1
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Shaik BB, Karpoormath R. Key challenges in TB drug discovery: A perspective. Bioorg Med Chem Lett 2024; 109:129846. [PMID: 38857850 DOI: 10.1016/j.bmcl.2024.129846] [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: 04/16/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
Over the past 2000 years, tuberculosis (TB) has been responsible for more deaths than any other infectious disease. In recent years, there has been a recovery of research and development (R&D) efforts focused on TB drugs. This is driven by the pressing need to combat the global spread of the disease and develop improved therapies for both drug-sensitive and drug-resistant strains. Many new TB drug candidates have recently entered clinical trials, marking the beginning of a rebirth in this area after decades of neglect. The problem is that very few of the hundreds of compounds identified each year as potential anti-TB drugs really make it to the clinical development stage. This perspective focuses on the primary obstacles and approaches involved in the development of new medications for TB. This will help medicinal chemists better understand TB drug challenges and develop novel drug candidates.
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Affiliation(s)
- Baji Baba Shaik
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban 4000, South Africa.
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2
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Rs N, Sinha SK, Batra S, Regatti PR, Syal K. Promoter characterization of relZ-bifunctional (pp)pGpp synthetase in mycobacteria. Genes Cells 2024. [PMID: 38923083 DOI: 10.1111/gtc.13135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The second messenger guanosine 3',5'-bis(diphosphate)/guanosine tetraphosphate (ppGpp) and guanosine 3'-diphosphate 5'-triphosphate/guanosine pentaphosphate (pppGpp) ((p)ppGpp) has been shown to be crucial for the survival of mycobacteria under hostile conditions. Unexpectedly, deletion of primary (p)ppGpp synthetase-Rel did not completely diminish (p)ppGpp levels leading to the discovery of novel bifunctional enzyme-RelZ, which displayed guanosine 5'-monophosphate,3'-diphosphate (pGpp), ppGpp, and pppGpp ((pp)pGpp) synthesis and RNAseHII activity. What conditions does it express itself under, and does it work in concert with Rel? The regulation of its transcription and whether the Rel enzyme plays a role in such regulation remain unclear. In this article, we have studied relZ promoter and compared its activity with rel promoter in different growth conditions. We observed that the promoter activity of relZ was constitutive; it is weaker than rel promoter, lies within 200 bp upstream of translation-start site, and it increased under carbon starvation. Furthermore, the promoter activity of relZ was compromised in the rel-knockout strain in the stationary phase. Our study unveils the dynamic regulation of relZ promoter activity by SigA and SigB sigma factors in different growth phases in mycobacteria. Importantly, elucidating the regulatory network of RelZ would enable the development of the targeted interventions for treating mycobacterial infections.
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Affiliation(s)
- Neethu Rs
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
| | - Shubham Kumar Sinha
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
| | - Sakshi Batra
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
- Department of Pulmonary Medicine, Malla Reddy Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Pavan Reddy Regatti
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
| | - Kirtimaan Syal
- Genetics and Molecular Microbiology Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, Telangana, India
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3
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Bao J, Tang Y, Chen Y, Jin J, Wang X, An G, Cao L, Zhang H, Cheng G, Pan G, Zhou Z. E. hellem Ser/Thr protein phosphatase PP1 targets the DC MAPK pathway and impairs immune functions. Life Sci Alliance 2024; 7:e202302375. [PMID: 38199846 PMCID: PMC10781585 DOI: 10.26508/lsa.202302375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
Microsporidia are difficult to be completely eliminated once infected, and the persistence disrupts host cell functions. Here in this study, we aimed to elucidate the impairing effects and consequences of microsporidia on host DCs. Enterocytozoon hellem, one of the most commonly diagnosed zoonotic microsporidia species, was applied. In vivo models demonstrated that E. hellem-infected mice were more susceptible to further pathogenic challenges, and DCs were identified as the most affected groups of cells. In vitro assays revealed that E. hellem infection impaired DCs' immune functions, reflected by down-regulated cytokine expressions, lower extent of maturation, phagocytosis ability, and antigen presentations. E. hellem infection also detained DCs' potencies to prime and stimulate T cells; therefore, host immunities were disrupted. We found that E. hellem Ser/Thr protein phosphatase PP1 directly interacts with host p38α (MAPK14) to manipulate the p38α(MAPK14)/NFAT5 axis of the MAPK pathway. Our study is the first to elucidate the molecular mechanisms of the impairing effects of microsporidia on host DCs' immune functions. The emergence of microsporidiosis may be of great threat to public health.
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Affiliation(s)
- Jialing Bao
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Yunlin Tang
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Yebo Chen
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Jiangyan Jin
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Xue Wang
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guozhen An
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Lu Cao
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Huarui Zhang
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Gong Cheng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Guoqing Pan
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Zeyang Zhou
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
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4
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Kathayat D, VanderVen BC. Exploiting cAMP signaling in Mycobacterium tuberculosis for drug discovery. Trends Microbiol 2024:S0966-842X(24)00008-8. [PMID: 38360432 PMCID: PMC11322422 DOI: 10.1016/j.tim.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Mycobacterium tuberculosis (Mtb) replicates within host macrophages by adapting to the stressful and nutritionally constrained environments in these cells. Exploiting these adaptations for drug discovery has revealed that perturbing cAMP signaling can restrict Mtb growth in macrophages. Specifically, compounds that agonize or stimulate the bacterial enzyme, Rv1625c/Cya, induce cAMP synthesis and this interferes with the ability of Mtb to metabolize cholesterol. In murine tuberculosis (TB) infection models, Rv1625c/Cya agonists contribute to reducing relapse and shortening combination treatments, highlighting the therapeutic potential for this class of compounds. More recently, cAMP signaling has been implicated in regulating fatty acid utilization by Mtb. Thus, a new model is beginning to emerge in which cAMP regulates the utilization of host lipids by Mtb during infection, and this could provide new targets for TB drug development. Here, we summarize the current understanding of cAMP signaling in Mtb with a focus on our understanding of how cAMP signaling impacts Mtb physiology during infection. We also discuss additional cAMP-related drug targets in Mtb and other bacterial pathogens that may have therapeutic potential.
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Affiliation(s)
- Dipak Kathayat
- Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Brian C VanderVen
- Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA.
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Zhang M, Wang P, Li C, Segev O, Wang J, Wang X, Yue L, Jiang X, Sheng Y, Levy A, Jiang C, Chen F. Comparative genomic analysis reveals differential genomic characteristics and featured genes between rapid- and slow-growing non-tuberculous mycobacteria. Front Microbiol 2023; 14:1243371. [PMID: 37808319 PMCID: PMC10551460 DOI: 10.3389/fmicb.2023.1243371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Non-tuberculous mycobacteria (NTM) is a major category of environmental bacteria in nature that can be divided into rapidly growing mycobacteria (RGM) and slowly growing mycobacteria (SGM) based on their distinct growth rates. To explore differential molecular mechanisms between RGM and SGM is crucial to understand their survival state, environmental/host adaptation and pathogenicity. Comparative genomic analysis provides a powerful tool for deeply investigating differential molecular mechanisms between them. However, large-scale comparative genomic analysis between RGM and SGM is still uncovered. Methods In this study, we screened 335 high-quality, non-redundant NTM genome sequences covering 187 species from 3,478 online NTM genomes, and then performed a comprehensive comparative genomic analysis to identify differential genomic characteristics and featured genes/protein domains between RGM and SGM. Results Our findings reveal that RGM has a larger genome size, more genes, lower GC content, and more featured genes/protein domains in metabolism of some main substances (e.g. carbohydrates, amino acids, nucleotides, ions, and coenzymes), energy metabolism, signal transduction, replication, transcription, and translation processes, which are essential for its rapid growth requirements. On the other hand, SGM has a smaller genome size, fewer genes, higher GC content, and more featured genes/protein domains in lipid and secondary metabolite metabolisms and cellular defense mechanisms, which help enhance its genome stability and environmental adaptability. Additionally, orthogroup analysis revealed the important roles of bacterial division and bacteriophage associated genes in RGM and secretion system related genes for better environmental adaptation in SGM. Notably, PCoA analysis of the top 20 genes/protein domains showed precision classification between RGM and SGM, indicating the credibility of our screening/classification strategies. Discussion Overall, our findings shed light on differential underlying molecular mechanisms in survival state, adaptation and pathogenicity between RGM and SGM, show the potential for our comparative genomic pipeline to investigate differential genes/protein domains at whole genomic level across different bacterial species on a large scale, and provide an important reference and improved understanding of NTM.
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Affiliation(s)
- Menglu Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Peihan Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cuidan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Ofir Segev
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jie Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaotong Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Liya Yue
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Xiaoyuan Jiang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China
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6
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Li X, Long X, Chen L, Guo X, Lu L, Hu L, He ZG. Mycobacterial phage TM4 requires a eukaryotic-like Ser/Thr protein kinase to silence and escape anti-phage immunity. Cell Host Microbe 2023; 31:1469-1480.e4. [PMID: 37567169 DOI: 10.1016/j.chom.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/15/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023]
Abstract
In eukaryotic cells, serine/threonine protein kinases (StpKs) play important roles in limiting viral infections. StpKs are commonly activated upon infections, inhibiting the expression of genes central for viral replication. Here, we report that a eukaryotic-like StpK7 encoded by MSMEG_1200 in M. smegmatis is required for mycobacteriophage TM4 to escape bacterial defense. stpK7 is located within a gene island, MSMEG_1191-MSMEG_1200, containing multiple anti-phage genes resembling the BREX (bacteriophage exclusion) phage-resistance system. StpK7 negatively regulates the expression of this gene island. Following phage TM4 infection, StpK7 is induced, directly phosphorylating the transcriptional regulator MSMEG_1198 and inhibiting its positive regulatory activity, thus reducing the expression of multiple downstream genes in the BREX-like gene island. Further analysis showed that genes within this anti-phage island critically regulate mycobacterial lipid hemostasis and phage adsorption. Collectively, this work characterizes a regulatory network driven by StpK7, which is utilized by phage TM4 to escape from the host defense against mycobacteria.
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Affiliation(s)
- Xiaohui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiating Long
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liu Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiao Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Lining Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zheng-Guo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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7
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Krishnan V, Nath S, Nair P, Das B. Mycobacterium tuberculosis and its clever approaches to escape the deadly macrophage. World J Microbiol Biotechnol 2023; 39:300. [PMID: 37667129 DOI: 10.1007/s11274-023-03735-9] [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: 06/21/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Mycobacterium tuberculosis (Mt.b), a deadly disease causer, is a facultative parasite. This microorganism has developed several methods to defend itself, once internalized within specialised vacuoles in the macrophages. A wide array of receptors like the complement receptor mannose receptors, scavenger receptor assists the entry of the microbe within the phagocytic macrophages. However, Mt.b is clever enough to protect itself from the hostile environment of the macrophage thereby prevailing within it. The microbe can efficiently inhibit processes like phagosome-lysosome fusion, acidification of phagosomes, release of proinflammatory cytokines and stop crucial events like apoptosis. Additionally, it also adopts resistance to killing by reactive oxygen intermediates and reactive nitrogen intermediates. There are multiple genes both in host and the pathogen which are involved in this successful survival of Mt.b. The regulation of phagolysosome fusion is mediated by proteins such as Coronin, TlyA, SapM, PnkG, EsxH. The microbe has certain mechanisms to even acquire iron from the host cell, to withstand iron deprivation as a mode of host's defence mechanism. This review focuses on the various defensive adaptations acquired by Mt.b for fighting against the deprived conditions existing within the macrophages and their capability of proliferating successfully within it, thereby resulting in a diseased condition.
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Affiliation(s)
- Vinaya Krishnan
- Department of Biotechnology, Mount Carmel College Autonomous, Bengaluru, 560052, India
| | | | - Preetha Nair
- Department of Biotechnology, Mount Carmel College Autonomous, Bengaluru, 560052, India
| | - Bannhi Das
- Department of Biotechnology, Mount Carmel College Autonomous, Bengaluru, 560052, India.
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8
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Jaiswal S, Kumar S, Velarde de la Cruz E. Exploring the role of the protein tyrosine kinase a (PtkA) in mycobacterial intracellular survival. Tuberculosis (Edinb) 2023; 142:102398. [PMID: 37657276 DOI: 10.1016/j.tube.2023.102398] [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: 05/20/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
Mycobacterium tuberculosis (Mtb) continues to define new paradigms of host-pathogen interaction. There are several host proteins known which are regulated by Mtb infection. The proteins which regulate host biological processes like apoptosis, cell processes, stress proteins, metabolic enzymes, etc. are targeted by the pathogens. Mtb proteins interact directly or indirectly with host proteins and play an important role in their persistence and intracellular growth. Mtb is an intracellular pathogen. It remains dormant for years within the host without activating its immune system. Mtb Protein tyrosine kinase (PtkA) regulates host anti-apoptotic protein, metabolic enzymes, and several other proteins that are involved in stress regulation, cell proliferation, protein folding, DNA repair, etc. PtkA regulates other mycobacterial proteins and plays an important role in its growth and survival. Here we summarized the current knowledge of PtkA and reviewed its role in mycobacterial intracellular survival as it regulates several other mycobacterial proteins and host proteins. PtkA regulates PtpA secretion which is essential for mycobacterial virulence and could be used as an attractive drug target.
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Affiliation(s)
- Swati Jaiswal
- University of Massachusetts Chan Medical School, Worcester, United States.
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9
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Frando A, Boradia V, Gritsenko M, Beltejar C, Day L, Sherman DR, Ma S, Jacobs JM, Grundner C. The Mycobacterium tuberculosis protein O-phosphorylation landscape. Nat Microbiol 2023; 8:548-561. [PMID: 36690861 DOI: 10.1038/s41564-022-01313-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/16/2022] [Indexed: 01/25/2023]
Abstract
Bacterial phosphosignalling has been synonymous with two-component systems and their histidine kinases, but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignalling enzymes in eukaryotes but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria is untested. Here we explored the global signalling capacity of the STPKs in Mtb using a panel of STPK loss-of-function and overexpression strains combined with mass spectrometry-based phosphoproteomics. A deep phosphoproteome with >14,000 unique phosphosites shows that O-phosphorylation in Mtb is a vastly underexplored protein modification that affects >80% of the proteome and extensively interfaces with the transcriptional machinery. Mtb O-phosphorylation gives rise to an expansive, distributed and cooperative network of a complexity that has not previously been seen in bacteria and that is on par with eukaryotic phosphosignalling networks. A resource of >3,700 high-confidence direct substrate-STPK interactions and their transcriptional effects provides signalling context for >80% of Mtb proteins and allows the prediction and assembly of signalling pathways for mycobacterial physiology.
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Affiliation(s)
- Andrew Frando
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Vishant Boradia
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Claude Beltejar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Le Day
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - David R Sherman
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Shuyi Ma
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jon M Jacobs
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, USA.
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10
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Freeman AH, Tembiwa K, Brenner JR, Chase MR, Fortune SM, Morita YS, Boutte CC. Arginine methylation sites on SepIVA help balance elongation and septation in Mycobacterium smegmatis. Mol Microbiol 2023; 119:208-223. [PMID: 36416406 PMCID: PMC10023300 DOI: 10.1111/mmi.15006] [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: 10/27/2021] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022]
Abstract
The growth of mycobacterial cells requires successful coordination between elongation and septation. However, it is not clear which factors mediate this coordination. Here, we studied the function and post-translational modification of an essential division factor, SepIVA, in Mycobacterium smegmatis. We find that SepIVA is arginine methylated, and that alteration of its methylation sites affects both septation and polar elongation of Msmeg. Furthermore, we show that SepIVA regulates the localization of MurG and that this regulation may impact polar elongation. Finally, we map SepIVA's two regulatory functions to different ends of the protein: the N-terminus regulates elongation while the C-terminus regulates division. These results establish SepIVA as a regulator of both elongation and division and characterize a physiological role for protein arginine methylation sites for the first time in mycobacteria.
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Affiliation(s)
- Angela H Freeman
- Department of Biology, University of Texas at Arlington,
Arlington, Texas, USA
| | - Karen Tembiwa
- Department of Biology, University of Texas at Arlington,
Arlington, Texas, USA
| | - James R Brenner
- Department of Microbiology, University of Massachusetts,
Amherst, Massachusetts, USA
| | - Michael R Chase
- Department of Immunology and Infectious Disease, Harvard TH
Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Disease, Harvard TH
Chan School of Public Health, Boston, Massachusetts, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts,
Amherst, Massachusetts, USA
| | - Cara C Boutte
- Department of Biology, University of Texas at Arlington,
Arlington, Texas, USA
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11
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Kaur K, Sharma S, Abhishek S, Kaur P, Saini UC, Dhillon MS, Karakousis PC, Verma I. Metabolic switching and cell wall remodelling of Mycobacterium tuberculosis during bone tuberculosis. J Infect 2023; 86:134-146. [PMID: 36549425 DOI: 10.1016/j.jinf.2022.12.014] [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: 04/13/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Bone tuberculosis (TB) is the third most common types of extrapulmonary tuberculosis. It is critical to understand mycobacterial adaptive strategies within bone lesions to identify mycobacterial factors that may have role in disease pathogenesis. METHODS Whole genome microarray was used to characterize the in-vivo transcriptome of Mycobacterium tuberculosis (M.tb) within bone TB specimens. Mycobacterial virulent proteins were identified by bioinformatic software. An in vitro osteoblast cell line model was used to study the role of these proteins in bone TB pathogenesis. RESULTS 914 mycobacterial genes were significantly overexpressed and 1688 were repressed in bone TB specimens. Pathway analysis of differentially expressed genes demonstrated a non-replicative and hypometabolic state of M.tb, reinforcement of the mycobacterial cell wall and induction of DNA damage repair responses, suggesting possible survival strategies of M.tb within bone. Bioinformatics mining of microarray data led to identification of five virulence proteins. The genes encoding these proteins were also upregulated in the in vitro MC3T3 osteoblast cell line model of bone TB. Further, exposure of osteoblast cells to two of these virulence proteins (Rv1046c and Rv3663c) significantly inhibited osteoblast differentiation. CONCLUSION M.tb alters its transcriptome to establish infection in bone by upregulating certain virulence genes which play a key role in disturbing bone homeostasis.
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Affiliation(s)
- Khushpreet Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sumedha Sharma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudhanshu Abhishek
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Prabhdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Uttam Chand Saini
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mandeep Singh Dhillon
- Department of Orthopaedics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Petros C Karakousis
- Centers for Tuberculosis Research and Systems Approaches for Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Indu Verma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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12
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Thongdee P, Hanwarinroj C, Pakamwong B, Kamsri P, Punkvang A, Leanpolchareanchai J, Ketrat S, Saparpakorn P, Hannongbua S, Ariyachaokun K, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Mukamolova GV, Blood RA, Takebayashi Y, Spencer J, Mulholland AJ, Pungpo P. Virtual Screening Identifies Novel and Potent Inhibitors of Mycobacterium tuberculosis PknB with Antibacterial Activity. J Chem Inf Model 2022; 62:6508-6518. [PMID: 35994014 DOI: 10.1021/acs.jcim.2c00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis protein kinase B (PknB) is essential to mycobacterial growth and has received considerable attention as an attractive target for novel anti-tuberculosis drug development. Here, virtual screening, validated by biological assays, was applied to select candidate inhibitors of M. tuberculosis PknB from the Specs compound library (www.specs.net). Fifteen compounds were identified as hits and selected for in vitro biological assays, of which three indoles (2, AE-848/42799159; 4, AH-262/34335013; 10, AP-124/40904362) inhibited growth of M. tuberculosis H37Rv with minimal inhibitory concentrations of 6.2, 12.5, and 6.2 μg/mL, respectively. Two compounds, 2 and 10, inhibited M. tuberculosis PknB activity in vitro, with IC50 values of 14.4 and 12.1 μM, respectively, suggesting this to be the likely basis of their anti-tubercular activity. In contrast, compound 4 displayed anti-tuberculosis activity against M. tuberculosis H37Rv but showed no inhibition of PknB activity (IC50 > 128 μM). We hypothesize that hydrolysis of its ethyl ester to a carboxylate moiety generates an active species that inhibits other M. tuberculosis enzymes. Molecular dynamics simulations of modeled complexes of compounds 2, 4, and 10 bound to M. tuberculosis PknB indicated that compound 4 has a lower affinity for M. tuberculosis PknB than compounds 2 and 10, as evidenced by higher calculated binding free energies, consistent with experiment. Compounds 2 and 10 therefore represent candidate inhibitors of M. tuberculosis PknB that provide attractive starting templates for optimization as anti-tubercular agents.
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Affiliation(s)
- Paptawan Thongdee
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Chayanin Hanwarinroj
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Bongkochawan Pakamwong
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | | | - Sombat Ketrat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, 21210, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Kanchiyaphat Ariyachaokun
- Department of Biological Science, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center, NSTDA, 111 Thailand Science Park, Klong Luang, Pathum Thani, 12120, Thailand
| | - Sanya Sureram
- Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok, 10210, Thailand
| | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Pitak Santanirand
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Maurice Shock Medical Sciences Building, University Road, Leicester, LE1 9HN, United Kingdom
| | - Rosemary A Blood
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
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13
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Sun M, Ge S, Li Z. The Role of Phosphorylation and Acylation in the Regulation of Drug Resistance in Mycobacterium tuberculosis. Biomedicines 2022; 10:biomedicines10102592. [PMID: 36289854 PMCID: PMC9599588 DOI: 10.3390/biomedicines10102592] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis is a chronic and lethal infectious disease caused by Mycobacterium tuberculosis. In previous decades, most studies in this area focused on the pathogenesis and drug targets for disease treatments. However, the emergence of drug-resistant strains has increased the difficulty of clinical trials over time. Now, more post-translational modified proteins in Mycobacterium tuberculosis have been discovered. Evidence suggests that these proteins have the ability to influence tuberculosis drug resistance. Hence, this paper systematically summarizes updated research on the impacts of protein acylation and phosphorylation on the acquisition of drug resistance in Mycobacterium tuberculosis through acylation and phosphorylation protein regulating processes. This provides us with a better understanding of the mechanism of antituberculosis drugs and may contribute to a reduction the harm that tuberculosis brings to society, as well as aiding in the discovery of new drug targets and therapeutic regimen adjustments in the future.
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Affiliation(s)
- Manluan Sun
- School of Medicine, Shanxi Datong University, Datong 037009, China
- Institute of Carbon Materials Science, Shanxi Datong University, Datong 037009, China
- Correspondence:
| | - Sai Ge
- Institute of Carbon Materials Science, Shanxi Datong University, Datong 037009, China
- Center of Academic Journal, Shanxi Datong University, Datong 037009, China
| | - Zhaoyang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Wang H, Bi J, Zhang Y, Pan M, Guo Q, Xiao G, Cui Y, Hu S, Chan CK, Yuan Y, Kaneko T, Zhang G, Chen S. Human Kinase IGF1R/IR Inhibitor Linsitinib Controls the In Vitro and Intracellular Growth of Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:2019-2027. [PMID: 36048501 DOI: 10.1021/acsinfecdis.2c00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
ATP provides energy in the biosynthesis of cellular metabolites as well as regulates protein functions through phosphorylation. Many ATP-dependent enzymes are antibacterial and anticancer targets including human kinases acted on by most of the successful drugs. In search of new chemotherapeutics for tuberculosis (TB), we screened repurposing compounds against the essential glutamine synthase (GlnA1) of Mycobacterium tuberculosis (Mtb) and identified linsitinib, a clinical-stage drug originally targeting kinase IGF1R/IR as a potent GlnA1 inhibitor. Linsitinib has direct antimycobacterial activity. Biochemical, molecular modeling, and target engagement analyses revealed the inhibition is ATP-competitive and specific in Mtb. Linsitinib also improves autophagy flux in both Mtb-infected and uninfected THP1 macrophages, as demonstrated by the decreased p-mTOR and p62 and the increased lipid-bound LC3B-II and autophagosome forming puncta. Linsitinib-mediated autophagy reduces intracellular growth of wild-type and isoniazid-resistant Mtb alone or in combination with bedaquiline. We have demonstrated that an IGF-IR/IR inhibitor can potentially be used to treat TB. Our study reinforces the concept of targeting ATP-dependent enzymes for novel anti-TB therapy.
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Affiliation(s)
- Heng Wang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Jing Bi
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Yuan Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Miaomiao Pan
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Qinglong Guo
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Genhui Xiao
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Yumeng Cui
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Song Hu
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Chi Kin Chan
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Ying Yuan
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, New York 10005, United States
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Shawn Chen
- Global Health Drug Discovery Institute, Haidian, Beijing 100192, China
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15
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Craggs PD, de Carvalho LPS. Bottlenecks and opportunities in antibiotic discovery against Mycobacterium tuberculosis. Curr Opin Microbiol 2022; 69:102191. [PMID: 35970040 DOI: 10.1016/j.mib.2022.102191] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/29/2022] [Accepted: 07/17/2022] [Indexed: 11/16/2022]
Abstract
Tuberculosis (TB) persists as a major global health issue and a leading cause of death by a single infectious agent. The global burden of TB is further exacerbated by the continuing emergence and dissemination of strains of Mycobacterium tuberculosis resistant to multiple antibiotics. The need for novel drugs that can be used to shorten the course for current TB drug regimens as well as combat the persistent threat of antibiotic resistance has never been greater. There have been significant advances in the discovery of de novo TB treatments, with the first TB-specific drugs in 45 years approved for use. However, there are still issues that restrict the pipeline of new antitubercular chemotherapies. The rate of failure of TB drug candidates in clinical trials remains high, while the validation of new TB drug targets and subsequent identification of novel inhibitors remains modest.
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Affiliation(s)
- Peter D Craggs
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; GSK-Francis Crick Institute Linklabs, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Luiz Pedro S de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom.
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16
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Giacalone D, Yap RE, Ecker AMV, Tan S. PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases. PLoS Genet 2022; 18:e1010331. [PMID: 35913986 PMCID: PMC9371303 DOI: 10.1371/journal.pgen.1010331] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/11/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia-responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK-phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function. Vital to successful host colonization by Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the bacterium’s ability to respond and adapt to changes in its local environment during infection. Here, we discover that the essential transcription factor PrrA, part of the PrrAB two-component system (TCS), modulates Mtb response to four important environmental cues encountered within the host: pH, chloride, nitric oxide, and hypoxia. PrrA acts as a rheostat, adjusting the amplitude of Mtb gene expression changes upon bacterial exposure to each of the four environmental signals. Further, we reveal a critical impact of serine/threonine protein kinases (STPKs) on PrrA function, with prevention of STPK phosphorylation of PrrA disrupting adaptive response of Mtb to growth-inhibiting cues and attenuating the bacterium’s ability to colonize its host. Our work uncovers PrrA as a regulator with broad impact across environmental signals, and highlights how two regulatory systems, TCSs and STPKs, critically interact in coordinating Mtb response to environmental cues.
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Affiliation(s)
- David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Rochelle E. Yap
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alwyn M. V. Ecker
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
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17
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Bar-Oz M, Meir M, Barkan D. Virulence-Associated Secretion in Mycobacterium abscessus. Front Immunol 2022; 13:938895. [PMID: 35880173 PMCID: PMC9308005 DOI: 10.3389/fimmu.2022.938895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are a heterogeneous group of originally environmental organi3sms, increasingly recognized as pathogens with rising prevalence worldwide. Knowledge of NTM’s mechanisms of virulence is lacking, as molecular research of these bacteria is challenging, sometimes more than that of M. tuberculosis (Mtb), and far less resources are allocated to their investigation. While some of the virulence mechanisms are common to several mycobacteria including Mtb, others NTM species-specific. Among NTMs, Mycobacterium abscessus (Mabs) causes some of the most severe and difficult to treat infections, especially chronic pulmonary infections. Mabs survives and proliferates intracellularly by circumventing host defenses, using multiple mechanisms, many of which remain poorly characterized. Some of these immune-evasion mechanisms are also found in Mtb, including phagosome pore formation, inhibition of phagosome maturation, cytokine response interference and apoptosis delay. While much is known of the role of Mtb-secreted effector molecules in mediating the manipulation of the host response, far less is known of the secreted effector molecules in Mabs. In this review, we briefly summarize the knowledge of secreted effectors in Mtb (such as ESX secretion, SecA2, TAT and others), and draw the parallel pathways in Mabs. We also describe pathways that are unique to Mabs, differentiating it from Mtb. This review will assist researchers interested in virulence-associated secretion in Mabs by providing the knowledge base and framework for their studies.
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Affiliation(s)
- Michal Bar-Oz
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Michal Meir
- The Ruth Rappaport Children’s Hospital, Rambam Medical Center, Haifa, Israel
| | - Daniel Barkan
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Daniel Barkan,
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18
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Griego A, Douché T, Gianetto QG, Matondo M, Manina G. RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness. iScience 2022; 25:104233. [PMID: 35521527 PMCID: PMC9062218 DOI: 10.1016/j.isci.2022.104233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 12/26/2022] Open
Abstract
RNA turnover is a primary source of gene expression variation, in turn promoting cellular adaptation. Mycobacteria leverage reversible mRNA stabilization to endure hostile conditions. Although RNase E is essential for RNA turnover in several species, its role in mycobacterial single-cell physiology and functional phenotypic diversification remains unexplored. Here, by integrating live-single-cell and quantitative-mass-spectrometry approaches, we show that RNase E forms dynamic foci, which are associated with cellular homeostasis and fate, and we discover a versatile molecular interactome. We show a likely interaction between RNase E and the nucleoid-associated protein HupB, which is particularly pronounced during drug treatment and infection, where phenotypic diversity increases. Disruption of RNase E expression affects HupB levels, impairing Mycobacterium tuberculosis growth homeostasis during treatment, intracellular replication, and host spread. Our work lays the foundation for targeting the RNase E and its partner HupB, aiming to undermine M. tuberculosis cellular balance, diversification capacity, and persistence. Single mycobacterial cells exhibit phenotypic variation in RNase E expression RNase E is implicated in the maintenance of mycobacterial cell growth homeostasis RNase E and HupB show a functional interplay in single mycobacterial cells RNase E-HupB disruption impairs Mycobacterium tuberculosis fate under drug and in macrophages
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19
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Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival. mBio 2022; 13:e0383621. [PMID: 35471080 PMCID: PMC9239209 DOI: 10.1128/mbio.03836-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis encodes ~200 transcription factors that modulate gene expression under different microenvironments in the host. Even though high-throughput chromatin immunoprecipitation sequencing and transcriptome sequencing (RNA-seq) studies have identified the regulatory network for ~80% of transcription factors, many transcription factors remain uncharacterized. EmbR is one such transcription factor whose in vivo regulon and biological function are yet to be elucidated. Previous in vitro studies suggested that phosphorylation of EmbR by PknH upregulates the embCAB operon. Using a gene replacement mutant of embR, we investigated its role in modulating cellular morphology, antibiotic resistance, and survival in the host. Contrary to the prevailing hypothesis, under normal growth conditions, EmbR is neither phosphorylated nor impacted by ethambutol resistance through the regulation of the embCAB operon. The embR deletion mutant displayed attenuated M. tuberculosis survival in vivo. RNA-seq analysis suggested that EmbR regulates operons involved in the secretion pathway, lipid metabolism, virulence, and hypoxia, including well-known hypoxia-inducible genes devS and hspX. Lipidome analysis revealed that EmbR modulates levels of all lysophospholipids, several phospholipids, and M. tuberculosis-specific lipids, which is more pronounced under hypoxic conditions. We found that the EmbR mutant is hypersusceptible to hypoxic stress, and RNA sequencing performed under hypoxic conditions indicated that EmbR majorly regulates genes involved in response to acidic pH, hypoxia, and fatty acid metabolism. We observed condition-specific phosphorylation of EmbR, which contributes to EmbR-mediated transcription of several essential genes, ensuring enhanced survival. Collectively, the study establishes EmbR as a key modulator of hypoxic response that facilitates mycobacterial survival in the host.
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20
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Baindara P, Agrawal S, Franco OL. Host-directed therapies for malaria and tuberculosis: common infection strategies and repurposed drugs. Expert Rev Anti Infect Ther 2022; 20:849-869. [DOI: 10.1080/14787210.2022.2044794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Piyush Baindara
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Missouri, Columbia, MO, USA
| | - Sonali Agrawal
- Immunology Division, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - O. L. Franco
- Proteomics Analysis and Biochemical Center, Catholic University of Brasilia, Brasilia, Brazil; S-Inova Biotech, Catholic University Dom Bosco, Campo Grande, MS, Brazil
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21
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Implementation of System Pharmacology and Molecular Docking Approaches to Explore Active Compounds and Mechanism of Ocimum Sanctum against Tuberculosis. Processes (Basel) 2022. [DOI: 10.3390/pr10020298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Worldwide, Tuberculosis (TB) is caused by Mycobacterium tuberculosis bacteria. Ocimum sanctum, commonly known as holy basil (Tulsi), is an herbaceous perennial that belongs to the family Lamiaceae and is considered one of the most important sources of medicine and drugs for the treatment of various diseases. The presented study aims to discover the potential phenomenon of Ocimum sanctum in the medicament of tuberculosis using a network pharmacology approach. Active ingredients of Ocimum sanctum were fetched through two different databases and from literature review and then targets of these compounds were harvested by SwissTargetPrediction. Potential targets of TB were downloaded from GeneCards and DisGNet databases. After screening of mutual targets, enrichment analysis through DAVID was performed. Protein–protein interaction was performed using the String database and visualized by Cytoscape. Then the target-compound-pathway network was constructed with Cytoscape. In the end, molecular docking was performed to get the potential active ingredients against tuberculosis. Eight active ingredients with 776 potential therapeutic targets were obtained from O. sanctum, 632 intersected targets from two databases were found in TB, 72 common potential targets were found from TB and O. sanctum. The topological analysis exposes those ten targets that formed the core PPI network. Furthermore, molecular docking analysis reveals that active compounds have the greater binding ability with the potential target to suppress TB.
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22
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Yamsani N, Sundararajan R. Design, Molecular Docking, Synthesis, Characterization and Biological Activities of Novel Thiazole Derivatives. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220105151308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aim:
The study aims to design & synthesize novel thiazole derivatives as potent antitubercular agents with minimal side effects.
Background:
The emergence and rapid spread of multi-drug resistant infectious microbial flora embracing a variety of bacterial as well as mycobacterium strains are causing a threat to public health worldwide.
Objective:
Owing to the importance, we designed compounds with thiazole functionality coupled with Schiff base and thiosemicarbazide, predicted the molecular properties and antitubercular potency of designed compounds by the in-silico method, and synthesized fifteen novel thiazole analogs, characterized and tested in vivo antitubercular, antibacterial and antioxidant potencies.
Methods:
Molinspiration online tool was used to predict the molecular properties and molecular docking was used to predict the antitubercular potency. FT-IR, 1H-NMR, 13C-NMR, Mass spectroscopy and bases of elemental analysis are employed to confirm the structure of compounds. 10-Fold serial dilution method, agar streak dilution test and DPPH radical scavenging methods are used to estimate antitubercular, antibacterial and antioxidant potency of title analogs, respectively.
Results:
Multi-step synthesis was used to synthesize a variety of novel thiazole derivatives coupled with Schiff base and thiosemicarbazide. Synthesized title compounds displayed a varying degree of antitubercular, antibacterial and antioxidant activities (mild to good). The title compounds possessing deactivating group exhibited superior activities than activating group, while unsubstituted analogs displayed intermediate activities. In addition, para-substituted analogs showed slightly higher activity than the corresponding meta substituted analogs.
Conclusion:
Among fifteen tested title compounds, the potent compound of this series was found to be 1-(4-nitrobenzylidene)-4-(4-(4-methoxyphenyl)thiazol-2-yl)thiosemicarbazide (BTS14), which might be extended as a novel class of antitubercular and antibacterial agents.
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Affiliation(s)
- Neeharika Yamsani
- Department of Pharmaceutical Chemistry, GITAM Institute of Pharmacy, GITAM (Deemed to be University), Gandhi Nagar, Rushikonda, Visakhapatnam-530 045, Andhra Pradesh, India
| | - Raja Sundararajan
- Department of Pharmaceutical Chemistry, GITAM Institute of Pharmacy, GITAM (Deemed to be University), Gandhi Nagar, Rushikonda, Visakhapatnam-530 045, Andhra Pradesh, India
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23
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Phosphoproteomics of Mycobacterium-host interaction and inspirations for novel measures against tuberculosis. Cell Signal 2022; 91:110238. [PMID: 34986388 DOI: 10.1016/j.cellsig.2021.110238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/19/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (Mtb) remains a tremendous global public health concern. Deciphering the biology of the pathogen and its interaction with host can inspire new measures against tuberculosis. Phosphorylation plays versatile and important role in the pathogen and host physiology, such as virulence, signaling and immune response. Proteome-wide phosphorylation of Mtb and its infected host cells, namely phosphoproteome, can inform the post-translational modification of the interaction network between the pathogen and the host, key targets for novel antibiotics. We summarized the phosphoproteome of Mtb, as well as the host, focusing on potential application for new measures against tuberculosis.
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24
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Burastero O, Niebling S, Defelipe LA, Günther C, Struve A, Garcia Alai MM. eSPC: an online data-analysis platform for molecular biophysics. Acta Crystallogr D Struct Biol 2021; 77:1241-1250. [PMID: 34605428 PMCID: PMC8489228 DOI: 10.1107/s2059798321008998] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
All biological processes rely on the formation of protein-ligand, protein-peptide and protein-protein complexes. Studying the affinity, kinetics and thermodynamics of binding between these pairs is critical for understanding basic cellular mechanisms. Many different technologies have been designed for probing interactions between biomolecules, each based on measuring different signals (fluorescence, heat, thermophoresis, scattering and interference, among others). Evaluation of the data from binding experiments and their fitting is an essential step towards the quantification of binding affinities. Here, user-friendly online tools to analyze biophysical data from steady-state fluorescence spectroscopy, microscale thermophoresis and differential scanning fluorimetry experiments are presented. The modules of the data-analysis platform (https://spc.embl-hamburg.de/) contain classical thermodynamic models and clear user guidelines for the determination of equilibrium dissociation constants (Kd) and thermal unfolding parameters such as melting temperatures (Tm).
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Affiliation(s)
- Osvaldo Burastero
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina
- IQUIBICEN–UBA/CONICET, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina
| | - Stephan Niebling
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lucas A. Defelipe
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Günther
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Angelica Struve
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maria M. Garcia Alai
- European Molecular Biology Laboratory, EMBL Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology, Notkestrasse 85, 22607 Hamburg, Germany
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25
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Rastogi S, Ellinwood S, Augenstreich J, Mayer-Barber KD, Briken V. Mycobacterium tuberculosis inhibits the NLRP3 inflammasome activation via its phosphokinase PknF. PLoS Pathog 2021; 17:e1009712. [PMID: 34324582 PMCID: PMC8321130 DOI: 10.1371/journal.ppat.1009712] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved to evade host innate immunity by interfering with macrophage functions. Interleukin-1β (IL-1β) is secreted by macrophages after the activation of the inflammasome complex and is crucial for host defense against Mtb infections. We have previously shown that Mtb is able to inhibit activation of the AIM2 inflammasome and subsequent pyroptosis. Here we show that Mtb is also able to inhibit host cell NLRP3 inflammasome activation and pyroptosis. We identified the serine/threonine kinase PknF as one protein of Mtb involved in the NLRP3 inflammasome inhibition, since the pknF deletion mutant of Mtb induces increased production of IL-1β in bone marrow-derived macrophages (BMDMs). The increased production of IL-1β was dependent on NLRP3, the adaptor protein ASC and the protease caspase-1, as revealed by studies performed in gene-deficient BMDMs. Additionally, infection of BMDMs with the pknF deletion mutant resulted in increased pyroptosis, while the IL-6 production remained unchanged compared to Mtb-infected cells, suggesting that the mutant did not affect the priming step of inflammasome activation. In contrast, the activation step was affected since potassium efflux, chloride efflux and the generation of reactive oxygen species played a significant role in inflammasome activation and subsequent pyroptosis mediated by the Mtb pknF mutant strain. In conclusion, we reveal here that the serine/threonine kinase PknF of Mtb plays an important role in innate immune evasion through inhibition of the NLRP3 inflammasome. Mycobacterium tuberculosis (Mtb) infections are causing millions of deaths per year and the pathogen is highly adapted to its human host. Host cell phagocytes take up Mtb but the bacterium is capable of manipulating the host cell to enhance its own survival. In the current study we discover a novel pathway of host cell manipulation and innate immune evasion by Mtb. We show that the activation of a host cell defense complex, the inflammasome, is limited after Mtb infection. Most importantly, we identify a bacterial protein, PknF, that is involved in inflammasome inhibition.
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Affiliation(s)
- Shivangi Rastogi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Sarah Ellinwood
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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26
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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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27
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Ge P, Lei Z, Yu Y, Lu Z, Qiang L, Chai Q, Zhang Y, Zhao D, Li B, Pang Y, Liu CH, Wang J. M. tuberculosis PknG manipulates host autophagy flux to promote pathogen intracellular survival. Autophagy 2021; 18:576-594. [PMID: 34092182 DOI: 10.1080/15548627.2021.1938912] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The eukaryotic-type protein kinase G (PknG), one of the eleven eukaryotic type serine-threonine protein kinase (STPK) in Mycobacterium tuberculosis (Mtb), is involved in mycobacterial survival within macrophages, presumably by suppressing phagosome and autophagosome maturation, which makes PknG an attractive drug target. However, the exact mechanism by which PknG inhibits pathogen clearance during mycobacterial infection remains largely unknown. Here, we show that PknG promotes macroautophagy/autophagy induction but inhibits autophagosome maturation, causing an overall effect of blocked autophagy flux and enhanced pathogen intracellular survival. PknG prevents the activation of AKT (AKT serine/threonine kinase) via competitively binding to its pleckstrin homology (PH) domain, leading to autophagy induction. Remarkably, PknG could also inhibit autophagosome maturation to block autophagy flux via targeting host small GTPase RAB14. Specifically, PknG directly interacts with RAB14 to block RAB14-GTP hydrolysis. Furthermore, PknG phosphorylates TBC1D4/AS160 (TBC1 domain family member 4) to suppress its GTPase-activating protein (GAP) activity toward RAB14. In macrophages and in vivo, PknG promotes Mtb intracellular survival through blocking autophagy flux, which is dependent on RAB14. Taken together, our data unveil a dual-functional bacterial effector that tightly regulates host autophagy flux to benefit pathogen intracellular survival.Abbreviations: AKT: AKT serine/threonine kinase; ATG5: autophagy related 5; BMDMs: bone marrow-derived macrophages; DTT: dithiothreitol; FBS: fetal calf serum; GAP: GTPase-activating protein; MOI: multiplicity of infection; Mtb: Mycobacterium tuberculosis; MTOR: mechanistic target of rapamycin kinase; OADC: oleic acid-albumin-dextrose-catalase; PC, phosphatidylcholine; PH: pleckstrin homology; PI3K: phosphoinositide 3-kinase; PknG: protein kinase G; PtdIns(3,4,5)P3: phosphatidylinositol(3,4,5)-trisphosphate; SQSTM1: sequestosome 1; STPK: serine-threonine protein kinase; TB: tuberculosis; TBC1D4: TBC1 domain family member 4; TPR: tetratricopeptide repeat; ULK1: unc-51 like autophagy activating kinase 1; WT: wild-type.
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Affiliation(s)
- Pupu Ge
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Zehui Lei
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Yu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Lihua Qiang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qiyao Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Dongdong Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bingxi Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Yu Pang
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
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28
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Wang J, Ge P, Lei Z, Lu Z, Qiang L, Chai Q, Zhang Y, Zhao D, Li B, Su J, Peng R, Pang Y, Shi Y, Zhang Y, Gao GF, Qiu XB, Liu CH. Mycobacterium tuberculosis protein kinase G acts as an unusual ubiquitinating enzyme to impair host immunity. EMBO Rep 2021; 22:e52175. [PMID: 33938130 DOI: 10.15252/embr.202052175] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
Upon Mycobacterium tuberculosis (Mtb) infection, protein kinase G (PknG), a eukaryotic-type serine-threonine protein kinase (STPK), is secreted into host macrophages to promote intracellular survival of the pathogen. However, the mechanisms underlying this PknG-host interaction remain unclear. Here, we demonstrate that PknG serves both as a ubiquitin-activating enzyme (E1) and a ubiquitin ligase (E3) to trigger the ubiquitination and degradation of tumor necrosis factor receptor-associated factor 2 (TRAF2) and TGF-β-activated kinase 1 (TAK1), thereby inhibiting the activation of NF-κB signaling and host innate responses. PknG promotes the attachment of ubiquitin (Ub) to the ubiquitin-conjugating enzyme (E2) UbcH7 via an isopeptide bond (UbcH7 K82-Ub), rather than the usual C86-Ub thiol-ester bond. PknG induces the discharge of Ub from UbcH7 by acting as an isopeptidase, before attaching Ub to its substrates. These results demonstrate that PknG acts as an unusual ubiquitinating enzyme to remove key components of the innate immunity system, thus providing a potential target for tuberculosis treatment.
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Affiliation(s)
- Jing Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Pupu Ge
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Zehui Lei
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Lihua Qiang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qiyao Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Dongdong Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bingxi Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Su
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Yu Pang
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Bo Qiu
- Ministry of Education Key Laboratory of Cell Proliferation and Regulation Biology, Department of Cell Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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29
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Sharma A, De Rosa M, Singla N, Singh G, Barnwal RP, Pandey A. Tuberculosis: An Overview of the Immunogenic Response, Disease Progression, and Medicinal Chemistry Efforts in the Last Decade toward the Development of Potential Drugs for Extensively Drug-Resistant Tuberculosis Strains. J Med Chem 2021; 64:4359-4395. [PMID: 33826327 DOI: 10.1021/acs.jmedchem.0c01833] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis (TB) is a slow growing, potentially debilitating disease that has plagued humanity for centuries and has claimed numerous lives across the globe. Concerted efforts by researchers have culminated in the development of various strategies to combat this malady. This review aims to raise awareness of the rapidly increasing incidences of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis, highlighting the significant modifications that were introduced in the TB treatment regimen over the past decade. A description of the role of pathogen-host immune mechanisms together with strategies for prevention of the disease is discussed. The struggle to develop novel drug therapies has continued in an effort to reduce the treatment duration, improve patient compliance and outcomes, and circumvent TB resistance mechanisms. Herein, we give an overview of the extensive medicinal chemistry efforts made during the past decade toward the discovery of new chemotypes, which are potentially active against TB-resistant strains.
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Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India.,UIPS, Panjab University, Chandigarh 160014, India
| | - Maria De Rosa
- Drug Discovery Unit, Ri.MED Foundation, Palermo 90133, Italy
| | - Neha Singla
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- UIPS, Panjab University, Chandigarh 160014, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
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30
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Abundant Monovalent Ions as Environmental Signposts for Pathogens during Host Colonization. Infect Immun 2021; 89:IAI.00641-20. [PMID: 33526568 DOI: 10.1128/iai.00641-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Host colonization by a pathogen requires proper sensing and response to local environmental cues, to ensure adaptation and continued survival within the host. The ionic milieu represents a critical potential source of environmental cues, and indeed, there has been extensive study of the interplay between host and pathogen in the context of metals such as iron, zinc, and manganese, vital ions that are actively sequestered by the host. The inherent non-uniformity of the ionic milieu also extends, however, to "abundant" ions such as chloride and potassium, whose concentrations vary greatly between tissue and cellular locations, and with the immune response. Despite this, the concept of abundant ions as environmental cues and key players in host-pathogen interactions is only just emerging. Focusing on chloride and potassium, this review brings together studies across multiple bacterial and parasitic species that have begun to define both how these abundant ions are exploited as cues during host infection, and how they can be actively manipulated by pathogens during host colonization. The close links between ion homeostasis and sensing/response to different ionic signals, and the importance of studying pathogen response to cues in combination, are also discussed, while considering the fundamental insight still to be uncovered from further studies in this nascent area of inquiry.
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31
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Oh S, Trifonov L, Yadav VD, Barry CE, Boshoff HI. Tuberculosis Drug Discovery: A Decade of Hit Assessment for Defined Targets. Front Cell Infect Microbiol 2021; 11:611304. [PMID: 33791235 PMCID: PMC8005628 DOI: 10.3389/fcimb.2021.611304] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/20/2022] Open
Abstract
More than two decades have elapsed since the publication of the first genome sequence of Mycobacterium tuberculosis (Mtb) which, shortly thereafter, enabled methods to determine gene essentiality in the pathogen. Despite this, target-based approaches have not yielded drugs that have progressed to clinical testing. Whole-cell screening followed by elucidation of mechanism of action has to date been the most fruitful approach to progressing inhibitors into the tuberculosis drug discovery pipeline although target-based approaches are gaining momentum. This review discusses scaffolds that have been identified over the last decade from screens of small molecule libraries against Mtb or defined targets where mechanism of action investigation has defined target-hit couples and structure-activity relationship studies have described the pharmacophore.
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Affiliation(s)
- Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Lena Trifonov
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Veena D Yadav
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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32
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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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33
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Augenstreich J, Briken V. Host Cell Targets of Released Lipid and Secreted Protein Effectors of Mycobacterium tuberculosis. Front Cell Infect Microbiol 2020; 10:595029. [PMID: 33194845 PMCID: PMC7644814 DOI: 10.3389/fcimb.2020.595029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is a very successful pathogen, strictly adapted to humans and the cause of tuberculosis. Its success is associated with its ability to inhibit host cell intrinsic immune responses by using an arsenal of virulence factors of different nature. It has evolved to synthesize a series of complex lipids which form an outer membrane and may also be released to enter host cell membranes. In addition, secreted protein effectors of Mtb are entering the host cell cytosol to interact with host cell proteins. We briefly discuss the current model, involving the ESX-1 type seven secretion system and the Mtb lipid phthiocerol dimycoserosate (PDIM), of how Mtb creates pores in the phagosomal membrane to allow Mtb proteins to access to the host cell cytosol. We provide an exhaustive list of Mtb secreted proteins that have effector functions. They modify (mostly inhibit but sometimes activate) host cell pathways such as: phagosome maturation, cell death, cytokine response, xenophagy, reactive oxygen species (ROS) response via NADPH oxidase 2 (NOX2), nitric oxide (NO) response via NO Synthase 2 (NOS2) and antigen presentation via MHC class I and class II molecules. We discuss the host cell targets for each lipid and protein effector and the importance of the Mtb effector for virulence of the bacterium.
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Affiliation(s)
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
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34
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Stokas H, Rhodes HL, Purdy GE. Modulation of the M. tuberculosis cell envelope between replicating and non-replicating persistent bacteria. Tuberculosis (Edinb) 2020; 125:102007. [PMID: 33035766 DOI: 10.1016/j.tube.2020.102007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022]
Abstract
The success of Mycobacterium tuberculosis as a human pathogen depends on the bacterium's ability to persist in a quiescent form in oxygen and nutrient-poor host environments. In vitro studies have demonstrated that these restricting environments induce a shift from bacterial replication to non-replicating persistence (NRP). Entry into NRP involves changes in bacterial metabolism and remodeling of the cell envelope. Findings consistent with the phenotypes observed in vitro have been observed in patient and animal model samples. This review focuses on the cell envelope differences seen between replicating and NRP M. tuberculosis and summarizes the ways in which serine/threonine protein kinases (STPKs) may mediate this process.
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Affiliation(s)
- Haley Stokas
- Oregon Health & Science University, Department of Molecular Microbiology & Immunology, Portland, OR, 97239, United States
| | - Heather L Rhodes
- Oregon Health & Science University, Department of Molecular Microbiology & Immunology, Portland, OR, 97239, United States
| | - Georgiana E Purdy
- Oregon Health & Science University, Department of Molecular Microbiology & Immunology, Portland, OR, 97239, United States.
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35
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Olotu FA, Soliman ME. Probing the Highly Disparate Dual Inhibitory Mechanisms of Novel Quinazoline Derivatives against Mycobacterium tuberculosis Protein Kinases A and B. Molecules 2020; 25:E4247. [PMID: 32947886 PMCID: PMC7571077 DOI: 10.3390/molecules25184247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) serine/threonine (Ser/Thr) Protein kinases A (PknA) and B (PknB) have been identified as highly attractive targets for overcoming drug resistant tuberculosis. A recent lead series optimization study yielded compound 33 which exhibited potencies ~1000 times higher than compound 57. This huge discrepancy left us curious to investigate the mechanistic 'dual' (in)activities of the compound using computational methods, as carried out in this study. Findings revealed that 33 stabilized the PknA and B conformations and reduced their structural activities relative to 57. Optimal stability of 33 in the hydrophobic pockets further induced systemic alterations at the P-loops, catalytic loops, helix Cs and DFG motifs of PknA and B. Comparatively, 57 was more surface-bound with highly unstable motions. Furthermore, 33 demonstrated similar binding patterns in PknA and B, involving conserved residues of their binding pockets. Both π and hydrogen interactions played crucial roles in the binding of 33, which altogether culminated in high ΔGs for both proteins. On the contrary, the binding of 57 was characterized by unfavorable interactions with possible repulsive effects on its optimal dual binding to both proteins, as evidenced by the relatively lowered ΔGs. These findings would significantly contribute to the rational structure-based design of novel and highly selective dual inhibitors of Mtb PknA and B.
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Affiliation(s)
| | - Mahmoud E. Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa;
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36
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Chai Q, Wang L, Liu CH, Ge B. New insights into the evasion of host innate immunity by Mycobacterium tuberculosis. Cell Mol Immunol 2020; 17:901-913. [PMID: 32728204 PMCID: PMC7608469 DOI: 10.1038/s41423-020-0502-z] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/22/2020] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an extremely successful intracellular pathogen that causes tuberculosis (TB), which remains the leading infectious cause of human death. The early interactions between Mtb and the host innate immune system largely determine the establishment of TB infection and disease development. Upon infection, host cells detect Mtb through a set of innate immune receptors and launch a range of cellular innate immune events. However, these innate defense mechanisms are extensively modulated by Mtb to avoid host immune clearance. In this review, we describe the emerging role of cytosolic nucleic acid-sensing pathways at the host-Mtb interface and summarize recently revealed mechanisms by which Mtb circumvents host cellular innate immune strategies such as membrane trafficking and integrity, cell death and autophagy. In addition, we discuss the newly elucidated strategies by which Mtb manipulates the host molecular regulatory machinery of innate immunity, including the intranuclear regulatory machinery, the ubiquitin system, and cellular intrinsic immune components. A better understanding of innate immune evasion mechanisms adopted by Mtb will provide new insights into TB pathogenesis and contribute to the development of more effective TB vaccines and therapies.
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Affiliation(s)
- Qiyao Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 100101, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, 101408, Beijing, China
| | - Lin Wang
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 100101, Beijing, China. .,Savaid Medical School, University of Chinese Academy of Sciences, 101408, Beijing, China.
| | - Baoxue Ge
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, China.
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37
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Structure-Based Drug Design for Tuberculosis: Challenges Still Ahead. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-based and computer-aided drug design approaches are commonly considered to have been successful in the fields of cancer and antiviral drug discovery but not as much for antibacterial drug development. The search for novel anti-tuberculosis agents is indeed an emblematic example of this trend. Although huge efforts, by consortiums and groups worldwide, dramatically increased the structural coverage of the Mycobacterium tuberculosis proteome, the vast majority of candidate drugs included in clinical trials during the last decade were issued from phenotypic screenings on whole mycobacterial cells. We developed here three selected case studies, i.e., the serine/threonine (Ser/Thr) kinases—protein kinase (Pkn) B and PknG, considered as very promising targets for a long time, and the DNA gyrase of M. tuberculosis, a well-known, pharmacologically validated target. We illustrated some of the challenges that rational, target-based drug discovery programs in tuberculosis (TB) still have to face, and, finally, discussed the perspectives opened by the recent, methodological developments in structural biology and integrative techniques.
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38
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Characterization of a toxin-antitoxin system in Mycobacterium tuberculosis suggests neutralization by phosphorylation as the antitoxicity mechanism. Commun Biol 2020; 3:216. [PMID: 32382148 PMCID: PMC7205606 DOI: 10.1038/s42003-020-0941-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/10/2020] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) encodes an exceptionally large number of toxin-antitoxin (TA) systems, supporting the hypothesis that TA systems are involved in pathogenesis. We characterized the putative Mtb Rv1044-Rv1045 TA locus structurally and functionally, demonstrating that it constitutes a bona fide TA system but adopts a previously unobserved antitoxicity mechanism involving phosphorylation of the toxin. While Rv1045 encodes the guanylyltransferase TglT functioning as a toxin, Rv1044 encodes the novel atypical serine protein kinase TakA, which specifically phosphorylates the cognate toxin at residue S78, thereby neutralizing its toxicity. In contrast to previous predictions, we found that Rv1044-Rv1045 does not belong to the type IV TA family because TglT and TakA interact with each other as substrate and kinase, suggesting an unusual type of TA system. Protein homology analysis suggests that other COG5340-DUF1814 protein pairs, two highly associated but uncharacterized protein families widespread in prokaryotes, might share this unusual antitoxicity mechanism. Xia Yu et al. report the characterization of a toxin-antitoxin system with an unusual mechanism in Mycobacterium tuberculosis. They find that the antitoxin locus Rv1044 encodes an atypical serine protein kinase that phosphorylates the toxin to neutralize toxicity.
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39
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Zeng J, Platig J, Cheng TY, Ahmed S, Skaf Y, Potluri LP, Schwartz D, Steen H, Moody DB, Husson RN. Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility. PLoS Pathog 2020; 16:e1008452. [PMID: 32255801 PMCID: PMC7164672 DOI: 10.1371/journal.ppat.1008452] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/17/2020] [Accepted: 03/03/2020] [Indexed: 01/28/2023] Open
Abstract
The Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB are essential for growth and have been proposed as possible drug targets. We used a titratable conditional depletion system to investigate the functions of these kinases. Depletion of PknA or PknB or both kinases resulted in growth arrest, shortening of cells, and time-dependent loss of acid-fast staining with a concomitant decrease in mycolate synthesis and accumulation of trehalose monomycolate. Depletion of PknA and/or PknB resulted in markedly increased susceptibility to β-lactam antibiotics, and to the key tuberculosis drug rifampin. Phosphoproteomic analysis showed extensive changes in protein phosphorylation in response to PknA depletion and comparatively fewer changes with PknB depletion. These results identify candidate substrates of each kinase and suggest specific and coordinate roles for PknA and PknB in regulating multiple essential physiologies. These findings support these kinases as targets for new antituberculosis drugs and provide a valuable resource for targeted investigation of mechanisms by which protein phosphorylation regulates pathways required for growth and virulence in M. tuberculosis.
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Affiliation(s)
- Jumei Zeng
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - John Platig
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Brigham & Women’s Hospital, Harvard Medical School, Boston MA, United States of America
| | - Saima Ahmed
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Yara Skaf
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States of America
| | - Lakshmi-Prasad Potluri
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Daniel Schwartz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States of America
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - D. Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Brigham & Women’s Hospital, Harvard Medical School, Boston MA, United States of America
| | - Robert N. Husson
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
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40
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Intelligent Mechanisms of Macrophage Apoptosis Subversion by Mycobacterium. Pathogens 2020; 9:pathogens9030218. [PMID: 32188164 PMCID: PMC7157668 DOI: 10.3390/pathogens9030218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/12/2020] [Accepted: 03/15/2020] [Indexed: 02/07/2023] Open
Abstract
Macrophages are one of the first innate defense barriers and play an indispensable role in communication between innate and adaptive immune responses, leading to restricted Mycobacterium tuberculosis (Mtb) infection. The macrophages can undergo programmed cell death (apoptosis), which is a crucial step to limit the intracellular growth of bacilli by liberating them into extracellular milieu in the form of apoptotic bodies. These bodies can be taken up by the macrophages for the further degradation of bacilli or by the dendritic cells, thereby leading to the activation of T lymphocytes. However, Mtb has the ability to interplay with complex signaling networks to subvert macrophage apoptosis. Here, we describe the intelligent strategies of Mtb inhibition of macrophages apoptosis. This review provides a platform for the future study of unrevealed Mtb anti-apoptotic mechanisms and the design of therapeutic interventions.
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41
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Maslov DA, Shur KV, Vatlin AA, Danilenko VN. MmpS5-MmpL5 Transporters Provide Mycobacterium smegmatis Resistance to imidazo[1,2- b][1,2,4,5]tetrazines. Pathogens 2020; 9:E166. [PMID: 32121069 PMCID: PMC7157563 DOI: 10.3390/pathogens9030166] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
The emergence and spread of drug-resistant Mycobacterium tuberculosis strains (including MDR, XDR, and TDR) force scientists worldwide to search for new anti-tuberculosis drugs. We have previously reported a number of imidazo[1,2-b][1,2,4,5]tetrazines - putative inhibitors of mycobacterial eukaryotic-type serine-threonine protein-kinases, active against M. tuberculosis. Whole genomic sequences of spontaneous drug-resistant M. smegmatis mutants revealed four genes possibly involved in imidazo[1,2-b][1,2,4,5]tetrazines resistance; however, the exact mechanism of resistance remain unknown. We used different approaches (construction of targeted mutants, overexpression of the wild-type (w.t.) and mutant genes, and gene-expression studies) to assess the role of the previously identified mutations. We show that mutations in MSMEG_1380 gene lead to overexpression of the mmpS5-mmpL5 operon in M. smegmatis, thus providing resistance to imidazo[1,2-b][1,2,4,5]tetrazines by increased efflux through the MmpS5-MmpL5 system, similarly to the mechanisms of resistance described for M. tuberculosis and M. abscessus. Mycobacterial MmpS5-MmpL5 transporters should be considered as an MDR-efflux system and they should be taken into account at early stages of anti-tuberculosis drug development.
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Affiliation(s)
- Dmitry A. Maslov
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia; (K.V.S.); (A.A.V.); (V.N.D.)
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42
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Baros SS, Blackburn JM, Soares NC. Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases. Mol Cell Proteomics 2020; 19:233-244. [PMID: 31839597 PMCID: PMC7000118 DOI: 10.1074/mcp.r119.001668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Mycobacterial Ser/Thr protein kinases (STPKs) play a critical role in signal transduction pathways that ultimately determine mycobacterial growth and metabolic adaptation. Identification of key physiological substrates of these protein kinases is, therefore, crucial to better understand how Ser/Thr phosphorylation contributes to mycobacterial environmental adaptation, including response to stress, cell division, and host-pathogen interactions. Various substrate detection methods have been employed with limited success, with direct targets of STPKs remaining elusive. Recently developed mass spectrometry (MS)-based phosphoproteomic approaches have expanded the list of potential STPK substrate identifications, yet further investigation is required to define the most functionally significant phosphosites and their physiological importance. Prior to the application of MS workflows, for instance, GarA was the only known and validated physiological substrate for protein kinase G (PknG) from pathogenic mycobacteria. A subsequent list of at least 28 candidate PknG substrates has since been reported with the use of MS-based analyses. Herein, we integrate and critically review MS-generated datasets available on novel STPK substrates and report new functional and subcellular localization enrichment analyses on novel candidate protein kinase A (PknA), protein kinase B (PknB) and PknG substrates to deduce the possible physiological roles of these kinases. In addition, we assess substrate specificity patterns across different mycobacterial STPKs by analyzing reported sets of phosphopeptides, in order to determine whether novel motifs or consensus regions exist for mycobacterial Ser/Thr phosphorylation sites. This review focuses on MS-based techniques employed for STPK substrate identification in mycobacteria, while highlighting the advantages and challenges of the various applications.
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Affiliation(s)
- Seanantha S Baros
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa; Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.
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43
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Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA. Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members. Sci Rep 2019; 9:19259. [PMID: 31848383 PMCID: PMC6917791 DOI: 10.1038/s41598-019-55464-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 11/09/2022] Open
Abstract
Nontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern “omics” approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, MmucT, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.
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Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Malavika Ramesh
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden.
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44
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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: 162] [Impact Index Per Article: 32.4] [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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45
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Qasaymeh RM, Rotondo D, Oosthuizen CB, Lall N, Seidel V. Predictive Binding Affinity of Plant-Derived Natural Products Towards the Protein Kinase G Enzyme of Mycobacterium tuberculosis ( MtPknG). PLANTS 2019; 8:plants8110477. [PMID: 31698813 PMCID: PMC6918344 DOI: 10.3390/plants8110477] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a growing public health concern worldwide, especially with the emerging challenge of drug resistance to the current drugs. Efforts to discover and develop novel, more effective, and safer anti-TB drugs are urgently needed. Products from natural sources, such as medicinal plants, have played an important role in traditional medicine and continue to provide some inspiring templates for the design of new drugs. Protein kinase G, produced by M. tuberculosis (MtPKnG), is a serine/threonine kinase, that has been reported to prevent phagosome-lysosome fusion and help prolong M. tuberculosis survival within the host’s macrophages. Here, we used an in silico, target-based approach (docking) to predict the interactions between MtPknG and 84 chemical constituents from two medicinal plants (Pelargonium reniforme and Pelargonium sidoides) that have a well-documented historical use as natural remedies for TB. Docking scores for ligands towards the target protein were calculated using AutoDock Vina as the predicted binding free energies. Ten flavonoids present in the aerial parts of P. reniforme and/or P.sidoides showed docking scores ranging from −11.1 to −13.2 kcal/mol. Upon calculation of all ligand efficiency indices, we observed that the (−ΔG/MW) ligand efficiency index for flavonoids (4), (5) and (7) was similar to the one obtained for the AX20017 control. When taking all compounds into account, we observed that the best (−ΔG/MW) efficiency index was obtained for coumaric acid, coumaraldehyde, p-hydroxyphenyl acetic acid and p-hydroxybenzyl alcohol. We found that methyl gallate and myricetin had ligand efficiency indices superior and equal to the AX20017 control efficiency, respectively. It remains to be seen if any of the compounds screened in this study exert an effect in M. tuberculosis-infected macrophages.
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Affiliation(s)
- Rana M. Qasaymeh
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (R.M.Q.); (D.R.)
| | - Dino Rotondo
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (R.M.Q.); (D.R.)
| | - Carel B. Oosthuizen
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
| | - Namrita Lall
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
- College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570015, India
| | - Veronique Seidel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (R.M.Q.); (D.R.)
- Correspondence: ; Tel.: +44-141-548-2751
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Veyron-Churlet R, Locht C. In Vivo Methods to Study Protein-Protein Interactions as Key Players in Mycobacterium Tuberculosis Virulence. Pathogens 2019; 8:pathogens8040173. [PMID: 31581602 PMCID: PMC6963305 DOI: 10.3390/pathogens8040173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Studies on protein–protein interactions (PPI) can be helpful for the annotation of unknown protein functions and for the understanding of cellular processes, such as specific virulence mechanisms developed by bacterial pathogens. In that context, several methods have been extensively used in recent years for the characterization of Mycobacterium tuberculosis PPI to further decipher tuberculosis (TB) pathogenesis. This review aims at compiling the most striking results based on in vivo methods (yeast and bacterial two-hybrid systems, protein complementation assays) for the specific study of PPI in mycobacteria. Moreover, newly developed methods, such as in-cell native mass resonance and proximity-dependent biotinylation identification, will have a deep impact on future mycobacterial research, as they are able to perform dynamic (transient interactions) and integrative (multiprotein complexes) analyses.
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Affiliation(s)
- Romain Veyron-Churlet
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Camille Locht
- Institut Pasteur de Lille, CHU Lille, CNRS, Inserm, Université de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G. Antimicrob Agents Chemother 2019; 63:AAC.00996-19. [PMID: 31285226 DOI: 10.1128/aac.00996-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/30/2019] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a global health concern, and this situation has further worsened due to the emergence of drug-resistant strains and the failure of BCG vaccine to impart protection. There is an imperative need to develop highly sensitive, specific diagnostic tools, novel therapeutics, and vaccines for the eradication of TB. In the present study, a chemical screen of a pharmacologically active compound library was performed to identify antimycobacterial compounds. The phenotypic screen identified a few novel small-molecule inhibitors, including NU-6027, a known CDK-2 inhibitor. We demonstrate that NU-6027 inhibits Mycobacterium bovis BCG growth in vitro and also displayed cross-reactivity with Mycobacterium tuberculosis protein kinase D (PknD) and protein kinase G (PknG). Comparative structural and sequence analysis along with docking simulation suggest that the unique binding site stereochemistry of PknG and PknD accommodates NU-6027 more favorably than other M. tuberculosis Ser/Thr protein kinases. Further, we also show that NU-6027 treatment induces the expression of proapoptotic genes in macrophages. Finally, we demonstrate that NU-6027 inhibits M. tuberculosis growth in both macrophage and mouse tissues. Taken together, these results indicate that NU-6027 can be optimized further for the development of antimycobacterial agents.
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Mori M, Sammartino JC, Costantino L, Gelain A, Meneghetti F, Villa S, Chiarelli LR. An Overview on the Potential Antimycobacterial Agents Targeting Serine/Threonine Protein Kinases from Mycobacterium tuberculosis. Curr Top Med Chem 2019; 19:646-661. [PMID: 30827246 DOI: 10.2174/1568026619666190227182701] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/27/2018] [Accepted: 10/09/2018] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), still remains an urgent global health issue, mainly due to the emergence of multi-drug resistant strains. Therefore, there is a pressing need to develop novel and more efficient drugs to control the disease. In this context, targeting the pathogen virulence factors, and particularly signal mechanisms, seems to be a promising approach. An important transmembrane signaling system in Mtb is represented by receptor-type Serine/ Threonine protein kinases (STPKs). Mtb has 11 different STPKs, two of them, PknA and PknB, are essential. By contrast PknG and PknH are involved in Mtb virulence and adaptation, and are fundamental for the pathogen growth in infection models. Therefore, STPKs represent a very interesting group of pharmacological targets in M. tuberculosis. In this work, the principal inhibitors of the mycobacterial STPKs will be presented and discussed. In particular, medicinal chemistry efforts have been focused on discovering new antimycobacterial compounds, targeting three of these kinases, namely PknA, PknB and PknG. Generally, the inhibitory effect on these enzymes do not correlate with a significant antimycobacterial action in whole-cell assays. However, compounds with activity in the low micromolar range have been obtained, demonstrating that targeting Mtb STPKs could be a new promising strategy for the development of drugs to treat TB infections.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - José Camilla Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Luca Costantino
- Dipartimento Scienze della Vita, Universita degli Studi di Modena e Reggio Emilia, via Campi 103, 41121 Modena, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Laurent Roberto Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100 Pavia, Italy
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49
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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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50
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Melly G, Purdy GE. MmpL Proteins in Physiology and Pathogenesis of M. tuberculosis. Microorganisms 2019; 7:microorganisms7030070. [PMID: 30841535 PMCID: PMC6463170 DOI: 10.3390/microorganisms7030070] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/14/2019] [Accepted: 03/03/2019] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains an important human pathogen. The Mtb cell envelope is a critical bacterial structure that contributes to virulence and pathogenicity. Mycobacterial membrane protein large (MmpL) proteins export bulky, hydrophobic substrates that are essential for the unique structure of the cell envelope and directly support the ability of Mtb to infect and persist in the host. This review summarizes recent investigations that have enabled insight into the molecular mechanisms underlying MmpL substrate export and the role that these substrates play during Mtb infection.
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Affiliation(s)
- Geoff Melly
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.
| | - Georgiana E Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.
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