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Savková K, Danchenko M, Fabianová V, Bellová J, Bencúrová M, Huszár S, Korduláková J, Siváková B, Baráth P, Mikušová K. Compartmentalization of galactan biosynthesis in mycobacteria. J Biol Chem 2024; 300:105768. [PMID: 38367664 PMCID: PMC10951656 DOI: 10.1016/j.jbc.2024.105768] [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: 11/27/2023] [Revised: 01/31/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024] Open
Abstract
Galactan polymer is a prominent component of the mycobacterial cell wall core. Its biogenesis starts at the cytoplasmic side of the plasma membrane by a build-up of the linker disaccharide [rhamnosyl (Rha) - N-acetyl-glucosaminyl (GlcNAc) phosphate] on the decaprenyl-phosphate carrier. This decaprenyl-P-P-GlcNAc-Rha intermediate is extended by two bifunctional galactosyl transferases, GlfT1 and GlfT2, and then it is translocated to the periplasmic space by an ABC transporter Wzm-Wzt. The cell wall core synthesis is finalized by the action of an array of arabinosyl transferases, mycolyl transferases, and ligases that catalyze an attachment of the arabinogalactan polymer to peptidoglycan through the linker region. Based on visualization of the GlfT2 enzyme fused with fluorescent tags it was proposed that galactan polymerization takes place in a specific compartment of the mycobacterial cell envelope, the intracellular membrane domain, representing pure plasma membrane free of cell wall components (previously denoted as the "PMf" domain), which localizes to the polar region of mycobacteria. In this work, we examined the activity of the galactan-producing cellular machine in the cell-wall containing cell envelope fraction and in the cell wall-free plasma membrane fraction prepared from Mycobacterium smegmatis by the enzyme assays using radioactively labeled substrate UDP-[14C]-galactose as a tracer. We found that despite a high abundance of GlfT2 in both of these fractions as confirmed by their thorough proteomic analyses, galactan is produced only in the reaction mixtures containing the cell wall components. Our findings open the discussion about the distribution of GlfT2 and the regulation of its activity in mycobacteria.
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Affiliation(s)
- Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Maksym Danchenko
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Viktória Fabianová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jana Bellová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Mária Bencúrová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Stanislav Huszár
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Barbara Siváková
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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Juárez-Cepeda J, Valenzuela O, Garibay-Valdez E, Velazquez C, Garibay-Escobar A. Gene expression during the development of Mycobacterium smegmatis biofilms on hydroxyapatite surfaces. Int Microbiol 2024; 27:257-263. [PMID: 37311924 DOI: 10.1007/s10123-023-00385-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/19/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Bacterial biofilms are a consortium of bacteria that are strongly bound to each other and the surface on which they developed irreversibly. Bacteria can survive adverse environmental conditions and undergo changes when transitioning from a planktonic form to community cells. The process of mycobacteria adhesion is complex, involving characteristics and properties of bacteria, surfaces, and environmental factors; therefore, the formation of different biofilms is possible. Cell wall-, lipid-, and lipid transporter-related genes (glycopeptidolipids, GroEL1, protein kinase) are important in mycobacterial biofilm development. We investigated gene expression during in vitro development of Mycobacterium smegmatis biofilms on a hydroxyapatite (HAP) surface. Biofilm formation by M. smegmatis cells was induced for 1, 2, 3, and 5 days on the HAP surface. Mycobacteria on polystyrene generated an air-liquid interface biofilm, and on the fifth day, it increased by 35% in the presence of HAP. Six genes with key roles in biofilm formation were analyzed by real-time RT‒qPCR during the biofilm formation of M. smegmatis on both abiotic surfaces. The expression of groEL1, lsr2, mmpL11, mps, pknF, and rpoZ genes during biofilm formation on the HAP surface did not exhibit significant changes compared to the polystyrene surface. These genes involved in biofilm formation are not affected by HAP.
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Affiliation(s)
- Jacqueline Juárez-Cepeda
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México
| | - Olivia Valenzuela
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México
| | - Estefanía Garibay-Valdez
- Centro de Investigación en Alimentación y Desarrollo, A. C. Km 0.6 Carretera a La Victoria, Hermosillo, Sonora, México
| | - Carlos Velazquez
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departmento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas S/N, 83000, Hermosillo, Sonora, México.
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Angrish N, Lalwani N, Khare G. In silico virtual screening for the identification of novel inhibitors against dihydrodipicolinate reductase (DapB) of Mycobacterium tuberculosis, a key enzyme of diaminopimelate pathway. Microbiol Spectr 2023; 11:e0135923. [PMID: 37855602 PMCID: PMC10714930 DOI: 10.1128/spectrum.01359-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/02/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Non-compliance to lengthy antituberculosis (TB) treatment regimen, associated side effects, and emergence of drug-resistant strains of Mycobacterium tuberculosis (M. tb) emphasize the need to develop more effective anti-TB drugs. Here, we have evaluated the role of M. tb dihydrodipicolinate reductase (DapB), a component of the diaminopimelate pathway, which is involved in the biosynthesis of both lysine and mycobacterial cell wall. We showed that DapB is essential for the in vitro as well as intracellular growth of M. tb. We further utilized M. tb DapB, as a target for identification of inhibitors by employing in silico virtual screening, and conducted various in vitro screening assays to identify inhibitors with potential to inhibit DapB activity and in vitro and intracellular growth of M. tb with no significant cytotoxicity against various mammalian cell lines. Altogether, M. tb DapB serves as an important drug target and a hit molecule, namely, 4-(3-Phenylazoquinoxalin-2-yl) butanoic acid methyl ester has been identified as an antimycobacterial molecule in our study.
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Affiliation(s)
- Nupur Angrish
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Neha Lalwani
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
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The Bacterial MtrAB Two-Component System Regulates the Cell Wall Homeostasis Responding to Environmental Alkaline Stress. Microbiol Spectr 2022; 10:e0231122. [PMID: 36073914 PMCID: PMC9602371 DOI: 10.1128/spectrum.02311-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Throughout the course of evolution, bacteria have developed signal transduction tools such as two-component systems (TCSs) to meet their demands to thrive even under the most challenging environmental conditions. One TCS called MtrAB is commonly found in Actinobacteria and is implicated in cell wall metabolism, osmoprotection, cell proliferation, antigen secretion, and biosynthesis of secondary metabolites. However, precisely how the MtrAB TCS regulates the bacterial responses to external environments remains unclear. Here, we report that the MtrAB TCS regulates the cell envelope response of alkali-tolerant bacterium Dietzia sp. strain DQ12-45-1b to extreme alkaline stimuli. We found that under alkaline conditions, an mtrAB mutant exhibited both reduced growth and abnormal morphology compared to the wild-type strain. Electrophoretic mobility shift assay analysis showed that MtrA binds the promoter of the mraZ gene critical for cell wall homeostasis, suggesting that MtrA directly controls transcription of this regulator. In conclusion, our findings demonstrate that MtrAB TCS is involved in controlling the bacterial response to alkaline stimuli by regulating the expression of the cell wall homeostasis regulator MraZ in Dietzia sp. DQ12-45-1b, providing novel details critical for a mechanistic understanding of how cell wall homeostasis is controlled. IMPORTANCE Microorganisms can be found in most extreme environments, and they have to adapt to a wide range of environmental stresses. The two-component systems (TCSs) found in bacteria detect environmental stimuli and regulate physiological pathways for survival. The MtrAB TCS conserved in Corynebacterineae is critical for maintaining the metabolism of the cell wall components that protects bacteria from diverse environmental stresses. However, how the MtrAB TCS regulates cell wall homeostasis and adaptation under stress conditions is unclear. Here, we report that the MtrAB TCS in Dietzia sp. DQ12-45-1b plays a critical role in alkaline resistance by modulating the cell wall homeostasis through the MtrAB-MraZ pathway. Thus, our work provides a novel regulatory pathway used by bacteria for adaptation and survival under extreme alkaline stresses.
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Abstract
Pyroptosis, a regulated form of pro-inflammatory cell death, is characterised by cell lysis and by the release of cytokines, damage- and pathogen-associated molecular patterns. It plays an important role during bacterial infection, where it can promote an inflammatory response and eliminate the replicative niche of intracellular pathogens. Recent work, using a variety of bacterial pathogens, has illuminated the versatility of pyroptosis, revealing unexpected and important concepts underlying host defence. In this Review, we overview the molecular mechanisms underlying pyroptosis and discuss their role in host defence, from the single cell to the whole organism. We focus on recent studies using three cellular microbiology paradigms - Mycobacterium tuberculosis, Salmonella Typhimurium and Shigella flexneri - that have transformed the field of pyroptosis. We compare insights discovered in tissue culture, zebrafish and mouse models, highlighting the advantages and disadvantages of using these complementary infection models to investigate pyroptosis and for modelling human infection. Moving forward, we propose that in-depth knowledge of pyroptosis obtained from complementary infection models can better inform future studies using higher vertebrates, including humans, and help develop innovative host-directed therapies to combat bacterial infection.
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Affiliation(s)
- Dominik Brokatzky
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Liao F, Huang Z, Xu R, Luo Z, Qi W, Fan B, Yu J. Analysis of misdiagnosis and 18F-FDG PET/CT findings of lymph node tuberculosis. JOURNAL OF X-RAY SCIENCE AND TECHNOLOGY 2022; 30:941-951. [PMID: 35694951 DOI: 10.3233/xst-221195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To investigate 18F-FDG PET/CT findings of tuberculous lymphadenitis and analyze the causes of misdiagnosis. METHOD Between 2013 and 2021, a retrospective review was conducted on 22 patients at Jiangxi Provincial People's Hospital Affiliated with Nanchang University who had lymph node tuberculosis confirmed by histology or clinical investigation. Subjective judgment and quantitative analysis were adopted. RESULTS Out of 22 patients, 14 are male and 8 are female. The average age was 55.5 years (55.5±12.4). The most common site of lymph node tuberculosis (LNTB) is the mediastinum (41.5%), followed by the neck (24.4%) and the abdominal cavity (21.9%). Half of the patients have more than one site affected. More than half of LNTB patients (54.5%) are concurrent with other types of TB, especially PTB. Among the 41 biggest affected lymph nodes, the average maximum diameter, minimum diameter, SUVmax and the lesion SUVmax/SUVmean liver ratio are 22.04±8.39, 16.93±6.75, 9.72±5.04 and 6.72±3.60, respectively. There is a poor correlation coefficient of 0.236 between the FDG uptake and the size of the biggest affected lymph node. Patients who are concurrent with no other TB have the significantly higher FDG uptake than patients who are concurrent with other TB (12.42 vs 8.02) (p = 0.005). Among these cases, 6 cases (27.3%) are accurately diagnosed with LNTB, all of which have pulmonary tuberculosis as a complication. However, 16 cases (72.7%) are misdiagnosed as lymphoma (50%), sarcoidosis (13.6%), and lymph node metastasis (9%). CONCLUSIONS This study demonstrates that 18F-FDG PET/CT is very useful in detecting LNTB because tuberculous granulomas show significant levels of glucose uptake. It proves to be an effective method for revealing lesion extent and discovering additional lesions that morphological imaging is missed. However, 18F-FDG PET/CT is not able to reliably distinguish LNTB from lymphoma, sarcoidosis, and metastatic lymph nodes. Nonetheless, 18F-FDG PET/CT allows for the selection of the most optimal biopsy location, and thus has potential to detect early treatment response and distinguish between active and inactive lesions.
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Affiliation(s)
- Fengxiang Liao
- Department of Nuclear Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Zizhen Huang
- Sterilization and Supply Center, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Rong Xu
- Department of Nuclear Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Zhehuang Luo
- Department of Nuclear Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Wanling Qi
- Department of Nuclear Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Bing Fan
- Department of Radiology, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Juhong Yu
- Department of Radiology, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
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Cabarca S, Frazão de Souza M, Albert de Oliveira A, Vignoli Muniz GS, Lamy MT, Vinicius Dos Reis C, Takarada J, Effer B, Souza LS, Iriarte de la Torre L, Couñago R, Pinto Oliveira CL, Balan A. Structure of the Mycobacterium tuberculosis cPknF and conformational changes induced in forkhead-associated regulatory domains. Curr Res Struct Biol 2021; 3:165-178. [PMID: 34382010 PMCID: PMC8339232 DOI: 10.1016/j.crstbi.2021.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has 11 Serine-Threonine Protein Kinases (STPK) that control numerous physiological processes, including cell growth, cell division, metabolic flow, and transcription. PknF is one of the 11 Mtb STPKs that has, among other substrates, two FHA domains (FHA-1 and FHA-2) of the ATP-Binding Cassette (ABC) transporter Rv1747. Phosphorylation in T152 and T210 located in a non-structured linker that connects Rv1747 FHA domains is considerate to be the regulatory mechanism of the transporter. In this work, we resolved the three-dimensional structure of the PknF catalytic domain (cPknF) in complex with the human kinase inhibitor IKK16. cPknF is conserved when compared to other STPKs but shows specific residues in the binding site where the inhibitor is positioned. In addition, using Small Angle X-Ray Scattering analysis we monitored the behavior of the wild type and three FHA-phosphomimetic mutants in solution, and measured the cPknF affinity for these domains. The kinase showed higher affinity for the non-phosphorylated wild type domain and preference for phosphorylation of T152 inducing the rapprochement of the domains and significant structural changes. The results shed some light on the process of regulating the transporter's activity by phosphorylation and arises important questions about evolution and importance of this mechanism for the bacillus. Rv1747 is an ABC transporter which activity is regulated by PknF. cPknF is a typical Serine/Threonine Protein Kinase that can be explored as drug target. The higher affinity of cPknF for FHA-2 is important for further conformational changes. Rv1747 activation model reveals a concatenated activity essential for the system.
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Affiliation(s)
- Sindy Cabarca
- Programa de Pós-graduação em Genética, Universidade Estadual de Campinas, Campinas, 13083-862, SP, Brazil.,Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.,Grupo Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, 700001, Sucre, Colombia
| | - Maximilia Frazão de Souza
- Grupo de Fluidos Complexos, Departamento de Física Experimental, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, SP, Brazil
| | - Andrew Albert de Oliveira
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14049-900, SP, Brazil
| | - Gabriel S Vignoli Muniz
- Departamento de Física Geral, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - M Teresa Lamy
- Departamento de Física Geral, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - Caio Vinicius Dos Reis
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, 13083-886, São Paulo, Brazil
| | - Jessica Takarada
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, 13083-886, São Paulo, Brazil
| | - Brian Effer
- Center of Excellence in Traslational Medicine (CEMT) and Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de la Frontera, Temuco, 01145, Chile
| | - Lucas Santos Souza
- Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Lilia Iriarte de la Torre
- Programa de Pós-graduação em Genética, Universidade Estadual de Campinas, Campinas, 13083-862, SP, Brazil.,Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.,Grupo Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, 700001, Sucre, Colombia
| | - Rafael Couñago
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, 13083-886, São Paulo, Brazil
| | - Cristiano Luis Pinto Oliveira
- Grupo de Fluidos Complexos, Departamento de Física Experimental, Instituto de Física, Universidade de São Paulo, São Paulo, 05508-090, SP, Brazil
| | - Andrea Balan
- Laboratório de Biologia Estrutural Aplicada LBEA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
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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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Dulberger CL, Rubin EJ, Boutte CC. The mycobacterial cell envelope - a moving target. Nat Rev Microbiol 2019; 18:47-59. [PMID: 31728063 DOI: 10.1038/s41579-019-0273-7] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 01/12/2023]
Abstract
Mycobacterium tuberculosis, the leading cause of death due to infection, has a dynamic and immunomodulatory cell envelope. The cell envelope structurally and functionally varies across the length of the cell and during the infection process. This variability allows the bacterium to manipulate the human immune system, tolerate antibiotic treatment and adapt to the variable host environment. Much of what we know about the mycobacterial cell envelope has been gleaned from model actinobacterial species, or model conditions such as growth in vitro, in macrophages and in the mouse. In this Review, we combine data from different experimental systems to build a model of the dynamics of the mycobacterial cell envelope across space and time. We describe the regulatory pathways that control metabolism of the cell wall and surface lipids in M. tuberculosis during growth and stasis, and speculate about how this regulation might affect antibiotic susceptibility and interactions with the immune system.
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Affiliation(s)
- Charles L Dulberger
- Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Cara C Boutte
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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Sánchez-Montalvá A, Barios M, Salvador F, Villar A, Tórtola T, Molina-Morant D, Lorenzo-Bosquet C, Espinosa-Pereiro J, Molina I. Usefulness of FDG PET/CT in the management of tuberculosis. PLoS One 2019; 14:e0221516. [PMID: 31454368 PMCID: PMC6711521 DOI: 10.1371/journal.pone.0221516] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/08/2019] [Indexed: 11/18/2022] Open
Abstract
Background The aim of our study is to describe the FDG-PET/CT findings in patients with tuberculosis and to correlate them with the patient’s prognosis. Methods We retrospectively collected data from patients with tuberculosis, who had an FDG-PET/CT performed prior to treatment initiation from 2010 to 2015. Results Forty-seven out of 504 patients with active tuberculosis diagnosis (9.33%) underwent an FDG-PET/CT. The reasons for performing the FDG-PET/CT were: characterization of a pulmonary nodule (24; 51.1%), study of fever of unknown origin (12; 25.5%), study of lymph node enlargement (5; 10.6%) and others (6; 12.8%). Median age was 64 (IQR 50–74) years and 31 (66%) patients were male. Twenty-six (55.3%) patients had an immunosuppressant condition. According to the FDG-PET/CT, 48.6% of the patients had more than 1 organ affected and 46.8% had lymph node involvement. Median SUVmax of the main lesion was 5 (IQR 0.28–11.85). We found an association between the FDG accumulation and the size of the main lesion with a correlation coefficient of 0.54 (p<0.002). Patients with an unsuccessful outcome had a higher ratio SUVmax main lesion / SUVmean liver (1.92 vs 7.67, p<0.02). Conclusions In our cohort, almost half of the patients had more than 1 organ affected and 46.8% of them had lymph node involvement. FDG uptake was associated with the size of the main lesion and seems to be related to the treatment outcome. The extent of its potential to be used as an early predictor of treatment success still needs to be defined.
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Affiliation(s)
- Adrián Sánchez-Montalvá
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
- Grupo de Estudio de micobacterias (GEIM), Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- * E-mail:
| | - Marta Barios
- Nuclear Medicine Department, Vall d’Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fernando Salvador
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
- Grupo de Estudio de micobacterias (GEIM), Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Ana Villar
- Pneumology Department, Vall d’Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Teresa Tórtola
- Microbiology Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Daniel Molina-Morant
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carles Lorenzo-Bosquet
- Nuclear Medicine Department, Vall d’Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Espinosa-Pereiro
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
- Grupo de Estudio de micobacterias (GEIM), Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Israel Molina
- Infectious Diseases Department, Vall d’Hebron University Hospital, PROSICS Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
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Alsayed SSR, Beh CC, Foster NR, Payne AD, Yu Y, Gunosewoyo H. Kinase Targets for Mycolic Acid Biosynthesis in Mycobacterium tuberculosis. Curr Mol Pharmacol 2019; 12:27-49. [PMID: 30360731 DOI: 10.2174/1874467211666181025141114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mycolic acids (MAs) are the characteristic, integral building blocks for the mycomembrane belonging to the insidious bacterial pathogen Mycobacterium tuberculosis (M.tb). These C60-C90 long α-alkyl-β-hydroxylated fatty acids provide protection to the tubercle bacilli against the outside threats, thus allowing its survival, virulence and resistance to the current antibacterial agents. In the post-genomic era, progress has been made towards understanding the crucial enzymatic machineries involved in the biosynthesis of MAs in M.tb. However, gaps still remain in the exact role of the phosphorylation and dephosphorylation of regulatory mechanisms within these systems. To date, a total of 11 serine-threonine protein kinases (STPKs) are found in M.tb. Most enzymes implicated in the MAs synthesis were found to be phosphorylated in vitro and/or in vivo. For instance, phosphorylation of KasA, KasB, mtFabH, InhA, MabA, and FadD32 downregulated their enzymatic activity, while phosphorylation of VirS increased its enzymatic activity. These observations suggest that the kinases and phosphatases system could play a role in M.tb adaptive responses and survival mechanisms in the human host. As the mycobacterial STPKs do not share a high sequence homology to the human's, there have been some early drug discovery efforts towards developing potent and selective inhibitors. OBJECTIVE Recent updates to the kinases and phosphatases involved in the regulation of MAs biosynthesis will be presented in this mini-review, including their known small molecule inhibitors. CONCLUSION Mycobacterial kinases and phosphatases involved in the MAs regulation may serve as a useful avenue for antitubercular therapy.
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Affiliation(s)
- Shahinda S R Alsayed
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA 6102, Australia
| | - Chau C Beh
- Western Australia School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Bentley 6102 WA, Australia.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, United States
| | - Neil R Foster
- Western Australia School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Bentley 6102 WA, Australia
| | - Alan D Payne
- School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Yu Yu
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA 6102, Australia
| | - Hendra Gunosewoyo
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA 6102, Australia
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12
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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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13
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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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14
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Khan MZ, Kaur P, Nandicoori VK. Targeting the messengers: Serine/threonine protein kinases as potential targets for antimycobacterial drug development. IUBMB Life 2018; 70:889-904. [DOI: 10.1002/iub.1871] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/22/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Mehak Zahoor Khan
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
| | - Prabhjot Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
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15
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Chhotaray C, Tan Y, Mugweru J, Islam MM, Adnan Hameed HM, Wang S, Lu Z, Wang C, Li X, Tan S, Liu J, Zhang T. Advances in the development of molecular genetic tools for Mycobacterium tuberculosis. J Genet Genomics 2018; 45:S1673-8527(18)30114-0. [PMID: 29941353 DOI: 10.1016/j.jgg.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference (CRISPRi), a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.
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Affiliation(s)
- Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, P.O Box 6 -60100, Embu, Kenya
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Khan MZ, Bhaskar A, Upadhyay S, Kumari P, Rajmani RS, Jain P, Singh A, Kumar D, Bhavesh NS, Nandicoori VK. Protein kinase G confers survival advantage to Mycobacterium tuberculosis during latency-like conditions. J Biol Chem 2017; 292:16093-16108. [PMID: 28821621 DOI: 10.1074/jbc.m117.797563] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/16/2017] [Indexed: 11/06/2022] Open
Abstract
Protein kinase G (PknG), a thioredoxin-fold-containing eukaryotic-like serine/threonine protein kinase, is a virulence factor in Mycobacterium tuberculosis, required for inhibition of phagolysosomal fusion. Here, we unraveled novel functional facets of PknG during latency-like conditions. We found that PknG mediates persistence under stressful conditions like hypoxia and abets drug tolerance. PknG mutant displayed minimal growth in nutrient-limited conditions, suggesting its role in modulating cellular metabolism. Intracellular metabolic profiling revealed that PknG is necessary for efficient metabolic adaptation during hypoxia. Notably, the PknG mutant exhibited a reductive shift in mycothiol redox potential and compromised stress response. Exposure to antibiotics and hypoxic environment resulted in higher oxidative shift in mycothiol redox potential of PknG mutant compared with the wild type. Persistence during latency-like conditions required kinase activity and thioredoxin motifs of PknG and is mediated through phosphorylation of a central metabolic regulator GarA. Finally, using a guinea pig model of infection, we assessed the in vivo role of PknG in manifestation of disease pathology and established a role for PknG in the formation of stable granuloma, hallmark structures of latent tuberculosis. Taken together, PknG-mediated GarA phosphorylation is important for maintenance of both mycobacterial physiology and redox poise, an axis that is dispensable for survival under normoxic conditions but is critical for non-replicating persistence of mycobacteria. In conclusion, we propose that PknG probably acts as a modulator of latency-associated signals.
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Affiliation(s)
| | | | | | - Pooja Kumari
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Raju S Rajmani
- the Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Preeti Jain
- From the National Institute of Immunology and
| | - Amit Singh
- the Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Dhiraj Kumar
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067 and
| | - Neel Sarovar Bhavesh
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067 and
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17
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Abstract
Reversible protein phosphorylation is the most common type of epigenetic posttranslational modification in living cells used as a major regulation mechanism of biological processes. The Mycobacterium tuberculosis genome encodes for 11 serine/threonine protein kinases that are responsible for sensing environmental signals to coordinate a cellular response to ensure the pathogen's infectivity, survival, and growth. To overcome killing mechanisms generated within the host during infection, M. tuberculosis enters a state of nonreplicating persistence that is characterized by arrested growth, limited metabolic activity, and phenotypic resistance to antimycobacterial drugs. In this article we focus our attention on the role of M. tuberculosis serine/threonine protein kinases in sensing the host environment to coordinate the bacilli's physiology, including growth, cell wall components, and central metabolism, to establish a persistent infection.
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18
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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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19
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Zhang C, Sun W, Tan M, Dong M, Liu W, Gao T, Li L, Xu Z, Zhou R. The Eukaryote-Like Serine/Threonine Kinase STK Regulates the Growth and Metabolism of Zoonotic Streptococcus suis. Front Cell Infect Microbiol 2017; 7:66. [PMID: 28326294 PMCID: PMC5339665 DOI: 10.3389/fcimb.2017.00066] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/21/2017] [Indexed: 12/21/2022] Open
Abstract
Like eukaryotes, bacteria express one or more serine/threonine kinases (STKs) that initiate diverse signaling networks. The STK from Streptococcus suis is encoded by a single-copy stk gene, which is crucial in stress response and virulence. To further understand the regulatory mechanism of STK in S. suis, a stk deletion strain (Δstk) and its complementary strain (CΔstk) were constructed to systematically decode STK characteristics by applying whole transcriptome RNA sequencing (RNA-Seq) and phosphoproteomic analysis. Numerous genes were differentially expressed in Δstk compared with the wild-type parental strain SC-19, including 320 up-regulated and 219 down-regulated genes. Particularly, 32 virulence-associated genes (VAGs) were significantly down-regulated in Δstk. Seven metabolic pathways relevant to bacterial central metabolism and translation are significantly repressed in Δstk. Phosphoproteomic analysis further identified 12 phosphoproteins that exhibit differential phosphorylation in Δstk. These proteins are associated with cell growth and division, glycolysis, and translation. Consistently, phenotypic assays confirmed that the Δstk strain displayed deficient growth and attenuated pathogenicity. Thus, STK is a central regulator that plays an important role in cell growth and division, as well as S. suis metabolism.
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Affiliation(s)
- Chunyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Wen Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Meifang Tan
- Veterinary Medicine Laboratory, Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences Nanchang, China
| | - Mengmeng Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Wanquan Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Ting Gao
- Veterinary Medicine Laboratory, Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences Wuhan, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Cooperative Innovation Center of Sustainable Pig ProductionWuhan, China
| | - Zhuofei Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Cooperative Innovation Center of Sustainable Pig ProductionWuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Cooperative Innovation Center of Sustainable Pig ProductionWuhan, China
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20
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Refaya AK, Sharma D, Kumar V, Bisht D, Narayanan S. A Serine/threonine kinase PknL, is involved in the adaptive response of Mycobacterium tuberculosis. Microbiol Res 2016; 190:1-11. [PMID: 27393993 DOI: 10.1016/j.micres.2016.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 02/05/2016] [Accepted: 02/22/2016] [Indexed: 12/28/2022]
Abstract
Mycobacterium tuberculosis adapts itself to various environmental stress conditions to thrive inside the phagosome for establishing a chronic infection. Serine/threonine protein kinases (STPKs) play a major role in the physiology and pathogenesis of Mycobacterium tuberculosis. Some of these STPKs are involved in regulating the growth of the mycobacterium under nutrient stress and starvation conditions. In this study, we have investigated the role of PknL, a STPK in the adaptive responses of M. tuberculosis by conditional inactivation of the gene using antisense technology. The inhibition of PknL in the knockdown strain was validated by RT-PCR. The in vitro growth kinetics of M. tuberculosis strain following inhibition of PknL was found to be bacteriostatic. The knock down strain of PknL exhibited a better survival in pH 5.5 when compared to its growth in pH 7.0. Similarly, it also exhibited more resistance to both SDS(0.01%) and Lysozyme stress (2.5mg/ml), indicating that loss of PknL enhances the growth of mycobacterium under stress conditions. SEM pictographs also represent an increase in the cell length of the knock down strain compared to Wild type stressing its role in cellular integrity. Lastly, the proteome analysis of differentially expressing PknL strains by 2D gel electrophoresis and mass spectrometry identified 19 differentially expressed proteins. Our findings have shown that PknL plays an important role in sensing the host environment and adapting itself in slowing down the growth of the pathogen and persisting within the host.
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Affiliation(s)
- Ahmed Kabir Refaya
- Department of Immunology, National Institute for Research in Tuberculosis, #1, Mayor Sathiyamoorthy road, Chetpet, Chennai, 600 031, India.
| | - Divakar Sharma
- National JALMA Institute for Leprosy & other Mycobacterial Diseases, Taj Ganj, Agra 282004, India.
| | - Virendra Kumar
- National JALMA Institute for Leprosy & other Mycobacterial Diseases, Taj Ganj, Agra 282004, India.
| | - Deepa Bisht
- National JALMA Institute for Leprosy & other Mycobacterial Diseases, Taj Ganj, Agra 282004, India.
| | - Sujatha Narayanan
- Department of Immunology, National Institute for Research in Tuberculosis, #1, Mayor Sathiyamoorthy road, Chetpet, Chennai, 600 031, India.
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21
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Kirsebom LA, Dasgupta S, Fredrik Pettersson BM. Pleiomorphism in Mycobacterium. ADVANCES IN APPLIED MICROBIOLOGY 2016; 80:81-112. [PMID: 22794145 DOI: 10.1016/b978-0-12-394381-1.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.
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22
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Choudhary E, Lunge A, Agarwal N. Strategies of genome editing in mycobacteria: Achievements and challenges. Tuberculosis (Edinb) 2016; 98:132-8. [PMID: 27156629 DOI: 10.1016/j.tube.2016.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/14/2016] [Accepted: 03/21/2016] [Indexed: 01/07/2023]
Abstract
Tremendous amount of physiological and functional complexities acquired through decades of evolutionary pressure makes Mycobacterium tuberculosis (Mtb) one of the most dreadful microorganisms infecting humans from centuries. Astonishing advances in genomics and genome editing tools substantially grew our knowledge about Mtb as an organism but dramatically failed to completely understand it as a pathogen. Though conventional tools based on homologous recombination, antisense, controlled proteolysis, etc. have made important contributions in advancing our understanding of the pathophysiology of Mtb, yet these approaches have not accentuated our exploration of mycobacterium on account of certain technical limitations. In this review article we have compiled various approaches implemented in genome editing of mycobacteria along with the latest adaptation of clustered regularly interspaced short palindromic repeat (CRISPR)-interference (CRISPRi), emphasizing the achievements and challenges associated with these techniques.
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Affiliation(s)
- Eira Choudhary
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India; Symbiosis School of Biomedical Sciences, Symbiosis International University, Lavale, Pune 412115, Maharashtra, India
| | - Ajitesh Lunge
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India; Jawaharlal Nehru University, New Mehrauli Road, Near Munirka, New Delhi 110067, Delhi, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India.
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23
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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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24
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Fan X, Duan X, Tong Y, Huang Q, Zhou M, Wang H, Zeng L, Young RF, Xie J. The Global Reciprocal Reprogramming between Mycobacteriophage SWU1 and Mycobacterium Reveals the Molecular Strategy of Subversion and Promotion of Phage Infection. Front Microbiol 2016; 7:41. [PMID: 26858712 PMCID: PMC4729954 DOI: 10.3389/fmicb.2016.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/11/2016] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages are the viruses of bacteria, which have contributed extensively to our understanding of life and modern biology. The phage-mediated bacterial growth inhibition represents immense untapped source for novel antimicrobials. Insights into the interaction between mycobacteriophage and Mycobacterium host will inform better utilizing of mycobacteriophage. In this study, RNA sequencing technology (RNA-seq) was used to explore the global response of Mycobacterium smegmatis mc2155 at an early phase of infection with mycobacteriophage SWU1, key host metabolic processes of M. smegmatis mc2155 shut off by SWU1, and the responsible phage proteins. The results of RNA-seq were confirmed by Real-time PCR and functional assay. 1174 genes of M. smegmatis mc2155 (16.9% of the entire encoding capacity) were differentially regulated by phage infection. These genes belong to six functional categories: (i) signal transduction, (ii) cell energetics, (iii) cell wall biosynthesis, (iv) DNA, RNA, and protein biosynthesis, (v) iron uptake, (vi) central metabolism. The transcription patterns of phage SWU1 were also characterized. This study provided the first global glimpse of the reciprocal reprogramming between the mycobacteriophage and Mycobacterium host.
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Affiliation(s)
- Xiangyu Fan
- 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 UniversityChongqing, China; Department of Biotechnology, School of Biological Science and Technology, University of JinanJinan, China
| | - Xiangke Duan
- 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 Chongqing, China
| | - Yan Tong
- 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 Chongqing, China
| | - 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 Chongqing, China
| | - Mingliang Zhou
- 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 Chongqing, China
| | - Huan Wang
- 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 Chongqing, China
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University College Station, TX, USA
| | - Ry F Young
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University College Station, TX, USA
| | - Jianping Xie
- 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 Chongqing, China
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Manuse S, Fleurie A, Zucchini L, Lesterlin C, Grangeasse C. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis. FEMS Microbiol Rev 2015; 40:41-56. [DOI: 10.1093/femsre/fuv041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2015] [Indexed: 11/14/2022] Open
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26
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Nakedi KC, Nel AJM, Garnett S, Blackburn JM, Soares NC. Comparative Ser/Thr/Tyr phosphoproteomics between two mycobacterial species: the fast growing Mycobacterium smegmatis and the slow growing Mycobacterium bovis BCG. Front Microbiol 2015; 6:237. [PMID: 25904896 PMCID: PMC4389566 DOI: 10.3389/fmicb.2015.00237] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
Ser/Thr/Tyr protein phosphorylation plays a critical role in regulating mycobacterial growth and development. Understanding the mechanistic link between protein phosphorylation signaling network and mycobacterial growth rate requires a global view of the phosphorylation events taking place at a given time under defined conditions. In the present study we employed a phosphopeptide enrichment and high throughput mass spectrometry-based strategy to investigate and qualitatively compare the phosphoproteome of two mycobacterial model organisms: the fast growing Mycobacterium smegmatis and the slow growing Mycobacterium bovis BCG. Cells were harvested during exponential phase and our analysis detected a total of 185 phospho-sites in M. smegmatis, of which 106 were confidently localized [localization probability (LP) = 0.75; PEP = 0.01]. By contrast, in M. bovis BCG the phosphoproteome comprised 442 phospho-sites, of which 289 were confidently localized. The percentage distribution of Ser/Thr/Tyr phosphorylation was 39.47, 57.02, and 3.51% for M. smegmatis and 35, 61.6, and 3.1% for M. bovis BCG. Moreover, our study identified a number of conserved Ser/Thr phosphorylated sites and conserved Tyr phosphorylated sites across different mycobacterial species. Overall a qualitative comparison of the fast and slow growing mycobacteria suggests that the phosphoproteome of M. smegmatis is a simpler version of that of M. bovis BCG. In particular, M. bovis BCG exponential cells exhibited a much more complex and sophisticated protein phosphorylation network regulating important cellular cycle events such as cell wall biosynthesis, elongation, cell division including immediately response to stress. The differences in the two phosphoproteomes are discussed in light of different mycobacterial growth rates.
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Affiliation(s)
| | | | | | - Jonathan M. Blackburn
- Blackburn Lab, Applied Proteomics and Chemical Biology Group, Division of Medical Biochemistry, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa
| | - Nelson C. Soares
- Blackburn Lab, Applied Proteomics and Chemical Biology Group, Division of Medical Biochemistry, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa
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Nagarajan SN, Upadhyay S, Chawla Y, Khan S, Naz S, Subramanian J, Gandotra S, Nandicoori VK. Protein kinase A (PknA) of Mycobacterium tuberculosis is independently activated and is critical for growth in vitro and survival of the pathogen in the host. J Biol Chem 2015; 290:9626-45. [PMID: 25713147 DOI: 10.1074/jbc.m114.611822] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Indexed: 01/09/2023] Open
Abstract
The essential mycobacterial protein kinases PknA and PknB play crucial roles in modulating cell shape and division. However, the precise in vivo functional aspects of PknA have not been investigated. This study aims to dissect the role of PknA in mediating cell survival in vitro as well as in vivo. We observed aberrant cell shape and severe growth defects when PknA was depleted. Using the mouse infection model, we observe that PknA is essential for survival of the pathogen in the host. Complementation studies affirm the importance of the kinase, juxtamembrane, and transmembrane domains of PknA. Surprisingly, the extracytoplasmic domain is dispensable for cell growth and survival in vitro. We find that phosphorylation of the activation loop at Thr(172) of PknA is critical for bacterial growth. PknB has been previously suggested to be the receptor kinase, which activates multiple kinases, including PknA, by trans-phosphorylating their activation loop residues. Using phospho-specific PknA antibodies and conditional pknB mutant, we find that PknA autophosphorylates its activation loop independent of PknB. Fluorescently tagged PknA and PknB show distinctive distribution patterns within the cell, suggesting that although both kinases are known to modulate cell shape and division, their modes of action are likely to be different. This is supported by our findings that expression of kinase-dead PknA versus kinase-dead PknB in mycobacterial cells leads to different cellular phenotypes. Data indicate that although PknA and PknB are expressed as part of the same operon, they appear to be regulating cellular processes through divergent signaling pathways.
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Affiliation(s)
- Sathya Narayanan Nagarajan
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India, the Department of Biotechnology, Nehru Arts and Science College, Coimbatore 641105, India, and
| | - Sandeep Upadhyay
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Yogesh Chawla
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shazia Khan
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saba Naz
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jayashree Subramanian
- the Department of Biotechnology, Nehru Arts and Science College, Coimbatore 641105, India, and
| | - Sheetal Gandotra
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Vinay Kumar Nandicoori
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India,
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28
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Calmodulin-like protein from M. tuberculosis H37Rv is required during infection. Sci Rep 2014; 4:6861. [PMID: 25359006 PMCID: PMC4215301 DOI: 10.1038/srep06861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 09/01/2014] [Indexed: 11/08/2022] Open
Abstract
M. tuberculosis constitutes very sophisticated signaling systems that convert the environment signals into appropriate cellular response and helps the bacilli to overcome the onslaught of host defence mechanisms. Although mycobacterial two-component systems and STPKs have gained lot of attention as virulence factors, mycobacterial calcium signaling has not been very well studied. Calcium signaling has been the primary mechanism in eukaryotes for regulation of kinases, however in prokaryotes auto-phosphorylation of number of kinases has been reported. We have previously reported a small calmodulin-like-protein (CAMLP) from M. tuberculosis regulating enzymes of heterogeneous origin. To understand its role in both viability and virulence, we have assessed the effect of reduced expression of CAMLP coding gene Rv1211 on M. tb growth in vitro and ex vivo. Further, we have also studied the expression profile of Rv1211 in various conditions simulating host microenvironments. Our results highlight the possible role of CAMLP in growth and survival of M. tb during infection.
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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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30
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Phosphorylation of pyruvate kinase A by protein kinase J leads to the altered growth and differential rate of intracellular survival of mycobacteria. Appl Microbiol Biotechnol 2014; 98:10065-76. [PMID: 24934223 DOI: 10.1007/s00253-014-5859-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/26/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
PknJ (Rv2088) is a serine/threonine protein kinase of mycobacteria which is present in Mycobacterium tuberculosis (MTB), but its gene is absent in Mycobacterium smegmatis (MS); a fast grower and nonpathogenic species of mycobacteria. The heterologous expression of MTB-specific PknJ in MS altered the growth of recombinant mycobacteria highlighting one of the characteristics of this protein. This nature of the protein was further confirmed when Mycobacterium bovis BCG (BCG) containing antisense copy of pknJ resulted in the increased growth of BCG. The real-time RNA quantification analysis pointed out toward increased expression of this protein during infection of THP-1 macrophage cells which further emphasized that the protein is essential for the intracellular survival of mycobacteria. The differential in gel electrophoresis (DIGE) data followed by mass spectroscopy suggested that PknJ is involved in regulation of pyruvate kinase A (Rv1617). Since pyruvate kinase (PK) A is one of the key enzymes which controls glycolytic cycle in mycobacteria, we looked for its interaction with PknJ during extracellular and intracellular growth of mycobacteria. In order to identify the specific residue(s) involved in post-translational modification, the phospho-null mutants of PK were generated, and their substrate specificities in response to PknJ were assessed through kinase assay. The findings thus underlined that the PK activity is predominantly dependent on the threonine residue at the 94(th) position and further suggested that this site may be plausible in intracellular survival of mycobacteria upon phosphorylation with PknJ.
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31
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Homology modelling, docking, pharmacophore and site directed mutagenesis analysis to identify the critical amino acid residue of PknI from Mycobacterium tuberculosis. J Mol Graph Model 2014; 52:11-9. [PMID: 24955490 DOI: 10.1016/j.jmgm.2014.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 11/22/2022]
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis, an intracellular pathogen. PknI is one of the 11 functional Serine/Threonine Protein Kinases which is predicted to regulate the cell division of M. tuberculosis. In order to find newer drugs and vaccine we need to understand the pathogenesis of the disease. We have used the bioinformatics approach to identify the functionally active residues of PknI and to confirm the same with wet lab experiments. In the current study, we have created homology model for PknI and have done comparative structural analysis of PknI with other kinases. Molecular docking studies were done with a library of kinase inhibitors and T95 was found as the potent inhibitor for PknI. Based on structure based pharmacophore analysis of kinase substrate complexes, Lys 41 along with Asp90, Val92 and Asp96 were identified as functionally important residues. Further, we used site directed mutagenesis technique to mutate Lys 41 to Met resulting in defective cell division of Mycobacterium smegmatis mc(2). Overall, the proposed model together with its binding features gained from pharmacophore docking studies helped in identifying ligand inhibitor specific to PknI which was confirmed by laboratory experiments.
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32
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Chawla Y, Upadhyay S, Khan S, Nagarajan SN, Forti F, Nandicoori VK. Protein kinase B (PknB) of Mycobacterium tuberculosis is essential for growth of the pathogen in vitro as well as for survival within the host. J Biol Chem 2014; 289:13858-75. [PMID: 24706757 DOI: 10.1074/jbc.m114.563536] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mycobacterium tuberculosis protein kinase B (PknB) comprises an intracellular kinase domain, connected through a transmembrane domain to an extracellular region that contains four PASTA domains. The present study describes the comprehensive analysis of different domains of PknB in the context of viability in avirulent and virulent mycobacteria. We find stringent regulation of PknB expression necessary for cell survival, with depletion or overexpression of PknB leading to cell death. Although PknB-mediated kinase activity is essential for cell survival, active kinase lacking the transmembrane or extracellular domain fails to complement conditional mutants not expressing PknB. By creating chimeric kinases, we find that the intracellular kinase domain has unique functions in the virulent strain, which cannot be substituted by other kinases. Interestingly, we find that although the presence of the C-terminal PASTA domain is dispensable in the avirulent M. smegmatis, all four PASTA domains are essential in M. tuberculosis. The differential behavior of PknB vis-à-vis the number of essential PASTA domains and the specificity of kinase domain functions suggest that PknB-mediated growth and signaling events differ in virulent compared with avirulent mycobacteria. Mouse infection studies performed to determine the role of PknB in mediating pathogen survival in the host demonstrate that PknB is not only critical for growth of the pathogen in vitro but is also essential for the survival of the pathogen in the host.
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Affiliation(s)
- Yogesh Chawla
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India and
| | - Sandeep Upadhyay
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India and
| | - Shazia Khan
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India and
| | | | - Francesca Forti
- the Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Vinay Kumar Nandicoori
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India and
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33
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Bhaduri A, Misra R, Maji A, Bhetaria PJ, Mishra S, Arora G, Singh LK, Dhasmana N, Dubey N, Virdi JS, Singh Y. Mycobacterium tuberculosis cyclophilin A uses novel signal sequence for secretion and mimics eukaryotic cyclophilins for interaction with host protein repertoire. PLoS One 2014; 9:e88090. [PMID: 24505389 PMCID: PMC3913756 DOI: 10.1371/journal.pone.0088090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 01/03/2014] [Indexed: 11/19/2022] Open
Abstract
Cyclophilins are prolyl isomerases with multitude of functions in different cellular processes and pathological conditions. Cyclophilin A (PpiA) of Mycobacterium tuberculosis is secreted during infection in intraphagosomal niche. However, our understanding about the evolutionary origin, secretory mechanism or the interactome of M. tuberculosis PpiA is limited. This study demonstrates through phylogenetic and structural analyses that PpiA has more proximity to human cyclophilins than the prokaryotic counterparts. We report a unique N-terminal sequence (MADCDSVTNSP) present in pathogenic mycobacterial PpiA and absent in non-pathogenic strains. This sequence stretch was shown to be essential for PpiA secretion. The overexpression of full-length PpiA from M. tuberculosis in non-pathogenic Mycobacterium smegmatis resulted in PpiA secretion while truncation of the N-terminal stretch obstructed the secretion. In addition, presence of an ESX pathway substrate motif in M. tuberculosis PpiA suggested possible involvement of Type VII secretion system. Site-directed mutagenesis of key residues in this motif in full-length PpiA also hindered the secretion in M. smegmatis. Bacterial two-hybrid screens with human lung cDNA library as target were utilized to identify interaction partners of PpiA from host repertoire, and a number of substrates with functional representation in iron storage, signal transduction and immune responses were detected. The extensive host interactome coupled with the sequence and structural similarity to human cyclophilins is strongly suggestive of PpiA being deployed by M. tuberculosis as an effector mimic against the host cyclophilins.
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Affiliation(s)
- Asani Bhaduri
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Department of Microbiology, University of Delhi, Delhi, India
| | - Richa Misra
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Abhijit Maji
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Sonakshi Mishra
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Gunjan Arora
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Neha Dhasmana
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Neha Dubey
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Yogendra Singh
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail: mail:
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Chandolia A, Rathor N, Sharma M, Saini NK, Sinha R, Malhotra P, Brahmachari V, Bose M. Functional analysis of mce4A gene of Mycobacterium tuberculosis H37Rv using antisense approach. Microbiol Res 2014; 169:780-7. [PMID: 24556072 DOI: 10.1016/j.micres.2013.12.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/17/2013] [Accepted: 12/28/2013] [Indexed: 01/21/2023]
Abstract
Antisense strategy is an attractive substitute for knockout mutations created for gene silencing. mce genes have been shown to be involved in mycobacterial uptake and intracellular survival. Here we report reduced expression of mce4A and mce1A genes of Mycobacterium tuberculosis using antisense technology. For this, 1.1 kb region of mce4A and mce1A was cloned in reverse orientation in pSD5 shuttle vector, resulting into antisense constructs pSD5-4AS and pSD5-1AS, respectively. In M. tuberculosis H37Rv approximately 60% reduction in Mce4A and 66% reduction in expression of Mce1A protein were observed. We also observed significantly reduced intracellular survival ability of both antisense strains in comparison to M. tuberculosis containing pSD5 alone. RT-PCR analysis showed antisense did not alter the transcription of upstream and downstream of mceA genes of the respective operon. The colony morphology, in vitro growth characteristics and drug susceptibility profile of the antisense construct remained unchanged. These results demonstrate that antisense can be a promising approach to assign function of a gene in a multiunit operon and could be suitably applied as a strategy.
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Affiliation(s)
- Amita Chandolia
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India.
| | - Nisha Rathor
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India.
| | - Monika Sharma
- Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
| | - Neeraj Kumar Saini
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India.
| | - Rajesh Sinha
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India.
| | - Pawan Malhotra
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Vani Brahmachari
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
| | - Mridula Bose
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India.
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Spivey VL, Whalan RH, Hirst EMA, Smerdon SJ, Buxton RS. An attenuated mutant of the Rv1747 ATP-binding cassette transporter of Mycobacterium tuberculosis and a mutant of its cognate kinase, PknF, show increased expression of the efflux pump-related iniBAC operon. FEMS Microbiol Lett 2013; 347:107-15. [PMID: 23915284 PMCID: PMC3908365 DOI: 10.1111/1574-6968.12230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 11/30/2022] Open
Abstract
The ATP-binding cassette transporter Rv1747 is required for the growth of Mycobacterium tuberculosis in mice and in macrophages. Its structure suggests it is an exporter. Rv1747 forms a two-gene operon with pknF coding for the serine/threonine protein kinase PknF, which positively modulates the function of the transporter. We show that deletion of Rv1747 or pknF results in a number of transcriptional changes which could be complemented by the wild type allele, most significantly up-regulation of the iniBAC genes. This operon is inducible by isoniazid and ethambutol and by a broad range of inhibitors of cell wall biosynthesis and is required for efflux pump functioning. However, neither the Rv1747 or pknF mutant showed increased susceptibility to a range of drugs and cell wall stress reagents including isoniazid and ethambutol, cell wall structure and cell division appear normal by electron microscopy, and no differences in lipoarabinomannan were found. Transcription from the pknF promoter was not induced by a range of stress reagents. We conclude that the loss of Rv1747 affects cell wall biosynthesis leading to the production of intermediates that cause induction of iniBAC transcription and implicates it in exporting a component of the cell wall, which is necessary for virulence.
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Affiliation(s)
- Vicky L Spivey
- Division of Mycobacterial Research, MRC National Institute for Medical Research, London, UK
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36
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High throughput phenotypic analysis of Mycobacterium tuberculosis and Mycobacterium bovis strains' metabolism using biolog phenotype microarrays. PLoS One 2013; 8:e52673. [PMID: 23326347 PMCID: PMC3542357 DOI: 10.1371/journal.pone.0052673] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/19/2012] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis is a major human and animal disease of major importance worldwide. Genetically, the closely related strains within the Mycobacterium tuberculosis complex which cause disease are well-characterized but there is an urgent need better to understand their phenotypes. To search rapidly for metabolic differences, a working method using Biolog Phenotype MicroArray analysis was developed. Of 380 substrates surveyed, 71 permitted tetrazolium dye reduction, the readout over 7 days in the method. By looking for ≥5-fold differences in dye reduction, 12 substrates differentiated M. tuberculosis H37Rv and Mycobacterium bovis AF2122/97. H37Rv and a Beijing strain of M. tuberculosis could also be distinguished in this way, as could field strains of M. bovis; even pairs of strains within one spoligotype could be distinguished by 2 to 3 substrates. Cluster analysis gave three clear groups: H37Rv, Beijing, and all the M. bovis strains. The substrates used agreed well with prior knowledge, though an unexpected finding that AF2122/97 gave greater dye reduction than H37Rv with hexoses was investigated further, in culture flasks, revealing that hexoses and Tween 80 were synergistic for growth and used simultaneously rather than in a diauxic fashion. Potential new substrates for growth media were revealed, too, most promisingly N-acetyl glucosamine. Osmotic and pH arrays divided the mycobacteria into two groups with different salt tolerance, though in contrast to the substrate arrays the groups did not entirely correlate with taxonomic differences. More interestingly, these arrays suggested differences between the amines used by the M. tuberculosis complex and enteric bacteria in acid tolerance, with some hydrophobic amino acids being highly effective. In contrast, γ-aminobutyrate, used in the enteric bacteria, had no effect in the mycobacteria. This study proved principle that Phenotype MicroArrays can be used with slow-growing pathogenic mycobacteria and already has generated interesting data worthy of further investigation.
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37
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Kumari R, Saxena R, Tiwari S, Tripathi DK, Srivastava KK. Rv3080c regulates the rate of inhibition of mycobacteria by isoniazid through FabD. Mol Cell Biochem 2012. [PMID: 23180244 DOI: 10.1007/s11010-012-1514-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mycobacterial FASII multi-enzyme complex has been identified to be a target of Ser/Thr protein kinases (STPKs) of Mycobacterium tuberculosis (MTB), with substrates, including the malonyl-CoA:ACP transacylase (FabD) and the β-ketoacyl-ACP synthases KasA and KasB. These proteins are phosphorylated by various kinases in vitro. The present study links the correlation of FASII pathway with serine threonine protein kinase of MTB. In the preliminary finding, we have shown that mycobacterial protein Rv3080c (PknK) phosphorylates FabD and the knockdown of PknK protein in mycobacteria down regulates FabD expression. This event leads to the differential inhibition of mycobacteria in the presence of isoniazid (INH), as the inhibition of growth of mycobacteria in the presence of INH is enhanced in PknK deficient mycobacteria.
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Affiliation(s)
- Ruma Kumari
- Department of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226001, India
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Kumar D, Palaniyandi K, Challu VK, Kumar P, Narayanan S. PknE, a serine/threonine protein kinase from Mycobacterium tuberculosis has a role in adaptive responses. Arch Microbiol 2012; 195:75-80. [DOI: 10.1007/s00203-012-0848-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 09/25/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
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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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The role of the mycobacterial DNA-binding protein 1 (MDP1) from Mycobacterium bovis BCG in host cell interaction. BMC Microbiol 2012; 12:165. [PMID: 22863261 PMCID: PMC3438132 DOI: 10.1186/1471-2180-12-165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/27/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mycobacterium tuberculosis differs from most pathogens in its ability to multiply inside monocytes and to persist during long periods of time within granuloma in a status of latency. A class of proteins called mycobacterial histone-like proteins has been associated with regulation of replication and latency, but their precise role in the infection process has yet to be uncovered. Our study aimed at defining the impact of the histone-like protein MDP1 from M. bovis BCG (mycobacterial DNA-binding protein 1, corresponding to Rv2986c from M. tuberculosis) on early steps of infection. RESULTS Previously, a BCG (Bacillus Calmette Guérin) strain had been generated by antisense-technique exhibiting reduced MDP1 expression. This strain was now used to analyse the impact of reduced amount of MDP1 on the interaction with human blood monocytes, macrophage lines and PBMC (peripheral blood mononuclear cells). MDP1 was revealed to be required for growth at acidic pH and for intracellular replication in human blood monocytes. Down-regulation of MDP1 resulted in reduced secretion of the cytokine IL-1β by infected human PBMC. In addition, a reduction of MDP1 expression had a major impact on the formation of fused multi-nucleated macrophages. In monocyte preparations from human blood as well as in human and mouse macrophage cell lines, both the percentage of multi-nucleated cells and the number of nuclei per cell were much enhanced when the monocytes were infected with BCG expressing less MDP1. CONCLUSION MDP1 from M. bovis BCG affects the growth at acidic pH and the intracellular replication in human monocytes. It furthermore affects cytokine secretion by host cells, and the formation of fused multi-nucleated macrophages. Our results suggest an important role of MDP1 in persistent infection.
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Functional characterization delineates that a Mycobacterium tuberculosis specific protein kinase (Rv3080c) is responsible for the growth, phagocytosis and intracellular survival of avirulent mycobacteria. Mol Cell Biochem 2012; 369:67-74. [DOI: 10.1007/s11010-012-1369-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 06/12/2012] [Indexed: 11/25/2022]
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Oh JR, Song HC, Kang SR, Yoo SW, Kim J, Chong A, Min JJ, Bom HS, Lee SS, Park YW. The Clinical Usefulness of (18)F-FDG PET/CT in Patients with Systemic Autoimmune Disease. Nucl Med Mol Imaging 2011; 45:177-84. [PMID: 24900001 DOI: 10.1007/s13139-011-0094-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/22/2011] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Individuals with systemic autoimmune disease have an increased susceptibility to both inflammation and malignancy. The aim of this study was to evaluate the clinical usefulness of (18)F-FDG PET/CT in patients with systemic autoimmune disease. METHODS Forty patients diagnosed with systemic autoimmune disease were enrolled. Diagnostic accuracy of FDG PET/CT for detecting malignancy was assessed. FDG PET/CT findings, including maximum standardized uptake (SUVmax) of lymphadenopathy (LAP), liver, bone marrow, spleen, joint and muscles, were considered for the characterization of LAPs. RESULTS FDG PET/CT could detect metabolically activated lesions in 36 out of 40 patients (90%) including inflammatory lesions in 28 out of 32 patients (88%). The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of FDG PET/CT for the detection of malignancy were 100, 67, 70, 25, and 100%, respectively. Multiple LAPs were found in 25 of 40 patients (63%), and comprised three malignancies, four cases of tuberculosis, and 18 reactive changes. A SUVmax ratio of bone marrow to liver below 0.78 could distinguish malignancy from tuberculosis + reactive change (AUC = 1.000, sensitivity: 100%, specificity: 100%). The SUVmax ratio of spleen to liver in the reactive group was also significantly higher than that in the malignancy group (P = 0.014). SUVmax of LAP in the TB group was significantly higher than that in the reactive group (P = 0.040). CONCLUSIONS PET/CT is useful in detecting and differentiating inflammation and malignancy in patients with systemic autoimmune disease. Frequent false-positive interpretations can be minimized by consideration of FDG uptake in bone marrow and spleen.
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Affiliation(s)
- Jong-Ryool Oh
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Ho-Chun Song
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Sae-Ryung Kang
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Su-Woong Yoo
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Jahae Kim
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Ari Chong
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Jung-Joon Min
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Hee-Seung Bom
- Department of Nuclear Medicine, Chonnam National University Medical School and Hospital, 8 Hakdong, Dongku, Gwangju 501-757 South Korea
| | - Shin-Seok Lee
- Department of Rheumatology, Chonnam National University Hospital, Gwangju, South Korea
| | - Yong-Wook Park
- Department of Rheumatology, Chonnam National University Hospital, Gwangju, South Korea
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Spivey VL, Molle V, Whalan RH, Rodgers A, Leiba J, Stach L, Walker KB, Smerdon SJ, Buxton RS. Forkhead-associated (FHA) domain containing ABC transporter Rv1747 is positively regulated by Ser/Thr phosphorylation in Mycobacterium tuberculosis. J Biol Chem 2011; 286:26198-209. [PMID: 21622570 PMCID: PMC3138270 DOI: 10.1074/jbc.m111.246132] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/24/2011] [Indexed: 12/22/2022] Open
Abstract
One major signaling method employed by Mycobacterium tuberculosis, the causative agent of tuberculosis, is through reversible phosphorylation of proteins mediated by protein kinases and phosphatases. This study concerns one of these enzymes, the serine/threonine protein kinase PknF, that is encoded in an operon with Rv1747, an ABC transporter that is necessary for growth of M. tuberculosis in vivo and contains two forkhead-associated (FHA) domains. FHA domains are phosphopeptide recognition motifs that specifically recognize phosphothreonine-containing epitopes. Experiments to determine how PknF regulates the function of Rv1747 demonstrated that phosphorylation occurs on two specific threonine residues, Thr-150 and Thr-208. To determine the in vivo consequences of phosphorylation, infection experiments were performed in bone marrow-derived macrophages and in mice using threonine-to-alanine mutants of Rv1747 that prevent specific phosphorylation and revealed that phosphorylation positively modulates Rv1747 function in vivo. The role of the FHA domains in this regulation was further demonstrated by isothermal titration calorimetry, using peptides containing both phosphothreonine residues. FHA-1 domain mutation resulted in attenuation in macrophages highlighting the critical role of this domain in Rv1747 function. A mutant deleted for pknF did not, however, have a growth phenotype in an infection, suggesting that other kinases can fulfill its role when it is absent. This study provides the first information on the molecular mechanism(s) regulating Rv1747 through PknF-dependent phosphorylation but also indicates that phosphorylation activates Rv1747, which may have important consequences in regulating growth of M. tuberculosis.
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Affiliation(s)
- Vicky L. Spivey
- From the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Universités de Montpellier II et I, CNRS, UMR 5235, Case 107, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Rachael H. Whalan
- From the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Angela Rodgers
- the Immunology and Cellular Immunity Section, Bacteriology Division, National Institute of Biological Standards and Control (A Centre of the Health Protection Agency), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom, and
| | - Jade Leiba
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Universités de Montpellier II et I, CNRS, UMR 5235, Case 107, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Lasse Stach
- the Division of Molecular Structure, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - K. Barry Walker
- the Immunology and Cellular Immunity Section, Bacteriology Division, National Institute of Biological Standards and Control (A Centre of the Health Protection Agency), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom, and
| | - Stephen J. Smerdon
- the Division of Molecular Structure, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Roger S. Buxton
- From the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
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Mészáros B, Tóth J, Vértessy BG, Dosztányi Z, Simon I. Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis. PLoS Comput Biol 2011; 7:e1002118. [PMID: 21814507 PMCID: PMC3140968 DOI: 10.1371/journal.pcbi.1002118] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 05/24/2011] [Indexed: 02/04/2023] Open
Abstract
Lengthy co-evolution of Homo sapiens and Mycobacterium tuberculosis, the main causative agent of tuberculosis, resulted in a dramatically successful pathogen species that presents considerable challenge for modern medicine. The continuous and ever increasing appearance of multi-drug resistant mycobacteria necessitates the identification of novel drug targets and drugs with new mechanisms of action. However, further insights are needed to establish automated protocols for target selection based on the available complete genome sequences. In the present study, we perform complete proteome level comparisons between M. tuberculosis, mycobacteria, other prokaryotes and available eukaryotes based on protein domains, local sequence similarities and protein disorder. We show that the enrichment of certain domains in the genome can indicate an important function specific to M. tuberculosis. We identified two families, termed pkn and PE/PPE that stand out in this respect. The common property of these two protein families is a complex domain organization that combines species-specific regions, commonly occurring domains and disordered segments. Besides highlighting promising novel drug target candidates in M. tuberculosis, the presented analysis can also be viewed as a general protocol to identify proteins involved in species-specific functions in a given organism. We conclude that target selection protocols should be extended to include proteins with complex domain architectures instead of focusing on sequentially unique and essential proteins only.
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Affiliation(s)
- Bálint Mészáros
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail: (ZD); (IS)
| | - István Simon
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail: (ZD); (IS)
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45
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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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46
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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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47
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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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48
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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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49
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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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50
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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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