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R. Ajay Kumar, PhD

Scientist E-II

+91-471-2529513

rakumar@rgcb.res.in

Ajay Portrait
Ajay Portrait

R. Ajay Kumar, PhD

Scientist E-II

+91-471-2529513

rakumar@rgcb.res.in

  • Profile

    • Ph.D Microbiology – 1992 (Madurai Kamaraj University, Madurai)
    • August-November, 2009: Visiting Scientist, Karolinska Institute, Stockholm and Swedish Institute for Infectious Disease Control (SMI), Solna, Sweden
    • 2002-2004: Visiting Scientist, University of Massachusetts Medical School, Worcester, MA, USA
    • 1995-1997: Postdoctoral, Sree Chitra Thirunal Institute for Medical Sciences and Technology, Thiruvananthapuram
    • 1992-1995: Postdoctoral, Indian Institute of Science, Bangalore
    • PhDs awarded: 2
    • Currently: 6
  • Research

    Mycobacterium tuberculosis-macrophage interactions

    M. tuberculosis (MTB) ) is a facultative intracellular pathogen that can reside within professional phagocytes such as macrophages and dendritic cells in the infected host. A number of virulence genes are known to be induced in intracellular bacteria at different stages following uptake by the host. Gene expression is altered in the host cells as well during infection. Our major interest is to understand how intracellular MTB regulates host gene expression. Chromatin modifications play a major role in the regulation of eukaryotic gene expression. Acetylation of histones is a major epigenetic modification and is maintained by two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs are generally associated with upregualtion of gene expression, and HDACs, with repression of gene expression. Intracellular bacteria can manipulate host defense gene expression by epigenetic modifications to facilitate infection and survival inside the host cell.
    Recently we have shown that Rv3423.1 of MTB is a histone acetyltransferase, secreted by intracellular bacteria, that directly enters the nucleus of macrophages and acetylates histone H3 at K9/K14 positions (Jose et al., 2015). Employing ChIP seq, we have identified some genes in the infected macrophages to whose promoters this HAT is recruited to upregulate their expression. However, the role of the products of these genes in infection or in the downstream events is not clear at present.
    In another study, we have observed that MTB infection causes significant upregulation of histone deacetylase 1 (HDAC1) in macrophages. Many host genes are known to be repressed during MTB infection. We have shown that some genes whose products play a key role in the initiation of Th1 responses following MTB infection are repressed by the recruitment of HDAC1 to their promoters. We demonstrated that HDAC1 hypoacetylates histone H3 at the promoter of IL-12B gene leading to the downregulation of its expression in macrophages infected with live, virulent MTB H37Rv, and not in those infected with MTB H37Ra or heat-killed MTB H37Rv (Chandran et al., 2015). Significantly our study showed that c-Jun is essential for HDAC1 expression, and is recruited to the promoter of HDAC1 gene only in macrophages infected with live MTB H37Rv. Currently our interest is in understanding how HDAC1 is recruited to the target promoters. Hopefully our studies will lead to the identification of novel targets in the host and the pathogen for therapeutic intervention to fight TB.

    Proteomics and lipidomics of M. tuberculosis during dormancy and reactivation

    MTB is capable of remaining in a state of dormancy in the infected host for a long time, leading to latent TB infection (LTBI). One of the reasons why TB still remains a major challenge is the ability of MTB to remain dormant in the body. The dormant bacilli are resistant to most of the anti-TB drugs, and becomes activated when the immune system of the body becomes weak. This is a major hindrance to TB control programmes. We carried out a comparative proteomic analysis to identify proteins that are differentially expressed during dormancy and reactivation of MTB. We made actively growing MTB dormant using Wayne's dormancy model, and developed a simple system to reactivate dormant bacteria. We extracted proteins at different stages of dormancy and reactivation, and carried out a label-free, one-dimensional LC-MS/MS analysis. Proteins were isolated from normoxic control, two phases of dormancy, and two phases of reactivation. One thousand, eight hundred and seventy one proteins (47% of the MTB proteome) were identified, and many of them were observed to be expressed differentially or uniquely during dormancy and reactivation. We analyzed various biological functions during these conditions. Fluctuations in the relative quantities of proteins involved in various metabolic processes such as energy metabolism, amino acid metabolism, lipid biosynthesis, lipid biodegradation, DNA replication, repair, transcription, protein synthesis etc. were observed during dormancy and reactivation (Gopinath et al., 2015). As we observed significantly low levels of proteins involved in the biosynthesis of mycolic acid and high levels of proteins associated with degradation of lipids during dormancy, we are currently investigating the changes in the lipidome of MTB during dormancy and reactivation. Also we have selected some transcriptional regulators that are uniquely expressed during reactivation for further study. Such proteins that are upregulated or uniquely expressed during reactivation from dormancy offer to be attractive drug targets to prevent reactivation of LTBI.

    Novel anti-TB molecules from Actinomycetes

    Despite the availability of BCG vaccine and effective anti-TB drugs, the incidence of TB has increased at an alarming rate in the past few decades. Currently BCG is the only approved vaccine against TB. However, it is found to be less effective in preventing the disease in adults, and the efficacy is relatively low in tropical countries. Long duration of treatment, and emergence of multidrug resistant (MDR), extensively drug-resistant (XDR) and recently of totally drug-resistant (TDR) strains of MTB render the current mode of treatment of TB very difficult, prohibitively expensive and often completely ineffective. The situation is made worse by the co-infection with HIV. This scenario calls for the development of novel and more effective anti-TB drugs at least until better vaccines or other forms of treatment are available. With financial support from OSDD/CSIR, we have screened hundreds of actinomycetes isolated from different parts of Kerala and Tamil Nadu for their inhibitory activity against MTB. We employ different chromatographic techniques to isolate molecules with inhibitory activity against MTB in vitro.

    Interested in a post-doctoral position?

    Please contact rakumar@rgcb.res.in

    Extramural grants

    1. Identification of transcriptional regulators expressed in Mycobacterium tuberculosis during reactivation from dormancy in vitro, and identification of their target sequences. (DBT, New Delhi, 2012-2015). Collaborators - Dr Abdul Jaleel and Dr Sathish Mundayoor (RGCB).
    2. Isolation and characterization of anti-mycobacterial molecules from Actinomycetes. (CSIR (OSDD), New Delhi, 2012-2015). Collaborator - Dr Sabu Thomas (RGCB).
  • Publications

    1. Gomez RL, Jose L, Ramachandran R, Raghunandanan S, Muralikrishnan B, Johnson JB, Krishnankutty SC, Mundayoor S and Kumar RA (2016). The multiple stress responsive transcriptional regulator Rv3334 of Mycobacterium tuberculosis is an autorepressor and a positive regulator of kstR. FEBS JDOI: 10.1111/febs.13791
    2. Dhanasooraj D, Kumar RA, Mundayoor S (2016). Subunit Protein Vaccine Delivery System for Tuberculosis Based on Hepatitis B Virus Core VLP (HBc-VLP) Particles. Methods Mol Biol. 2016;1404:377-92.
    3. Jose L, Ramachandran R, Bhagavat R, Gomez RL, Chandran A, Raghunandanan S, Omkumar RV, Chandra N, Mundayoor S, Kumar RA (2016). Hypothetical protein Rv3423.1 of Mycobacterium tuberculosis is a histone acetyltransferase. FEBS J. 283(2):265-81.
    4. Chandran A, Antony C, Jose L, Mundayoor S, Natarajan K, Kumar RA (2015). Mycobacterium tuberculosis Infection Induces HDAC1-Mediated Suppression of IL-12B Gene Expression in Macrophages. Front. Cell. Infect. Microbiol., http://dx.doi.org/10.3389/fcimb.2015.00090.
    5. Gopinath V, Raghunandanan S, Gomez RL, Jose L, Surendran A, Ramachandran R, Pushparajan AR, Mundayoor S, Jaleel A, Kumar RA (2015). Profiling the Proteome of Mycobacterium tuberculosis during Dormancy and Reactivation. Mol Cell Proteomics. 14(8):2160-2176.
    6. Augustine N, Goel AK, Sivakumar KC, Kumar RA, Thomas S (2014). Resveratrol - a potential inhibitor of biofilm formation in Vibrio cholerae. Phytomedicine. 2014 Feb 15;21(3):286-9.
    7. Dhanasooraj D, Kumar RA, Mundayoor S. Vaccine delivery system for tuberculosis based on nano-sized hepatitis B virus core protein particles. Int J Nanomedicine. 2013;8:835-43.
    8. Joseph BV, Soman S, Hill V, Kumar RA, Rastogi N, Mundayoor S (2013). Efficient discrimination by MIRU-VNTRs of Mycobacterium tuberculosis clinical isolates belonging to the predominant SIT11/EAI3-IND ancestral genotypic lineage in Kerala, India. Int J Mycobacteriol. 2(4):244-7.
    9. Joseph BV, Soman S, Radhakrishnan I, Hill V, Dhanasooraj D, Kumar RA, Rastogi N, Mundayoor S (2013). Molecular epidemiology of Mycobacterium tuberculosis isolates from Kerala, India using IS6110-RFLP, spoligotyping and MIRU-VNTRs. Infect Genet Evol. 16:157-64.
    10. Madhavilatha GK, Joseph BV, Paul LK, Kumar RA, Hariharan R, Mundayoor S (2012). Whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis from Kerala, South India. J Bacteriol. 194(16):4430. doi: 10.1128/JB.00453-12.
    11. Yamuna E, Kumar RA, Zeller M, Rajendra Prasad KJ (2012). Synthesis, antimicrobial, antimycobacterial and structure-activity relationship of substituted pyrazolo-, isoxazolo-, pyrimido- and mercaptopyrimidocyclohepta[b]indoles. Eur J Med Chem. 47(1):228-38.
    12. Joseph SV, Madhavilatha GK, Kumar RA, Mundayoor S (2012). Comparative analysis of mycobacterial truncated hemoglobin promoters and the groEL2 promoter in free-living and intracellular mycobacteria. Appl Environ Microbiol. 78(18):6499-506.
    13. Lakshmanan D, Werngren J, Jose L, Suja KP, Nair MS , Varma RL, Mundayoor S, Hoffner S, Kumar RA (2011). Ethyl p-methoxycinnamate isolated from a traditional anti-tuberculosis medicinal herb inhibits drug resistant strains of Mycobacterium tuberculosis in vitro. Fitoterapia 82: 757-761.
    14. James B, Viji S, Mathew S, Nair MS, Lakshmanan D, Kumar RA (2007). Synthesis of novel highly functionalized biologically active polycyclic caged amides. Tetrahedron Letters 48(35):6204-6208. 
    15. Kumar RA, Naidu SR, Wang X, Imbalzano AN, Androphy EJ (2007)  Interaction of papillomavirus E2 protein with the Brm chromatin remodeling complex leads to enhanced transcriptional activation. J Virol 81(5):2213-20.
    16. Kumar RA, Vaze MB, Chandra NR, Vijayan M, Muniyappa K (1996). Functional characterization of the precursor and spliced forms of RecA protein of Mycobacteriumtuberculosis. Biochemistry 35(6):1793-802.
    1. Streptomyces sp. OA161 16S ribosomal RNA gene, partial sequence. Accession number: KX364040.1
  • Team


    Roshna Lawrence Gomez, PhD Student

    Gene regulation in M. tuberculosis under stress

    To survive in stressful environments microorganisms must make appropriate adaptive responses which are reflected by changes in its transcriptional machinery. During infection, and intracellular residency, M. tuberculosis is exposed to different stress conditions as part of the host defence mechanisms that try to eliminate the bacterium. My work aims at the structural and functional characterization of a mycobacterial stress associated transcription factor that seems to play a role in the survival of the bacterium during dormancy.

    Roshna
    Roshna

    Roshna Lawrence Gomez, PhD Student

    Gene regulation in M. tuberculosis under stress

    To survive in stressful environments microorganisms must make appropriate adaptive responses which are reflected by changes in its transcriptional machinery. During infection, and intracellular residency, M. tuberculosis is exposed to different stress conditions as part of the host defence mechanisms that try to eliminate the bacterium. My work aims at the structural and functional characterization of a mycobacterial stress associated transcription factor that seems to play a role in the survival of the bacterium during dormancy.

    Ranjit Ramachandran, PhD Student

    Regulation of gene expression in macrophages during M. tuberculosis infection

    Histone modifications such as acetylation, methylation, phosphorylation etc. play a major role in the regulation of eukaryotic gene expression. I am interested in studying the histone acetylations in the host promoter regions during M. tuberculosis infection.

    Ranjit
    Ranjit

    Ranjit Ramachandran, PhD Student

    Regulation of gene expression in macrophages during M. tuberculosis infection

    Histone modifications such as acetylation, methylation, phosphorylation etc. play a major role in the regulation of eukaryotic gene expression. I am interested in studying the histone acetylations in the host promoter regions during M. tuberculosis infection.

    Sajith R, PhD Student

    Identification of transcriptional regulators expressed in M. tuberculosis during reactivation from dormancy

    In most cases infection with M. tuberculosis leads to asymptomatic latent tuberculosis. The bacilli remain dormant in structures called granuloma where they survive for long durations without actually causing any disease. However during immunosuppression (such as when co-infected with HIV) the dormant bacilli get reactivated and cause reactivation TB. Wayne’s model of dormancy is a well accepted system used to simulate dormancy in vitro. Using this model, I am interested in studying proteins that are uniquely expressed during dormancy and reactivation. We believe that the unique and physiologically important proteins that are overexpressed during dormancy and reactivation could be excellent drug targets to prevent reactivation TB.

    Sajith
    Sajith

    Sajith R, PhD Student

    Identification of transcriptional regulators expressed in M. tuberculosis during reactivation from dormancy

    In most cases infection with M. tuberculosis leads to asymptomatic latent tuberculosis. The bacilli remain dormant in structures called granuloma where they survive for long durations without actually causing any disease. However during immunosuppression (such as when co-infected with HIV) the dormant bacilli get reactivated and cause reactivation TB. Wayne’s model of dormancy is a well accepted system used to simulate dormancy in vitro. Using this model, I am interested in studying proteins that are uniquely expressed during dormancy and reactivation. We believe that the unique and physiologically important proteins that are overexpressed during dormancy and reactivation could be excellent drug targets to prevent reactivation TB.

    Akhil Raj P, PhD student

    Intracellular pathogens such as M. tuberculosis induce epigenetic changes that influence host cellular functions either to promote host defense or to support the survival and multiplication of the pathogen. For example, many host genes involved in immune responses are downregulated in TB patients. My interest is to identify and dissect the function of mycobacterial proteins that interact with host epigenetic factors leading to modulation of gene expression in human macrophages upon infection with M. tuberculosis.

    AKHIL RAJ P
    AKHIL RAJ P

    Akhil Raj P, PhD student

    Intracellular pathogens such as M. tuberculosis induce epigenetic changes that influence host cellular functions either to promote host defense or to support the survival and multiplication of the pathogen. For example, many host genes involved in immune responses are downregulated in TB patients. My interest is to identify and dissect the function of mycobacterial proteins that interact with host epigenetic factors leading to modulation of gene expression in human macrophages upon infection with M. tuberculosis.

    Balaji, PhD student

    Isolation and characterization of antimycobacterial molecules from Actinomycetes

    The first anti-TB antibiotic Streptomycin, discovered about seventy years ago, is still used as a first-line drug to treat TB. Existing first- and second-line drugs are ineffective against MDR/XDR/TDR forms of TB. The vaccine BCG is known to have its limitations in tropical countries and in preventing adult TB. Until more effective vaccines and other treatment modalities are available, drug therapy would be the main weapon to fight TB. My goal is to search for, isolate and test novel anti-mycobacterial molecules from Actinomycetes.

    Balaji
    Balaji

    Balaji, PhD student

    Isolation and characterization of antimycobacterial molecules from Actinomycetes

    The first anti-TB antibiotic Streptomycin, discovered about seventy years ago, is still used as a first-line drug to treat TB. Existing first- and second-line drugs are ineffective against MDR/XDR/TDR forms of TB. The vaccine BCG is known to have its limitations in tropical countries and in preventing adult TB. Until more effective vaccines and other treatment modalities are available, drug therapy would be the main weapon to fight TB. My goal is to search for, isolate and test novel anti-mycobacterial molecules from Actinomycetes.

    Aravind Madhavan, DBT Postdoctoral Fellow (2016)

    Identification and delineation of function of proteins that interact with HDAC1 in macrophages infected with M.tuberculosis.

    Recent studies reveal that intracellular pathogens target the host chromatin and epigenetic regulators to suppress host immune functions. My interest is to study the role of M. tuberculosis proteins that are involved in the modulation of HDAC1 expression and subsequent suppression of immune functions. Also I would like to understand how these proteins help HDAC1 to be recruited to the promoters of genes that are downregulated upon infection.

    Aravind
    Aravind

    Aravind Madhavan, DBT Postdoctoral Fellow (2016)

    Identification and delineation of function of proteins that interact with HDAC1 in macrophages infected with M.tuberculosis.

    Recent studies reveal that intracellular pathogens target the host chromatin and epigenetic regulators to suppress host immune functions. My interest is to study the role of M. tuberculosis proteins that are involved in the modulation of HDAC1 expression and subsequent suppression of immune functions. Also I would like to understand how these proteins help HDAC1 to be recruited to the promoters of genes that are downregulated upon infection.

    Jijimole G.R, PhD Student (2016)

    Characterization of transcriptional regulators expressed in M. tuberculosis during its reactivation from dormancy. 

    A previous study in our lab has identified a few transcriptional regulators that are specifically expressed during reactivation from dormancy. I will be focusing my study on characterising some of the key regulators, identifying their target genes to understand their physiological role during reactivation from dormancy. 

    Jijimol
    Jijimol

    Jijimole G.R, PhD Student (2016)

    Characterization of transcriptional regulators expressed in M. tuberculosis during its reactivation from dormancy. 

    A previous study in our lab has identified a few transcriptional regulators that are specifically expressed during reactivation from dormancy. I will be focusing my study on characterising some of the key regulators, identifying their target genes to understand their physiological role during reactivation from dormancy. 

    Leena Rajkumar Desai, PhD student (2016)

    Characterisation of acetyltransferases in M. tuberculosis.

    The lab has recently identified a histone acetyletransferase in M. tuberculosis. Bioinformatic analysis revealed that there are more acetyltrasferases in this pathogen. I am interested in characterising these proteins, identifying their substrates and understanding their physiological significance during infection.

    Leena Rajkumar Desai
    Leena Rajkumar Desai

    Leena Rajkumar Desai. PhD student (2016)

    Characterisation of acetyltransferases in M. tuberculosis.

    The lab has recently identified a histone acetyletransferase in M. tuberculosis . Bioinformatic analysis revealed that there are more acetyltrasferases in this pathogen. I am interested in characterising these proteins, identifying their substrates and understanding their physiological significance during infection.

    Annapoorna K, PhD student (S.M.)

    Annapoorna K, PhD student (S.M.)

    Retnakumar R J, SRF, ICMR (S.M.)

    Even though Bacillus Calmette-Guerin (BCG) is the only vaccine licensed for use against tuberculosis, its efficacy to provide protection from the disease is highly variable due to various host and bacterial factors. This is due to the inability of the bacterium to evoke adequate immune response. We hypothesize that BCG dampens the immune response of by downregulating the macrophage surface receptors. I am interested in determining Mycobacterium bovis BCG genes that alter the expression of macrophage surface receptors.

    Retnakumar
    Retnakumar

    Retnakumar R J, SRF, ICMR (S.M.)

    Even though Bacillus Calmette-Guerin (BCG) is the only vaccine licensed for use against tuberculosis, its efficacy to provide protection from the disease is highly variable due to various host and bacterial factors. This is due to the inability of the bacterium to evoke adequate immune response. We hypothesize that BCG dampens the immune response of by downregulating the macrophage surface receptors. I am interested in determining Mycobacterium bovis BCG genes that alter the expression of macrophage surface receptors.

  • Alumni


    Aneesh C (2011-2016)

    Title of the thesis: Epigenetic modifications associated with Mycobacterium tuberculosis infection in macrophages.
    Currently a postdoctoral fellow at the Faculty of Health and Medical Sciences, University of Surrey, UK.

    Aneesh
    Aneesh

    Aneesh C (2011-2016)

    Title of the thesis: Epigenetic modifications associated with Mycobacterium tuberculosis infection in macrophages.
    Currently a postdoctoral fellow at the Faculty of Health and Medical Sciences, University of Surrey, UK.

    Dr. Leny Jose (2007-2014)

    Title of the thesis: Isolation, identification and functional characterization of a Mycobacterium tuberculosis protein with histone acetyltransferase activity.
    Currently a postdoctoral fellow at the Department of Dermatology, Indiana University School of Medicine, Indianapolis, USA.

    Leny
    Leny

    Dr. Leny Jose (2007-2014)

    Title of the thesis: Isolation, identification and functional characterization of a Mycobacterium tuberculosis protein with histone acetyltransferase activity.
    Currently a postdoctoral fellow at the Department of Dermatology, Indiana University School of Medicine, Indianapolis, USA.

    Dr. Divya Lakhsmanan (2005-2011)

    Title of the thesis - Effect and Mechanism of Action of Natural Compounds on the Growth of Mycobacterium tuberculosis in vitro.
    Currently a postdoctoral fellow at the Department of Biochemistry and Molecular Biology, Pondicherry University, Kalapet,
    Puducherry - 605 014.

    Dr. Divya Lakhsmanan (2005-2011)

    Title of the thesis - Effect and Mechanism of Action of Natural Compounds on the Growth of Mycobacterium tuberculosis in vitro.
    Currently a postdoctoral fellow at the Department of Biochemistry and Molecular Biology, Pondicherry University, Kalapet,
    Puducherry - 605 014.

    Dr. Vipin Gopinath

    Research Associate (March 2013 - Oct 2015, DBT Project)
    Currently a postdoctoral fellow at Biochemistry and Molecular Biology Department, Louisiana State University Health Science Centre, Shreveport, LA 71130,USA.

    Vipin
    Vipin

    Dr. Vipin Gopinath

    Research Associate (March 2013 - Oct 2015, DBT Project)
    Currently a postdoctoral fellow at Biochemistry and Molecular Biology Department, Louisiana State University Health Science Centre, Shreveport, LA 71130,USA.

    Dr. Asha Bharathan

    Research Associate (2009-2011, CSIR-funded project)
    Currently Assistant Professor at NSS College
    Pandalam.

    AshaBharathan
    AshaBharathan

    Dr. Asha Bharathan

    Research Associate (2009-2011, CSIR-funded project)
    Currently Assistant Professor at NSS College
    Pandalam.

    Dr. Suja K P

    Research Associate (2009-2010, DBT-funded project)
    Currently Scientist at HLL Lifecare Limited, Trivandrum.

    suja kp
    suja kp

    Dr. Suja K P

    Research Associate (2009-2010, DBT-funded project)
    Currently Scientist at HLL Lifecare Limited, Trivandrum.

    Dr. Sindhu R

    Postdoctotral Fellow (2006-2008, KSCSTE-funded poject)
    Currently Contract Scientist at NIIST
    Trivandrum

    Dr. Sindhu R

    Postdoctotral Fellow (2006-2008, KSCSTE-funded poject)
    Currently Contract Scientist at NIIST
    Trivandrum