacterium tuberculosis Ser/Thr phosphatase by PknA and PknB. PLoS One 2011; 6:e17871. [PMID: 21423706 PMCID: PMC3052367 DOI: 10.1371/journal.pone.0017871] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 02/11/2011] [Indexed: 11/30/2022] Open
Abstract
Background The integrated functions of 11 Ser/Thr protein kinases (STPKs) and one
phosphatase manipulate the phosphorylation levels of critical proteins in
Mycobacterium tuberculosis. In this study, we show that
the lone Ser/Thr phosphatase (PstP) is regulated through phosphorylation by
STPKs. Principal Findings PstP is phosphorylated by PknA and PknB and phosphorylation is influenced by
the presence of Zn2+-ions and inorganic phosphate (Pi). PstP
is differentially phosphorylated on the cytosolic domain with
Thr137, Thr141, Thr174 and
Thr290 being the target residues of PknB while
Thr137 and Thr174 are phosphorylated by PknA. The
Mn2+-ion binding residues Asp38 and
Asp229 are critical for the optimal activity of PstP and
substitution of these residues affects its phosphorylation status. Native
PstP and its phosphatase deficient mutant PstPcD38G
are phosphorylated by PknA and PknB in E. coli and addition
of Zn2+/Pi in the culture conditions affect the
phosphorylation level of PstP. Interestingly, the phosphorylated phosphatase
is more active than its unphosphorylated equivalent. Conclusions and Significance This study establishes the novel mechanisms for regulation of mycobacterial
Ser/Thr phosphatase. The results indicate that STPKs and PstP may regulate
the signaling through mutually dependent mechanisms. Consequently, PstP
phosphorylation may play a critical role in regulating its own activity.
Since, the equilibrium between phosphorylated and non-phosphorylated states
of mycobacterial proteins is still unexplained, understanding the regulation
of PstP may help in deciphering the signal transduction pathways mediated by
STPKs and the reversibility of the phenomena.
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Affiliation(s)
- Andaleeb Sajid
- Institute of Genomics and Integrative Biology
(CSIR), Delhi, India
| | - Gunjan Arora
- Institute of Genomics and Integrative Biology
(CSIR), Delhi, India
| | - Meetu Gupta
- Institute of Genomics and Integrative Biology
(CSIR), Delhi, India
| | - Sandeep Upadhyay
- National Institute of Immunology, Aruna Asaf
Ali Marg, New Delhi, India
| | | | - Yogendra Singh
- Institute of Genomics and Integrative Biology
(CSIR), Delhi, India
- * E-mail:
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38
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Autoregulatory characteristics of a Bacillus anthracis serine/threonine kinase. J Bacteriol 2011; 193:1833-42. [PMID: 21296958 DOI: 10.1128/jb.01401-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BA-Stk1 is a serine/threonine kinase (STK) expressed by Bacillus anthracis. In previous studies, we found that BA-Stk1 activity is modulated through dephosphorylation by a partner phosphatase, BA-Stp1. In this study, we identified critical phosphorylation regions of BA-Stk1 and determined the contributions of these phosphodomains to autophosphorylation and substrate phosphorylation. The data indicate that BA-Stk1 undergoes trans-autophosphorylation within a regulatory domain, referred to as the activation loop, which carries eight putative regulatory serine and threonine residues. We identified activation loop mutants that impacted kinase activity in three different manners: regulation of autophosphorylation (T162), regulation of substrate phosphorylation (T159 and S169), and regulation of overall kinase activity (T163). Tandem mass spectrometry (MS/MS) analysis of the phosphorylation profile of each mutant revealed a second site of phosphorylation on the kinase that was influenced by the phosphorylation status of the activation loop. This second region of the kinase contained a single phosphorylation residue, S214. Previous work has shown S214 to be necessary for downstream substrate phosphorylation, and we have shown that this residue is subject to dephosphorylation by BA-Stp1. These findings indicate a connection between the phosphorylation status of the activation loop and phosphorylation of S214, and this suggests a previously undescribed model for how a bacterial STK shifts from a state of autophosphorylation to targeting downstream substrates.
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Sharma AK, Ye L, Baer CE, Shanmugasundaram K, Alber T, Alper SL, Rigby AC. Solution structure of the guanine nucleotide-binding STAS domain of SLC26-related SulP protein Rv1739c from Mycobacterium tuberculosis. J Biol Chem 2010; 286:8534-8544. [PMID: 21190940 DOI: 10.1074/jbc.m110.165449] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The structure and intrinsic activities of conserved STAS domains of the ubiquitous SulP/SLC26 anion transporter superfamily have until recently remained unknown. Here we report the heteronuclear, multidimensional NMR spectroscopy solution structure of the STAS domain from the SulP/SLC26 putative anion transporter Rv1739c of Mycobacterium tuberculosis. The 0.87-Å root mean square deviation structure revealed a four-stranded β-sheet with five interspersed α-helices, resembling the anti-σ factor antagonist fold. Rv1739c STAS was shown to be a guanine nucleotide-binding protein, as revealed by nucleotide-dependent quench of intrinsic STAS fluorescence and photoaffinity labeling. NMR chemical shift perturbation analysis partnered with in silico docking calculations identified solvent-exposed STAS residues involved in nucleotide binding. Rv1739c STAS was not an in vitro substrate of mycobacterial kinases or anti-σ factors. These results demonstrate that Rv1739c STAS binds guanine nucleotides at physiological concentrations and undergoes a ligand-induced conformational change but, unlike anti-σ factor antagonists, may not mediate signals via phosphorylation.
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Affiliation(s)
- Alok K Sharma
- From the Divison of Molecular and Vascular Medicine,; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215 and
| | - Liwen Ye
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215 and; Renal Division
| | - Christina E Baer
- the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Kumaran Shanmugasundaram
- From the Divison of Molecular and Vascular Medicine,; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215 and
| | - Tom Alber
- the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Seth L Alper
- From the Divison of Molecular and Vascular Medicine,; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215 and; Renal Division,.
| | - Alan C Rigby
- From the Divison of Molecular and Vascular Medicine,; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215 and.
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Khan S, Nagarajan SN, Parikh A, Samantaray S, Singh A, Kumar D, Roy RP, Bhatt A, Nandicoori VK. Phosphorylation of enoyl-acyl carrier protein reductase InhA impacts mycobacterial growth and survival. J Biol Chem 2010; 285:37860-71. [PMID: 20864541 DOI: 10.1074/jbc.m110.143131] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
InhA, the primary target for the first line anti-tuberculosis drug isoniazid, is a key enzyme of the fatty-acid synthase II system involved in mycolic acid biosynthesis in Mycobacterium tuberculosis. In this study, we show that InhA is a substrate for mycobacterial serine/threonine protein kinases. Using a novel approach to validate phosphorylation of a substrate by multiple kinases in a surrogate host (Escherichia coli), we have demonstrated efficient phosphorylation of InhA by PknA, PknB, and PknH, and to a lower extent by PknF. Additionally, the sites targeted by PknA/PknB have been identified and shown to be predominantly located at the C terminus of InhA. Results demonstrate in vivo phosphorylation of InhA in mycobacteria and validate Thr-266 as one of the key sites of phosphorylation. Significantly, our studies reveal that the phosphorylation of InhA by kinases modulates its biochemical activity, with phosphorylation resulting in decreased enzymatic activity. Co-expression of kinase and InhA alters the growth dynamics of Mycobacterium smegmatis, suggesting that InhA phosphorylation in vivo is an important event in regulating its activity. An InhA-T266E mutant, which mimics constitutive phosphorylation, is unable to rescue an M. smegmatis conditional inhA gene replacement mutant, emphasizing the critical role of Thr-266 in mediating post-translational regulation of InhA activity. The involvement of various serine/threonine kinases in modulating the activity of a number of enzymes of the mycolic acid synthesis pathway, including InhA, accentuates the intricacies of mycobacterial signaling networks in parallel with the changing environment.
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Affiliation(s)
- Shazia Khan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 India
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Mehra S, Dutta NK, Mollenkopf HJ, Kaushal D. Mycobacterium tuberculosis MT2816 encodes a key stress-response regulator. J Infect Dis 2010; 202:943-53. [PMID: 20701538 DOI: 10.1086/654820] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Sigma (sigma) factors are transcription initiation factors that modulate the response of Mycobacterium tuberculosis to changes in extracellular milieu, allowing it to survive stress. METHODS We analyzed the expression of MT2816/Rv2745c under various stress conditions that mimic the intracellular environment faced by M. tuberculosis. RESULTS MT2816/Rv2745c expression was induced in M. tuberculosis following redox stress, heat shock and acid shock and intracellular replication. Its expression was also induced by SDS and thioridazine, agents that impact M. tuberculosis cell-envelope. However, exposure to isoniazid or ethambutol, front-line antituberculosis drugs which also target the cell envelope, did not induce the expression of MT2816/Rv2745c. Studies using Delta-sigma(H) and Delta-sigma(E) mutants showed that sigma(H) was required for the induction of MT2816/Rv2745c. Conditional expression of the MT2816/Rv2745c in M. tuberculosis showed that apart from regulating proteolysis, this gene may control the expression of trehalose biosynthesis and impact the maintenance of cellular redox potential and energy generation. CONCLUSIONS The protein encoded by MT2816/Rv2745c is important for the pathogen's response to stress conditions that mimic in vivo growth and it is subject to complex regulation. The MT2816/Rv2745c encoded protein likely functions by protecting intracellular redox potential and by inducing the expression of trehalose, a constituent of M. tuberculosis cell walls that is important for defense against cell-surface and oxidative stress.
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Affiliation(s)
- Smriti Mehra
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Covington, Louisiana 70433, USA
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42
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Rajpurohit YS, Misra HS. Characterization of a DNA damage-inducible membrane protein kinase from Deinococcus radiodurans and its role in bacterial radioresistance and DNA strand break repair. Mol Microbiol 2010; 77:1470-82. [PMID: 20633226 DOI: 10.1111/j.1365-2958.2010.07301.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deinococcus radiodurans mutant lacking pyrroloquinoline-quinone (PQQ) synthesis shows sensitivity to γ-rays and impairment of DNA double strand break repair. The genome of this bacterium encodes five putative proteins having multiple PQQ binding motifs. The deletion mutants of corresponding genes were generated, and their response to DNA damage was monitored. Only the Δdr2518 mutant exhibited higher sensitivity to DNA damage. Survival of these cells decreased by 3-log cycle both at 6 kGy γ-rays and 1200 Jm(-2) UV (254 nm) radiation, and 2.5-log cycle upon 14 days desiccation at 5% humidity. The Δdr2518 mutant showed complete inhibition of DSB repair until 24 h PIR and disappearance of a few phosphoproteins. The Δdr2518pqqE:cat double mutant showed γ-ray sensitivity similar to Δdr2518 indicating functional interaction of these genes in D. radiodurans. DR2518 contains a eukaryotic type Ser/Thr kinase domain and structural topology suggesting stress responsive transmembrane protein. Its autokinase activity in solution was stimulated by nearly threefold with PQQ and twofold with linear DNA, but not with circular plasmid DNA. More than 15-fold increase in dr2518 transcription and several-fold enhanced in vivo phosphorylation of DR2518 were observed in response to γ irradiation. These results suggest that DR2518 as a DNA damage-responsive protein kinase plays an important role in radiation resistance and DNA strand break repair in D. radiodurans.
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43
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Malhotra V, Arteaga-Cortés LT, Clay G, Clark-Curtiss JE. Mycobacterium tuberculosis protein kinase K confers survival advantage during early infection in mice and regulates growth in culture and during persistent infection: implications for immune modulation. MICROBIOLOGY-SGM 2010; 156:2829-2841. [PMID: 20522497 PMCID: PMC3068690 DOI: 10.1099/mic.0.040675-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis serine/threonine protein kinases (STPKs) are key regulators of growth and metabolism; however, evidence for their roles in virulence is limited. In a preliminary screen based on comparative expression between strains H37Rv and H37Ra, six STPK genes, pknD, pknG, pknH, pknJ, pknK and pknL, showed higher expression in H37Rv. In the second screen, STPK expression was analysed in H37Rv-infected human macrophages. Interestingly, significant expression of pknK was detected only at 18 h post-infection, suggesting its involvement in early infection events. We have investigated the roles of PknK in vitro and in vivo. PknK levels were induced under stationary phase and deletion of pknK resulted in increased resistance of the mutant to acidic pH, hypoxia, oxidative and stationary-phase stresses in vitro. These results, together with the increased survival of the ΔpknK strain during persistent infection in mice, reveal a role for PknK in adaptive mechanisms that slow the growth of mycobacteria. A novel finding of this study was the inhibition of growth of ΔpknK strain during acute infection in mice that correlated with the significant upregulation of tumour necrosis factor as well as the simultaneous downregulation of interleukin-12p40, interferon-γ and induced nitric oxide synthase transcripts. Finally, we provide evidence for the localization of PknK during infection and discuss its implications in pathogenesis.
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Affiliation(s)
- Vandana Malhotra
- Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287, USA
| | - Lourdes T Arteaga-Cortés
- Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287, USA
| | - Gwendolyn Clay
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Josephine E Clark-Curtiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.,Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287, USA
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44
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Tyagi N, Anamika K, Srinivasan N. A framework for classification of prokaryotic protein kinases. PLoS One 2010; 5:e10608. [PMID: 20520783 PMCID: PMC2877116 DOI: 10.1371/journal.pone.0010608] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 04/13/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Overwhelming majority of the Serine/Threonine protein kinases identified by gleaning archaeal and eubacterial genomes could not be classified into any of the well known Hanks and Hunter subfamilies of protein kinases. This is owing to the development of Hanks and Hunter classification scheme based on eukaryotic protein kinases which are highly divergent from their prokaryotic homologues. A large dataset of prokaryotic Serine/Threonine protein kinases recognized from genomes of prokaryotes have been used to develop a classification framework for prokaryotic Ser/Thr protein kinases. METHODOLOGY/PRINCIPAL FINDINGS We have used traditional sequence alignment and phylogenetic approaches and clustered the prokaryotic kinases which represent 72 subfamilies with at least 4 members in each. Such a clustering enables classification of prokaryotic Ser/Thr kinases and it can be used as a framework to classify newly identified prokaryotic Ser/Thr kinases. After series of searches in a comprehensive sequence database we recognized that 38 subfamilies of prokaryotic protein kinases are associated to a specific taxonomic level. For example 4, 6 and 3 subfamilies have been identified that are currently specific to phylum proteobacteria, cyanobacteria and actinobacteria respectively. Similarly subfamilies which are specific to an order, sub-order, class, family and genus have also been identified. In addition to these, we also identify organism-diverse subfamilies. Members of these clusters are from organisms of different taxonomic levels, such as archaea, bacteria, eukaryotes and viruses. CONCLUSION/SIGNIFICANCE Interestingly, occurrence of several taxonomic level specific subfamilies of prokaryotic kinases contrasts with classification of eukaryotic protein kinases in which most of the popular subfamilies of eukaryotic protein kinases occur diversely in several eukaryotes. Many prokaryotic Ser/Thr kinases exhibit a wide variety of modular organization which indicates a degree of complexity and protein-protein interactions in the signaling pathways in these microbes.
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Affiliation(s)
- Nidhi Tyagi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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45
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Understanding the role of PknJ in Mycobacterium tuberculosis: biochemical characterization and identification of novel substrate pyruvate kinase A. PLoS One 2010; 5:e10772. [PMID: 20520732 PMCID: PMC2875399 DOI: 10.1371/journal.pone.0010772] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 04/29/2010] [Indexed: 11/19/2022] Open
Abstract
Reversible protein phosphorylation is a prevalent signaling mechanism which modulates cellular metabolism in response to changing environmental conditions. In this study, we focus on previously uncharacterized Mycobacterium tuberculosis Ser/Thr protein kinase (STPK) PknJ, a putative transmembrane protein. PknJ is shown to possess autophosphorylation activity and is also found to be capable of carrying out phosphorylation on the artificial substrate myelin basic protein (MyBP). Previous studies have shown that the autophosphorylation activity of M. tuberculosis STPKs is dependent on the conserved residues in the activation loop. However, our results show that apart from the conventional conserved residues, additional residues in the activation loop may also play a crucial role in kinase activation. Further characterization of PknJ reveals that the kinase utilizes unusual ions (Ni2+, Co2+) as cofactors, thus hinting at a novel mechanism for PknJ activation. Additionally, as shown for other STPKs, we observe that PknJ possesses the capability to dimerize. In order to elucidate the signal transduction cascade emanating from PknJ, the M. tuberculosis membrane-associated protein fraction is treated with the active kinase and glycolytic enzyme Pyruvate kinase A (mtPykA) is identified as one of the potential substrates of PknJ. The phospholabel is found to be localized on serine and threonine residue(s), with Ser37 identified as one of the sites of phosphorylation. Since Pyk is known to catalyze the last step of glycolysis, our study shows that the fundamental pathways such as glycolysis can also be governed by STPK-mediated signaling.
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46
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Jang J, Stella A, Boudou F, Levillain F, Darthuy E, Vaubourgeix J, Wang C, Bardou F, Puzo G, Gilleron M, Burlet-Schiltz O, Monsarrat B, Brodin P, Gicquel B, Neyrolles O. Functional characterization of the Mycobacterium tuberculosis serine/threonine kinase PknJ. MICROBIOLOGY-SGM 2010; 156:1619-1631. [PMID: 20185505 DOI: 10.1099/mic.0.038133-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Eukaryotic-like Ser/Thr protein kinases (STPKs) are present in many bacterial species, where they control various physiological and virulence processes by enabling microbial adaptation to specific environmental signals. PknJ is the only member of the 11 STPKs identified in Mycobacterium tuberculosis that still awaits characterization. Here we report that PknJ is a functional kinase that forms dimers in vitro, and contains a single transmembrane domain. Using a high-density peptide-chip-based technology, multiple potential mycobacterial targets were identified for PknJ. We confirmed PknJ-dependent phosphorylation of four of these targets: PknJ itself, which autophosphorylates at Thr(168), Thr(171) and Thr(173) residues; the transcriptional regulator EmbR; the methyltransferase MmaA4/Hma involved in mycolic acid biosynthesis; and the dipeptidase PepE, whose encoding gene is located next to pknJ in the mycobacterial genome. Our results provide a number of candidate phospho-targets for PknJ and possibly other mycobacterial STPKs that could be studied to investigate the role of STPKs in M. tuberculosis physiology and virulence.
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Affiliation(s)
- Jichan Jang
- Inserm Equipe Avenir Biology of Intracellular Pathogens, Institut Pasteur Korea, Seoul, Republic of Korea.,Unit of Mycobacterial Genetics, Institut Pasteur, Paris, France
| | - Alexandre Stella
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Frédéric Boudou
- Unit of Mycobacterial Genetics, Institut Pasteur, Paris, France
| | - Florence Levillain
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Eliette Darthuy
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Julien Vaubourgeix
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Chongzhen Wang
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Fabienne Bardou
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Germain Puzo
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Martine Gilleron
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Odile Burlet-Schiltz
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Bernard Monsarrat
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Priscille Brodin
- Inserm Equipe Avenir Biology of Intracellular Pathogens, Institut Pasteur Korea, Seoul, Republic of Korea
| | | | - Olivier Neyrolles
- Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France.,Unit of Mycobacterial Genetics, Institut Pasteur, Paris, France
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Sureka K, Hossain T, Mukherjee P, Chatterjee P, Datta P, Kundu M, Basu J. Novel role of phosphorylation-dependent interaction between FtsZ and FipA in mycobacterial cell division. PLoS One 2010; 5:e8590. [PMID: 20066037 PMCID: PMC2797604 DOI: 10.1371/journal.pone.0008590] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 12/09/2009] [Indexed: 11/26/2022] Open
Abstract
The bacterial divisome is a multiprotein complex. Specific protein-protein interactions specify whether cell division occurs optimally, or whether division is arrested. Little is known about these protein-protein interactions and their regulation in mycobacteria. We have investigated the interrelationship between the products of the Mycobacterium tuberculosis gene cluster Rv0014c-Rv0019c, namely PknA (encoded by Rv0014c) and FtsZ-interacting protein A, FipA (encoded by Rv0019c) and the products of the division cell wall (dcw) cluster, namely FtsZ and FtsQ. M. smegmatis strains depleted in components of the two gene clusters have been complemented with orthologs of the respective genes of M. tuberculosis. Here we identify FipA as an interacting partner of FtsZ and FtsQ and establish that PknA-dependent phosphorylation of FipA on T77 and FtsZ on T343 is required for cell division under oxidative stress. A fipA knockout strain of M. smegmatis is less capable of withstanding oxidative stress than the wild type and showed elongation of cells due to a defect in septum formation. Localization of FtsQ, FtsZ and FipA at mid-cell was also compromised. Growth and survival defects under oxidative stress could be functionally complemented by fipA of M. tuberculosis but not its T77A mutant. Merodiploid strains of M. smegmatis expressing the FtsZ(T343A) showed inhibition of FtsZ-FipA interaction and Z ring formation under oxidative stress. Knockdown of FipA led to elongation of M. tuberculosis cells grown in macrophages and reduced intramacrophage growth. These data reveal a novel role of phosphorylation-dependent protein-protein interactions involving FipA, in the sustenance of mycobacterial cell division under oxidative stress.
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Affiliation(s)
| | | | | | | | - Pratik Datta
- Department of Chemistry, Bose Institute, Kolkata, India
| | | | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
- * E-mail:
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48
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Barik S, Sureka K, Mukherjee P, Basu J, Kundu M. RseA, the SigE specific anti-sigma factor ofMycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. Mol Microbiol 2009; 75:592-606. [DOI: 10.1111/j.1365-2958.2009.07008.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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49
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Sachdeva P, Misra R, Tyagi AK, Singh Y. The sigma factors of Mycobacterium tuberculosis: regulation of the regulators. FEBS J 2009; 277:605-26. [DOI: 10.1111/j.1742-4658.2009.07479.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Cao XJ, Dai J, Xu H, Nie S, Chang X, Hu BY, Sheng QH, Wang LS, Ning ZB, Li YX, Guo XK, Zhao GP, Zeng R. High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans. Cell Res 2009; 20:197-210. [PMID: 19918266 DOI: 10.1038/cr.2009.127] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Leptospirosis is a widespread zoonotic disease caused by pathogenic spirochetes of the genus Leptospira that infects humans and a wide range of animals. By combining computational prediction and high-accuracy tandem mass spectra, we revised the genome annotation of Leptospira interrogans serovar Lai, a free-living pathogenic spirochete responsible for leptospirosis, providing substantial peptide evidence for novel genes and new gene boundaries. Subsequently, we presented a high-coverage proteome analysis of protein expression and multiple posttranslational modifications (PTMs). Approximately 64.3% of the predicted L. interrogans proteins were cataloged by detecting 2 540 proteins. Meanwhile, a profile of multiple PTMs was concurrently established, containing in total 32 phosphorylated, 46 acetylated and 155 methylated proteins. The PTM systems in the serovar Lai show unique features. Unique eukaryotic-like features of L. interrogans protein modifications were demonstrated in both phosphorylation and arginine methylation. This systematic analysis provides not only comprehensive information of high-coverage protein expression and multiple modifications in prokaryotes but also a view suggesting that the evolutionarily primitive L. interrogans shares significant similarities in protein modification systems with eukaryotes.
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Affiliation(s)
- Xing-Jun Cao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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