1
|
Arora G, Tang X, Cui Y, Yang J, Chuang YM, Joshi J, Sajid A, Dong Y, Cresswell P, Dimopoulos G, Fikrig E. mosGILT controls innate immunity and germ cell development in Anopheles gambiae. BMC Genomics 2024; 25:42. [PMID: 38191283 PMCID: PMC10775533 DOI: 10.1186/s12864-023-09887-0] [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: 09/05/2023] [Accepted: 12/09/2023] [Indexed: 01/10/2024] Open
Abstract
Gene-edited mosquitoes lacking a gamma-interferon-inducible lysosomal thiol reductase-like protein, namely (mosGILTnull) have lower Plasmodium infection, which is linked to impaired ovarian development and immune activation. The transcriptome of mosGILTnull Anopheles gambiae was therefore compared to wild type (WT) mosquitoes by RNA-sequencing to delineate mosGILT-dependent pathways. Compared to WT mosquitoes, mosGILTnull A. gambiae demonstrated altered expression of genes related to oogenesis, 20-hydroxyecdysone synthesis, as well as immune-related genes. Serendipitously, the zero population growth gene, zpg, an essential regulator of germ cell development was found to be one of the most downregulated genes in mosGILTnull mosquitoes. These results provide a crucial missing link between two previous studies on the role of zpg and mosGILT in ovarian development. This study further demonstrates that mosGILT has the potential to serve as a target for the biological control of mosquito vectors and to influence the Plasmodium life cycle within the vector.
Collapse
Affiliation(s)
- Gunjan Arora
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, 06520, USA.
| | - Xiaotian Tang
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, 06520, USA
| | - Yingjun Cui
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, 06520, USA
| | - Jing Yang
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, 06520, USA
- Current Affiliation: Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, Gansu, 730030, China
| | - Yu-Min Chuang
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, 06520, USA
| | - Jayadev Joshi
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, 44195, USA
| | - Andaleeb Sajid
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, 06520, USA
| | - Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21205, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, 06510, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21205, USA
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, 06520, USA.
| |
Collapse
|
2
|
Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
Collapse
Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
| |
Collapse
|
3
|
Ouyang Y, Huang J, Wang Y, Tang F, Hu Z, Zeng Z, Zhang S. Bioinformatic analysis of RNA-seq data from TCGA database reveals prognostic significance of immune-related genes in colon cancer. Medicine (Baltimore) 2022; 101:e29962. [PMID: 35945793 PMCID: PMC9351934 DOI: 10.1097/md.0000000000029962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The tumor immune microenvironment is of crucial importance in cancer progression and anticancer immune responses. Thus, systematic exploration of the expression landscape and prognostic significance of immune-related genes (IRGs) to assist in the prognosis of colon cancer is valuable and significant. The transcriptomic data of 470 colon cancer patients were obtained from The Cancer Genome Atlas database and the differentially expressed genes were analyzed. After an intersection analysis, the hub IRGs were identified and a prognostic index was further developed using multivariable Cox analysis. In addition, the discriminatory ability and prognostic significance of the constructed model were validated and the characteristics of IRGs associated overall survival were analyzed to elucidate the underlying molecular mechanisms. A total of 465 differentially expressed IRGs and 130 survival-associated IRGs were screened. Then, 46 hub IRGs were identified by an intersection analysis. A regulatory network displayed that most of these genes were unfavorable for the prognosis of colon cancer and were regulated by transcription factors. After a least absolute shrinkage and selection operator regression analysis, 14 hub IRGs were ultimately chose to construct a prognostic index. The validation results illustrated that this model could act as an independent indicator to moderately separate colon cancer patients into low- and high-risk groups. This study ascertained the prognostic significance of IRGs in colon cancer and successfully constructed an IRG-based prognostic signature for clinical prediction. Our results provide promising insight for the exploration of diagnostic markers and immunotherapeutic targets in colon cancer.
Collapse
Affiliation(s)
- Yan Ouyang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province/Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Jiangtao Huang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province/Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Yun Wang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province/Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Fuzhou Tang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province/Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Zuquan Hu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province/Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of China, Guizhou Medical University, Guiyang, China
- *Correspondence: Zuquan Hu, Department of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou, China (e-mail: )
| | - Zhu Zeng
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province/Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Shichao Zhang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province/Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| |
Collapse
|
4
|
Sharma V, Joshi J, Yeh IJ, Doughman Y, Blankenberg D, Wald D, Montano MM. Re-Expression of ERα and AR in Receptor Negative Endocrine Cancers via GSK3 Inhibition. Front Oncol 2022; 12:824594. [PMID: 35402240 PMCID: PMC8988137 DOI: 10.3389/fonc.2022.824594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/28/2022] [Indexed: 01/04/2023] Open
Abstract
DNA methylation, catalyzed by DNA methyltransferase (DNMT), is a well-characterized epigenetic modification in cancer cells. In particular, promoter hypermethylation of AR and ESR1 results in loss of expression on Androgen Receptor (AR) and Estrogen Receptor (ER), respectively, and is associated with a hormone refractory state. We now report that Glycogen Synthase Kinase 3 (GSK3) phosphorylates DNMT1 at S714, which is localized to a 62 amino acid region referred to as auto-inhibitory linker, which functions to occlude the DNA from the active site of DNMT1 to prevent the methylation of unmethylated DNA. Molecular Dynamics simulation indicates that phosphorylation at S714 resulted in conformational rearrangement of the autoinhibitory domain that inactivated its ability to block the methylation of unmethylated DNA and resulted in enhanced DNA binding. Treatment with a novel and more selective inhibitor of GSK3 resulted in decreased methylation of the promoter region of genes encoding the Androgen Receptor (AR) and Estrogen Receptor alpha (ERa) and re-expression of the AR and ERa in AR negative prostate cancer and ER negative breast cancer cells, respectively. As a result, concurrent treatment with the GSK3 inhibitor resulted in responsiveness of AR negative prostate cancer and ER negative breast cancer cells to inhibitors of the AR or ER, respectively, in in vitro and in vivo experimental models.
Collapse
Affiliation(s)
- Vikas Sharma
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Jayadev Joshi
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH, United States
| | - I-Ju Yeh
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - YongQiu Doughman
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH, United States
| | - David Wald
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Monica M. Montano
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- *Correspondence: Monica M. Montano,
| |
Collapse
|
5
|
Gupta KR, Arora G, Mattoo A, Sajid A. Stringent Response in Mycobacteria: From Biology to Therapeutic Potential. Pathogens 2021; 10:pathogens10111417. [PMID: 34832573 PMCID: PMC8622095 DOI: 10.3390/pathogens10111417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 01/16/2023] Open
Abstract
Mycobacterium tuberculosis is a human pathogen that can thrive inside the host immune cells for several years and cause tuberculosis. This is due to the propensity of M. tuberculosis to synthesize a sturdy cell wall, shift metabolism and growth, secrete virulence factors to manipulate host immunity, and exhibit stringent response. These attributes help M. tuberculosis to manage the host response, and successfully establish and maintain an infection even under nutrient-deprived stress conditions for years. In this review, we will discuss the importance of mycobacterial stringent response under different stress conditions. The stringent response is mediated through small signaling molecules called alarmones “(pp)pGpp”. The synthesis and degradation of these alarmones in mycobacteria are mediated by Rel protein, which is both (p)ppGpp synthetase and hydrolase. Rel is important for all central dogma processes—DNA replication, transcription, and translation—in addition to regulating virulence, drug resistance, and biofilm formation. Rel also plays an important role in the latent infection of M. tuberculosis. Here, we have discussed the literature on alarmones and Rel proteins in mycobacteria and highlight that (p)ppGpp-analogs and Rel inhibitors could be designed and used as antimycobacterial compounds against M. tuberculosis and non-tuberculous mycobacterial infections.
Collapse
Affiliation(s)
| | - Gunjan Arora
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Abid Mattoo
- Pharmaceutical Development, Ultragenyx Gene Therapy, Woburn, MA 01801, USA;
| | - Andaleeb Sajid
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA;
- Correspondence: or
| |
Collapse
|
6
|
Arora G, Joshi J, Mandal RS, Shrivastava N, Virmani R, Sethi T. Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19. Pathogens 2021; 10:1048. [PMID: 34451513 PMCID: PMC8399076 DOI: 10.3390/pathogens10081048] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare.
Collapse
Affiliation(s)
- Gunjan Arora
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jayadev Joshi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA;
| | - Rahul Shubhra Mandal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Nitisha Shrivastava
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10461, USA;
| | - Richa Virmani
- Confo Therapeutics, Technologiepark 94, 9052 Ghent, Belgium;
| | - Tavpritesh Sethi
- Indraprastha Institute of Information Technology, New Delhi 110020, India;
| |
Collapse
|
7
|
Arora G, Joshi J, Mandal RS, Shrivastava N, Virmani R, Sethi T. Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19. Pathogens 2021; 10:1048. [PMID: 34451513 PMCID: PMC8399076 DOI: 10.3390/pathogens10081048,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare.
Collapse
Affiliation(s)
- Gunjan Arora
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: or
| | - Jayadev Joshi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA;
| | - Rahul Shubhra Mandal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Nitisha Shrivastava
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10461, USA;
| | - Richa Virmani
- Confo Therapeutics, Technologiepark 94, 9052 Ghent, Belgium;
| | - Tavpritesh Sethi
- Indraprastha Institute of Information Technology, New Delhi 110020, India;
| |
Collapse
|
8
|
Virmani R, Sajid A, Singhal A, Gaur M, Joshi J, Bothra A, Garg R, Misra R, Singh VP, Molle V, Goel AK, Singh A, Kalia VC, Lee JK, Hasija Y, Arora G, Singh Y. The Ser/Thr protein kinase PrkC imprints phenotypic memory in Bacillus anthracis spores by phosphorylating the glycolytic enzyme enolase. J Biol Chem 2019; 294:8930-8941. [PMID: 30952697 DOI: 10.1074/jbc.ra118.005424] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 02/18/2019] [Indexed: 01/05/2023] Open
Abstract
Bacillus anthracis is the causative agent of anthrax in humans, bovine, and other animals. B. anthracis pathogenesis requires differentiation of dormant spores into vegetative cells. The spores inherit cellular components as phenotypic memory from the parent cell, and this memory plays a critical role in facilitating the spores' revival. Because metabolism initiates at the beginning of spore germination, here we metabolically reprogrammed B. anthracis cells to understand the role of glycolytic enzymes in this process. We show that increased expression of enolase (Eno) in the sporulating mother cell decreases germination efficiency. Eno is phosphorylated by the conserved Ser/Thr protein kinase PrkC which decreases the catalytic activity of Eno. We found that phosphorylation also regulates Eno expression and localization, thereby controlling the overall spore germination process. Using MS analysis, we identified the sites of phosphorylation in Eno, and substitution(s) of selected phosphorylation sites helped establish the functional correlation between phosphorylation and Eno activity. We propose that PrkC-mediated regulation of Eno may help sporulating B. anthracis cells in adapting to nutrient deprivation. In summary, to the best of our knowledge, our study provides the first evidence that in sporulating B. anthracis, PrkC imprints phenotypic memory that facilitates the germination process.
Collapse
Affiliation(s)
- Richa Virmani
- From the Department of Zoology, University of Delhi, Delhi 110007, India.,Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India.,Delhi Technological University, Delhi 110042, India
| | - Andaleeb Sajid
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Anshika Singhal
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Mohita Gaur
- From the Department of Zoology, University of Delhi, Delhi 110007, India
| | - Jayadev Joshi
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Ankur Bothra
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Richa Garg
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Richa Misra
- From the Department of Zoology, University of Delhi, Delhi 110007, India.,Sri Venkateswara College, University of Delhi, Delhi 110021, India
| | - Vijay Pal Singh
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Virginie Molle
- Dynamique des Interactions Membranaires Normales et Pathologiques (DIMNP), CNRS, University of Montpellier, Montpellier 34000, France
| | - Ajay K Goel
- Defence Research and Development Establishment, Gwalior 474002, India
| | - Archana Singh
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Vipin C Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea, and
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea, and
| | - Yasha Hasija
- Delhi Technological University, Delhi 110042, India
| | - Gunjan Arora
- From the Department of Zoology, University of Delhi, Delhi 110007, India, .,Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20851
| | - Yogendra Singh
- From the Department of Zoology, University of Delhi, Delhi 110007, India, .,Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi 110007, India
| |
Collapse
|
9
|
Zhai W, Wu F, Zhang Y, Fu Y, Liu Z. The Immune Escape Mechanisms of Mycobacterium Tuberculosis. Int J Mol Sci 2019; 20:ijms20020340. [PMID: 30650615 PMCID: PMC6359177 DOI: 10.3390/ijms20020340] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 01/15/2023] Open
Abstract
Epidemiological data from the Center of Disease Control (CDC) and the World Health Organization (WHO) statistics in 2017 show that 10.0 million people around the world became sick with tuberculosis. Mycobacterium tuberculosis (MTB) is an intracellular parasite that mainly attacks macrophages and inhibits their apoptosis. It can become a long-term infection in humans, causing a series of pathological changes and clinical manifestations. In this review, we summarize innate immunity including the inhibition of antioxidants, the maturation and acidification of phagolysosomes and especially the apoptosis and autophagy of macrophages. Besides, we also elaborate on the adaptive immune response and the formation of granulomas. A thorough understanding of these escape mechanisms is of major importance for the prevention, diagnosis and treatment of tuberculosis.
Collapse
Affiliation(s)
- Weijie Zhai
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, China.
| | - Fengjuan Wu
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, China.
| | - Yiyuan Zhang
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, China.
| | - Yurong Fu
- Department of Medical Microbiology, Weifang Medical University, Weifang 261053, China.
| | - Zhijun Liu
- Department of Medical Microbiology, Weifang Medical University, Weifang 261053, China.
| |
Collapse
|
10
|
GroEL Mediates Folding of Bacillus anthracis Serine/Threonine Protein Kinase, PrkC. Indian J Microbiol 2018; 58:520-524. [PMID: 30262963 DOI: 10.1007/s12088-018-0744-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 10/16/2022] Open
Abstract
Bacillus anthracis causes anthrax in human and animals. Both, signaling system such as two component system and endogenous chaperone system such as GroEL-GroES help bacteria to cope with the environmental challenges. Such molecular chaperones are the stress induced proteins that help bacteria to override unfavorable conditions by their moonlighting functions. Previous reports showed that PrkC and PrpC, the Ser/Thr kinase-phosphatase pair in B. anthracis, control phosphorylation of GroEL and regulate biofilm formation. In this study, we show that GroEL is involved in the folding of PrkC to active form. The proteins (GroEL, PrkC and PrpC) were expressed and purified by affinity chromatography. Purified GroEL was used for refolding of denatured PrkC and PrpC and observed that GroEL refolds PrkC but not PrpC as measured by their enzymatic activity. We also observed that purification of GroEL with six histidine tag using Cobalt-Agarose resin yielded superior quality GroEL protein with negligible contamination of non-specific proteins. Thus, cobalt resin can be a better choice for purification of many histidine tagged proteins, where Ni-NTA does not work very well.
Collapse
|
11
|
Effect of Homocysteine on Biofilm Formation by Mycobacteria. Indian J Microbiol 2018; 58:287-293. [PMID: 30013272 DOI: 10.1007/s12088-018-0739-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/03/2018] [Indexed: 12/29/2022] Open
Abstract
Mycobacteria show peculiar aggregated outgrowth like biofilm on the surface of solid or liquid media. Biofilms harbor antibiotic resistant bacteria in a self-produced extracellular matrix that signifies the bacterial fate to sedentary existence. Despite years of research, very little is known about the mechanisms that contribute to biofilm formation. LuxS has been previously known to play a role in biofilm formation in Autoinducer-2 dependent manner. We here show the effect of LuxS product-homocysteine, on the biofilm forming ability of non-tuberculous mycobacteria, Mycobacterium smegmatis and Mycobacterium bovis BCG showing AI-2 independent phenotypic effect of LuxS. Exogenous supplementation of homocysteine in the culture media leads to aberrant cording, pellicle outgrowth, and biofilm formation. Thus, our study contributes to the better understanding of the mechanism of mycobacterial biofilm formation and sheds light on the role of LuxS product homocysteine. In addition, we highlight the contribution of activated methyl cycle in bacterial quorum sensing.
Collapse
|
12
|
Ser/Thr protein kinase PrkC-mediated regulation of GroEL is critical for biofilm formation in Bacillus anthracis. NPJ Biofilms Microbiomes 2017. [PMID: 28649408 PMCID: PMC5460178 DOI: 10.1038/s41522-017-0015-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PrkC is a conserved Ser/Thr protein kinase encoded in Bacillus anthracis genome. PrkC is shown to be important for B. anthracis pathogenesis, but little is known about its other functions and phosphorylated substrates. Systemic analyses indicate the compelling role of PrkC in phosphorylating multiple substrates, including the essential chaperone GroEL. Through mass spectrometry, we identified that PrkC phosphorylates GroEL on six threonine residues that are distributed in three canonical regions. Phosphorylation facilitates the oligomerization of GroEL to the physiologically active tetradecameric state and increases its affinity toward the co-chaperone GroES. Deletion of prkC in B. anthracis abrogates its ability to form biofilm. Overexpression of native GroEL recovers the biofilm-forming ability of prkC deletion strain. Similar overexpression of GroEL phosphorylation site mutants (Thr to Ala) does not augment biofilm formation. Further analyses indicate the phosphorylation of GroEL in diverse bacterial species. Thus, our results suggest that PrkC regulates biofilm formation by modulating the GroEL activity in a phosphorylation-dependent manner. The study deciphers the molecular signaling events that are important for biofilm formation in B. anthracis. An enzyme that adds phosphate groups to other proteins, PrkC, mediates molecular signaling events that allow anthrax bacteria to form biofilms. Bacillus anthracis is widely used as a model to explore the formation of biofilms that allows many bacterial infections to resist immune defenses. An international research team led by Yogendra Singh and Andaleeb Sajid at the CSIR-Institute of Genomics and Integrative Biology in Delhi, India, studied the bacterial protein kinase PrkC. The researchers found that PrkC phosphorylates a “chaperone” protein that assist the assembly and disassembly of other protein-based structures. This signaling protein and the chaperone help in biofilm formation. Establishing this link in the signaling chain leading to biofilms will guide future research to combat the role of biofilms in disease.
Collapse
|
13
|
Sajid A, Arora G, Singhal A, Kalia VC, Singh Y. Protein Phosphatases of Pathogenic Bacteria: Role in Physiology and Virulence. Annu Rev Microbiol 2015; 69:527-47. [DOI: 10.1146/annurev-micro-020415-111342] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andaleeb Sajid
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Gunjan Arora
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Anshika Singhal
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Vipin C. Kalia
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Yogendra Singh
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| |
Collapse
|
14
|
Singhal A, Arora G, Virmani R, Kundu P, Khanna T, Sajid A, Misra R, Joshi J, Yadav V, Samanta S, Saini N, Pandey AK, Visweswariah SS, Hentschker C, Becher D, Gerth U, Singh Y. Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase. J Biol Chem 2015; 290:26218-34. [PMID: 26350458 DOI: 10.1074/jbc.m115.687269] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 02/02/2023] Open
Abstract
Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.
Collapse
Affiliation(s)
- Anshika Singhal
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Gunjan Arora
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India, the Translational Health Science and Technology Institute, Faridabad 121001, India
| | - Richa Virmani
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Parijat Kundu
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Tanya Khanna
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Andaleeb Sajid
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Richa Misra
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Jayadev Joshi
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Vikas Yadav
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Sintu Samanta
- the Indian Institute of Science, Bangalore 560012, India, and
| | - Neeru Saini
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Amit K Pandey
- the Translational Health Science and Technology Institute, Faridabad 121001, India,
| | | | - Christian Hentschker
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Dörte Becher
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Ulf Gerth
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Yogendra Singh
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India,
| |
Collapse
|