1
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Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [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: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
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Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
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2
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Singh PR, Goar H, Paul P, Mehta K, Bamniya B, Vijjamarri AK, Bansal R, Khan H, Karthikeyan S, Sarkar D. Dual functioning by the PhoR sensor is a key determinant to Mycobacterium tuberculosis virulence. PLoS Genet 2023; 19:e1011070. [PMID: 38100394 PMCID: PMC10723718 DOI: 10.1371/journal.pgen.1011070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
PhoP-PhoR, one of the 12 two-component systems (TCSs) that empower M. tuberculosis to sense and adapt to diverse environmental conditions, remains essential for virulence, and therefore, represents a major target to develop novel anti-TB therapies. Although both PhoP and PhoR have been structurally characterized, the signal(s) that this TCS responds to remains unknown. Here, we show that PhoR is a sensor of acidic pH/high salt conditions, which subsequently activate PhoP via phosphorylation. In keeping with this, transcriptomic data uncover that acidic pH- inducible expression of PhoP regulon is significantly inhibited in a PhoR-deleted M. tuberculosis. Strikingly, a set of PhoP regulon genes displayed a low pH-dependent activation even in the absence of PhoR, suggesting the presence of non-canonical mechanism(s) of PhoP activation. Using genome-wide interaction-based screening coupled with phosphorylation assays, we identify a non-canonical mechanism of PhoP phosphorylation by the sensor kinase PrrB. To investigate how level of P~PhoP is regulated, we discovered that in addition to its kinase activity PhoR functions as a phosphatase of P~PhoP. Our subsequent results identify the motif/residues responsible for kinase/phosphatase dual functioning of PhoR. Collectively, these results uncover that contrasting kinase and phosphatase functions of PhoR determine the homeostatic mechanism of regulation of intra-mycobacterial P~PhoP which controls the final output of the PhoP regulon. Together, these results connect PhoR to pH-dependent activation of PhoP with downstream functioning of the regulator. Thus, PhoR plays a central role in mycobacterial adaptation to low pH conditions within the host macrophage phagosome, and a PhoR-deleted M. tuberculosis remains significantly attenuated in macrophages and animal models.
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Affiliation(s)
| | - Harsh Goar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Partha Paul
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Khushboo Mehta
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bhanwar Bamniya
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Roohi Bansal
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Hina Khan
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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Giacalone D, Yap RE, Ecker AMV, Tan S. PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases. PLoS Genet 2022; 18:e1010331. [PMID: 35913986 PMCID: PMC9371303 DOI: 10.1371/journal.pgen.1010331] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/11/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia-responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK-phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function. Vital to successful host colonization by Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the bacterium’s ability to respond and adapt to changes in its local environment during infection. Here, we discover that the essential transcription factor PrrA, part of the PrrAB two-component system (TCS), modulates Mtb response to four important environmental cues encountered within the host: pH, chloride, nitric oxide, and hypoxia. PrrA acts as a rheostat, adjusting the amplitude of Mtb gene expression changes upon bacterial exposure to each of the four environmental signals. Further, we reveal a critical impact of serine/threonine protein kinases (STPKs) on PrrA function, with prevention of STPK phosphorylation of PrrA disrupting adaptive response of Mtb to growth-inhibiting cues and attenuating the bacterium’s ability to colonize its host. Our work uncovers PrrA as a regulator with broad impact across environmental signals, and highlights how two regulatory systems, TCSs and STPKs, critically interact in coordinating Mtb response to environmental cues.
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Affiliation(s)
- David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Rochelle E. Yap
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alwyn M. V. Ecker
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
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4
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Phosphoproteomics of Mycobacterium-host interaction and inspirations for novel measures against tuberculosis. Cell Signal 2022; 91:110238. [PMID: 34986388 DOI: 10.1016/j.cellsig.2021.110238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/19/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) remains a tremendous global public health concern. Deciphering the biology of the pathogen and its interaction with host can inspire new measures against tuberculosis. Phosphorylation plays versatile and important role in the pathogen and host physiology, such as virulence, signaling and immune response. Proteome-wide phosphorylation of Mtb and its infected host cells, namely phosphoproteome, can inform the post-translational modification of the interaction network between the pathogen and the host, key targets for novel antibiotics. We summarized the phosphoproteome of Mtb, as well as the host, focusing on potential application for new measures against tuberculosis.
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Unden G, Klein R. Sensing of O 2 and nitrate by bacteria: alternative strategies for transcriptional regulation of nitrate respiration by O 2 and nitrate. Environ Microbiol 2020; 23:5-14. [PMID: 33089915 DOI: 10.1111/1462-2920.15293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 12/28/2022]
Abstract
Many bacteria are able to use O2 and nitrate as alternative electron acceptors for respiration. Strategies for regulation in response to O2 and nitrate can vary considerably. In the paradigmatic system of E. coli (and γ-proteobacteria), regulation by O2 and nitrate is established by the O2 -sensor FNR and the two-component system NarX-NarL (for nitrate regulation). Expression of narGHJI is regulated by the binding of FNR and NarL to the promoter. A similar strategy by individual regulation in response to O2 and nitrate is verified in many genera by the use of various types of regulators. Otherwise, in the soil bacteria Bacillus subtilis (Firmicutes) and Streptomyces (Actinobacteria), nitrate respiration is subject to anaerobic induction, without direct nitrate induction. In contrast, the NreA-NreB-NreC two-component system of Staphylococcus (Firmicutes) performs joint sensing of O2 and nitrate by interacting O2 and nitrate sensors. The O2 -sensor NreB phosphorylates the response regulator NreC to activate narGHJI expression. NreC-P transmits the signal for anaerobiosis to the promoter. The nitrate sensor NreA modulates NreB function by converting NreB in the absence of nitrate from the kinase to a phosphatase that dephosphorylates NreC-P. Thus, widely different strategies for coordinating the response to O2 and nitrate have evolved in bacteria.
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Affiliation(s)
- Gottfried Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, 55099, Germany
| | - Robin Klein
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, 55099, Germany
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6
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Sousa EH, Carepo MS, Moura JJ. Nitrate-nitrite fate and oxygen sensing in dormant Mycobacterium tuberculosis: A bioinorganic approach highlighting the importance of transition metals. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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7
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Zheng H, Williams JT, Aleiwi B, Ellsworth E, Abramovitch RB. Inhibiting Mycobacterium tuberculosis DosRST Signaling by Targeting Response Regulator DNA Binding and Sensor Kinase Heme. ACS Chem Biol 2020; 15:52-62. [PMID: 31556993 PMCID: PMC6970277 DOI: 10.1021/acschembio.8b00849] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Mycobacterium
tuberculosis (Mtb) possesses a two-component
regulatory system, DosRST, that enables Mtb to sense host immune cues
and establish a state of nonreplicating persistence (NRP). NRP bacteria
are tolerant to several antimycobacterial drugs in vitro and are thought to play a role in the long course of tuberculosis
therapy. Previously, we reported the discovery of six novel chemical
inhibitors of DosRST, named HC101A–106A, from a whole cell,
reporter-based phenotypic high throughput screen. Here, we report
functional and mechanism of action studies of HC104A and HC106A. RNaseq
transcriptional profiling shows that the compounds downregulate genes
of the DosRST regulon. Both compounds reduce hypoxia-induced triacylglycerol
synthesis by ∼50%. HC106A inhibits Mtb survival during hypoxia-induced
NRP; however, HC104A did not inhibit survival during NRP. An electrophoretic
mobility assay shows that HC104A inhibits DosR DNA binding in a dose-dependent
manner, indicating that HC104A may function by directly targeting
DosR. In contrast, UV–visible spectroscopy studies suggest
HC106A directly targets the sensor kinase heme, via a mechanism that
is distinct from the oxidation and alkylation of heme previously observed
with artemisinin (HC101A). Synergistic interactions were observed
when DosRST inhibitors were examined in pairwise combinations with
the strongest potentiation observed between artemisinin paired with
HC102A, HC103A, or HC106A. Our data collectively show that the DosRST
pathway can be inhibited by multiple distinct mechanisms.
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8
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Veyron-Churlet R, Locht C. In Vivo Methods to Study Protein-Protein Interactions as Key Players in Mycobacterium Tuberculosis Virulence. Pathogens 2019; 8:pathogens8040173. [PMID: 31581602 PMCID: PMC6963305 DOI: 10.3390/pathogens8040173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Studies on protein–protein interactions (PPI) can be helpful for the annotation of unknown protein functions and for the understanding of cellular processes, such as specific virulence mechanisms developed by bacterial pathogens. In that context, several methods have been extensively used in recent years for the characterization of Mycobacterium tuberculosis PPI to further decipher tuberculosis (TB) pathogenesis. This review aims at compiling the most striking results based on in vivo methods (yeast and bacterial two-hybrid systems, protein complementation assays) for the specific study of PPI in mycobacteria. Moreover, newly developed methods, such as in-cell native mass resonance and proximity-dependent biotinylation identification, will have a deep impact on future mycobacterial research, as they are able to perform dynamic (transient interactions) and integrative (multiprotein complexes) analyses.
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Affiliation(s)
- Romain Veyron-Churlet
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Camille Locht
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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9
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Park EJ, Kwon YM, Lee JW, Kang HY, Oh JI. Dual control of RegX3 transcriptional activity by SenX3 and PknB. J Biol Chem 2019; 294:11023-11034. [PMID: 31160336 DOI: 10.1074/jbc.ra119.008232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The mycobacterial SenX3-RegX3 two-component system consists of the SenX3 sensor histidine kinase and its cognate RegX3 response regulator. This system is a phosphorelay-based regulatory system involved in sensing environmental Pi levels and induction of genes required for Pi acquisition under Pi-limiting conditions. Here we demonstrate that overexpression of the kinase domain of Mycobacterium tuberculosis PknB (PknB-KDMtb) inhibits the transcriptional activity of RegX3 of both M. tuberculosis and Mycobacterium smegmatis (RegX3Mtb and RegX3Ms, respectively). Mass spectrometry results, along with those of in vitro phosphorylation and complementation analyses, revealed that PknB kinase activity inhibits the transcriptional activity of RegX3Mtb through phosphorylation events at Thr-100, Thr-191, and Thr-217. Electrophoretic mobility shift assays disclosed that phosphorylation of Thr-191 and Thr-217 abolishes the DNA-binding ability of RegX3Mtb and that Thr-100 phosphorylation likely prevents RegX3Mtb from being activated through conformational changes induced by SenX3-mediated phosphorylation. We propose that the convergence of the PknB and SenX3-RegX3 signaling pathways might enable mycobacteria to integrate environmental Pi signals with the cellular replication state to adjust gene expression in response to Pi availability.
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Affiliation(s)
- Eun-Jin Park
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Yu-Mi Kwon
- Biomedical Research Institute, Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea, and; Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Ho-Young Kang
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea,.
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10
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Singh KK, Bhardwaj N, Sankhe GD, Udaykumar N, Singh R, Malhotra V, Saini DK. Acetylation of Response Regulator Proteins, TcrX and MtrA in M. tuberculosis Tunes their Phosphotransfer Ability and Modulates Two-Component Signaling Crosstalk. J Mol Biol 2019; 431:777-793. [DOI: 10.1016/j.jmb.2019.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/01/2019] [Accepted: 01/03/2019] [Indexed: 01/31/2023]
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11
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Lobão JBDS, Gondim ACS, Guimarães WG, Gilles‐Gonzalez M, Lopes LGDF, Sousa EHS. Oxygen triggers signal transduction in the DevS (DosS) sensor of
Mycobacterium tuberculosis
by modulating the quaternary structure. FEBS J 2019; 286:479-494. [DOI: 10.1111/febs.14734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/05/2018] [Accepted: 12/14/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Josiane Bezerra da Silva Lobão
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | - Ana C. S. Gondim
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | - Wellinson G. Guimarães
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | | | - Luiz Gonzaga de França Lopes
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | - Eduardo H. S. Sousa
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
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12
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Zondervan NA, van Dam JCJ, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M. Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story. Int J Mol Sci 2018; 19:E347. [PMID: 29364195 PMCID: PMC5855569 DOI: 10.3390/ijms19020347] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant M. tuberculosis strains makes treating tuberculosis increasingly challenging. In order to develop novel intervention strategies, detailed understanding of the molecular mechanisms behind the success of this pathogen is required. Here, we review recent literature to provide a systems level overview of the molecular and cellular components involved in divalent metal homeostasis and their role in regulating the three main virulence strategies of M. tuberculosis: immune modulation, dormancy and phagosomal rupture. We provide a visual and modular overview of these components and their regulation. Our analysis identified a single regulatory cascade for these three virulence strategies that respond to limited availability of divalent metals in the phagosome.
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Affiliation(s)
- Niels A Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Jesse C J van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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13
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Bae HJ, Lee HN, Baek MN, Park EJ, Eom CY, Ko IJ, Kang HY, Oh JI. Inhibition of the DevSR Two-Component System by Overexpression of Mycobacterium tuberculosis PknB in Mycobacterium smegmatis. Mol Cells 2017; 40:632-642. [PMID: 28843272 PMCID: PMC5638771 DOI: 10.14348/molcells.2017.0076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/11/2017] [Accepted: 07/24/2017] [Indexed: 01/29/2023] Open
Abstract
The DevSR (DosSR) two-component system, which is a major regulatory system involved in oxygen sensing in mycobacteria, plays an important role in hypoxic induction of many genes in mycobacteria. We demonstrated that overexpression of the kinase domain of Mycobacterium tuberculosis (Mtb) PknB inhibited transcriptional activity of the DevR response regulator in Mycobacterium smegmatis and that this inhibitory effect was exerted through phosphorylation of DevR on Thr180 within its DNA-binding domain. Moreover, the purified kinase domain of Mtb PknB significantly phosphorylated RegX3, NarL, KdpE, TrcR, DosR, and MtrA response regulators of Mtb that contain the Thr residues corresponding to Thr180 of DevR in their DNA-binding domains, implying that transcriptional activities of these response regulators might also be inhibited when the kinase domain of PknB is overexpressed.
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Affiliation(s)
- Hyun-Jung Bae
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Ha-Na Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Mi-Na Baek
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Eun-Jin Park
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Chi-Yong Eom
- Korea Basic Science Institute, Seoul 02855,
Korea
| | - In-Jeong Ko
- Korea Science Academy of KAIST, Busan 47162,
Korea
| | - Ho-Young Kang
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
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14
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Abstract
Two-component regulatory systems (2CRSs) are widely used by bacteria to sense and respond to environmental stimuli with coordinated changes in gene expression. Systems are normally comprised of a sensory kinase protein that activates a transcriptional regulator by phosphorylation. Mycobacteria have few 2CRSs, but they are of key importance for bacterial survival and play important roles in pathogenicity. Mycobacterium tuberculosis has 12 paired two-component regulatory systems (which include a system with two regulators and one sensor, and a split sensor system), as well as four orphan regulators. Several systems are involved in virulence, and disruption of different systems leads to attenuation or hypervirulence. PhoPR plays a major role in regulating cell wall composition, and its inactivation results in sufficient attenuation of M. tuberculosis that deletion strains are live vaccine candidates. MprAB controls the stress response and is required for persistent infections. SenX3-RegX3 is required for control of aerobic respiration and phosphate uptake, and PrrAB is required for adaptation to intracellular infection. MtrAB is an essential system that controls DNA replication and cell division. The remaining systems (KdpDE, NarL, TrcRS, TcrXY, TcrA, PdtaRS, and four orphan regulators) are less well understood. The structure and binding motifs for several regulators have been characterized, revealing variations in function and operation. The sensors are less well characterized, and stimuli for many remain to be confirmed. This chapter reviews our current understanding of the role of two-component systems in mycobacteria, in particular M. tuberculosis.
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15
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Kara A, Vickers M, Swain M, Whitworth DE, Fernandez-Fuentes N. Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. BMC Bioinformatics 2015; 16:297. [PMID: 26384938 PMCID: PMC4575426 DOI: 10.1186/s12859-015-0741-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 09/16/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Two component systems (TCS) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). They are the most abundant signalling pathways in prokaryotes and control a wide range of biological processes. The pairing of these two components is highly specific, often requiring costly and time-consuming experimental characterisation. Therefore, there is considerable interest in developing accurate prediction tools to lessen the burden of experimental work and cope with the ever-increasing amount of genomic information. RESULTS We present a novel meta-predictor, MetaPred2CS, which is based on a support vector machine. MetaPred2CS integrates six sequence-based prediction methods: in-silico two-hybrid, mirror-tree, gene fusion, phylogenetic profiling, gene neighbourhood, and gene operon. To benchmark MetaPred2CS, we also compiled a novel high-quality training dataset of experimentally deduced TCS protein pairs for k-fold cross validation, to act as a gold standard for TCS partnership predictions. Combining individual predictions using MetaPred2CS improved performance when compared to the individual methods and in comparison with a current state-of-the-art meta-predictor. CONCLUSION We have developed MetaPred2CS, a support vector machine-based metapredictor for prokaryotic TCS protein pairings. Central to the success of MetaPred2CS is a strategy of integrating individual predictors that improves the overall prediction accuracy, with the in-silico two-hybrid method contributing most to performance. MetaPred2CS outperformed other available systems in our benchmark tests, and is available online at http://metapred2cs.ibers.aber.ac.uk, along with our gold standard dataset of TCS interaction pairs.
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Affiliation(s)
- Altan Kara
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
| | - Martin Vickers
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
| | - Martin Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
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The two-component signalling networks of Mycobacterium tuberculosis display extensive cross-talk in vitro. Biochem J 2015; 469:121-34. [DOI: 10.1042/bj20150268] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/01/2015] [Indexed: 02/06/2023]
Abstract
Bacteria use two-component signalling systems (TCSs) to sense and respond to environmental changes. Currently, they are thought to be highly specific, with each TCS functioning independently. Here, unlike the prevalent paradigm, we show that the TCSs of M. tuberculosis cross-talk extensively, thereby proposing an alternative signalling scenario.
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Huang Q, Abdalla AE, Xie J. Phylogenomics of Mycobacterium Nitrate Reductase Operon. Curr Microbiol 2015; 71:121-8. [PMID: 25980349 DOI: 10.1007/s00284-015-0838-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022]
Abstract
NarGHJI operon encodes a nitrate reductase that can reduce nitrate to nitrite. This process enhances bacterial survival by nitrate respiration under anaerobic conditions. NarGHJI operon exists in many bacteria, especially saprophytic bacteria living in soil which play a key role in the nitrogen cycle. Most actinomycetes, including Mycobacterium tuberculosis, possess NarGHJI operons. M. tuberculosis is a facultative intracellular pathogen that expands in macrophages and has the ability to persist in a non-replicative form in granuloma lifelong. Nitrogen and nitrogen compounds play crucial roles in the struggle between M. tuberculosis and host. M. tuberculosis can use nitrate as a final electron acceptor under anaerobic conditions to enhance its survival. In this article, we reviewed the mechanisms regulating nitrate reductase expression and affecting its activity. Potential genes involved in regulating the nitrate reductase expression in M. tuberculosis were identified. The conserved NarG might be an alternative mycobacterium taxonomic marker.
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Affiliation(s)
- Qinqin Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, 1 Rd Tiansheng, Beibei, Chongqing, 400715, People's Republic of China
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18
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Cui T, He ZG. Improved understanding of pathogenesis from protein interactions inMycobacteriumtuberculosis. Expert Rev Proteomics 2014; 11:745-55. [DOI: 10.1586/14789450.2014.971762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Parandhaman DK, Sharma P, Bisht D, Narayanan S. Proteome and phosphoproteome analysis of the serine/threonine protein kinase E mutant of Mycobacterium tuberculosis. Life Sci 2014; 109:116-26. [PMID: 24972353 DOI: 10.1016/j.lfs.2014.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/23/2014] [Accepted: 06/09/2014] [Indexed: 01/04/2023]
Abstract
AIMS Serine/threonine protein kinases (STPKs) have prominent roles in the survival mechanisms of Mycobacterium tuberculosis (M. tuberculosis). Previous studies from our laboratory underscored the role of PknE, an STPK in virulence, adaptation and the suppression of host cell apoptosis. In this study, two-dimensional gel electrophoresis was used to study the proteome and phosphoproteome profiles of wild type M. tuberculosis and its isogenic pknE deletion mutant (ΔpknE) during growth in Middlebrook 7H9 and nitric oxide stress. MAIN METHODS Wild-type M. tuberculosis and its isogenic pknE deletion mutant strain were grown in Middlebrook 7H9 as well as subjected to nitric oxide stress using sodium nitroprusside. Whole cell lysates were prepared and analyzed by 2D-gel electrophoresis. Phosphoproteomes were analyzed using phospho serine and phospho threonine antibodies after subjecting the 2D-gels to western blotting. Proteins of interest were identified using mass spectrometry. KEY FINDINGS Our analysis provides insights into the targets that impose pro-apoptotic as well as altered cellular phenotypes on ΔpknE, revealing novel substrates and functions for PknE. SIGNIFICANCE For the first time, our proteome and phosphoproteome data decipher the function of PknE in cell division, virulence, dormancy, suppression of sigma factor B and its regulated genes, suppression of two-component systems and in the metabolic activity of M. tuberculosis.
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Affiliation(s)
- Dinesh Kumar Parandhaman
- Department of Immunology, National Institute for Research in Tuberculosis, Chennai,India; Department of Immunology, International Centre for Genetic Engineering and Biotechnology, Aruna Asif Ali Marg, New Delhi, 110067,India
| | - Prashant Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and other Mycobacterial Diseases, Tajganj, Agra,India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and other Mycobacterial Diseases, Tajganj, Agra,India
| | - Sujatha Narayanan
- Department of Immunology, National Institute for Research in Tuberculosis, Chennai,India.
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Agrawal R, Saini DK. Rv1027c-Rv1028c encode functional KdpDE two--component system in Mycobacterium tuberculosis. Biochem Biophys Res Commun 2014; 446:1172-8. [PMID: 24667597 DOI: 10.1016/j.bbrc.2014.03.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
Abstract
In Mycobacteriumtuberculosis Rv1027c-Rv1028c genes are predicted to encode KdpDE two component system, which is highly conserved across all bacterial species. Here, we show that the system is functionally active and KdpD sensor kinase undergoes autophosphorylation and transfers phosphoryl group to KdpE, response regulator protein. We identified His(642) and Asp(52) as conserved phosphorylation sites in KdpD and KdpE respectively and by SPR analysis confirmed the physical interaction between them. KdpD was purified with prebound divalent ions and their importance in phosphorylation was established using protein refolding and ion chelation approaches. Genetically a single transcript encoded both KdpD and KdpE proteins. Overall, we report that M. tuberculosis KdpDE system operates like a canonical two component system.
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Affiliation(s)
- Ruchi Agrawal
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India.
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Serine 83 in DosR, a response regulator from Mycobacterium tuberculosis, promotes its transition from an activated, phosphorylated state to an inactive, unphosphorylated state. Biochem Biophys Res Commun 2014; 444:651-5. [PMID: 24491537 DOI: 10.1016/j.bbrc.2014.01.128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 01/25/2014] [Indexed: 11/21/2022]
Abstract
A sensor kinase, DosS, and its corresponding response regulator, DosR, constitute a two component system for regulating gene expression under hypoxic conditions in Mycobacterium tuberculosis. Among response regulators in M. tuberculosis, NarL has high sequence similarity to DosR, and autophosphorylated DosS transfers its phosphate group not only to DosR but also to NarL. Phosphorylated DosR is more rapidly dephosphorylated than phosphorylated NarL. DosR and NarL differ with respect to the amino acids at positions T+1 and T+2 around the phosphorylation sites in the N-terminal phosphoacceptor domain; NarL has S83 and Y84, whereas DosR has A90 and H91. A DosR S83A mutant shows prolonged phosphorylation. Structural comparison with a histidinol phosphate phosphatase suggests that the hydroxyl group of DosR S83 could play a role in activating the water molecule involved in the triggering of autodephosphorylation.
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Lee HN, Lee NO, Ko IJ, Kim SW, Kang BS, Oh JI. Involvement of the catalytically important Asp54 residue of Mycobacterium smegmatis DevR in protein-protein interactions between DevR and DevS. FEMS Microbiol Lett 2013; 343:26-33. [PMID: 23480849 DOI: 10.1111/1574-6968.12122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 11/28/2022] Open
Abstract
The DevSR two-component system in Mycobacterium smegmatis consists of the DevS histidine kinase and the DevR response regulator. It is a regulatory system that is involved in the adaptation of mycobacteria to hypoxic and NO stresses. Using the yeast two-hybrid assay and pull-down assay, it was demonstrated that the phosphoaccepting Asp (Asp54) of DevR is important for protein-protein interactions between DevR and DevS. The negative charge of Asp54 of DevR was shown to play an important role in protein-protein interactions between DevR and DevS. When the Lys104 residue, which is involved in transmission of conformational changes induced by phosphorylation of the response regulator, was replaced with Ala, the mutant form of DevR was not phosphorylated by DevS and functionally inactive in vivo. However, the K104A mutation in DevR only slightly affected protein-protein interactions between DevR and DevS.
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Affiliation(s)
- Ha-Na Lee
- Department of Microbiology, Pusan National University, Busan, Korea
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