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Santoshi M, Tare P, Nagaraja V. Nucleoid-associated proteins of mycobacteria come with a distinctive flavor. Mol Microbiol 2024. [PMID: 38922783 DOI: 10.1111/mmi.15287] [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: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
In every bacterium, nucleoid-associated proteins (NAPs) play crucial roles in chromosome organization, replication, repair, gene expression, and other DNA transactions. Their central role in controlling the chromatin dynamics and transcription has been well-appreciated in several well-studied organisms. Here, we review the diversity, distribution, structure, and function of NAPs from the genus Mycobacterium. We highlight the progress made in our understanding of the effects of these proteins on various processes and in responding to environmental stimuli and stress of mycobacteria in their free-living as well as during distinctive intracellular lifestyles. We project them as potential drug targets and discuss future studies to bridge the information gap with NAPs from well-studied systems.
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Affiliation(s)
- Meghna Santoshi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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2
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Anam ZE, Joshi N, Gupta S, Yadav P, Chaurasiya A, Kahlon AK, Kaushik S, Munde M, Ranganathan A, Singh S. A De novo Peptide from a High Throughput Peptide Library Blocks Myosin A -MTIP Complex Formation in Plasmodium falciparum. Int J Mol Sci 2020; 21:ijms21176158. [PMID: 32859024 PMCID: PMC7503848 DOI: 10.3390/ijms21176158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/09/2020] [Accepted: 05/15/2020] [Indexed: 01/09/2023] Open
Abstract
Apicomplexan parasites, through their motor machinery, produce the required propulsive force critical for host cell-entry. The conserved components of this so-called glideosome machinery are myosin A and myosin A Tail Interacting Protein (MTIP). MTIP tethers myosin A to the inner membrane complex of the parasite through 20 amino acid-long C-terminal end of myosin A that makes direct contacts with MTIP, allowing the invasion of Plasmodium falciparum in erythrocytes. Here, we discovered through screening a peptide library, a de-novo peptide ZA1 that binds the myosin A tail domain. We demonstrated that ZA1 bound strongly to myosin A tail and was able to disrupt the native myosin A tail MTIP complex both in vitro and in vivo. We then showed that a shortened peptide derived from ZA1, named ZA1S, was able to bind myosin A and block parasite invasion. Overall, our study identified a novel anti-malarial peptide that could be used in combination with other antimalarials for blocking the invasion of Plasmodium falciparum.
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Affiliation(s)
- Zill e Anam
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; (Z.e.A.); (P.Y.); (A.C.); (A.K.K.); (S.K.)
| | - Nishant Joshi
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh 201304, India;
| | - Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (S.G.); (M.M.)
| | - Preeti Yadav
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; (Z.e.A.); (P.Y.); (A.C.); (A.K.K.); (S.K.)
| | - Ayushi Chaurasiya
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; (Z.e.A.); (P.Y.); (A.C.); (A.K.K.); (S.K.)
| | - Amandeep Kaur Kahlon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; (Z.e.A.); (P.Y.); (A.C.); (A.K.K.); (S.K.)
| | - Shikha Kaushik
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; (Z.e.A.); (P.Y.); (A.C.); (A.K.K.); (S.K.)
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (S.G.); (M.M.)
| | - Anand Ranganathan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; (Z.e.A.); (P.Y.); (A.C.); (A.K.K.); (S.K.)
- Correspondence: (A.R.); (S.S.)
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; (Z.e.A.); (P.Y.); (A.C.); (A.K.K.); (S.K.)
- Correspondence: (A.R.); (S.S.)
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3
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Ozeki Y, Igarashi M, Doe M, Tamaru A, Kinoshita N, Ogura Y, Iwamoto T, Sawa R, Umekita M, Enany S, Nishiuchi Y, Osada-Oka M, Hayashi T, Niki M, Tateishi Y, Hatano M, Matsumoto S. A New Screen for Tuberculosis Drug Candidates Utilizing a Luciferase-Expressing Recombinant Mycobacterium bovis Bacillus Calmette-Guéren. PLoS One 2015; 10:e0141658. [PMID: 26571296 PMCID: PMC4646695 DOI: 10.1371/journal.pone.0141658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/12/2015] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) is a serious infectious disease caused by a bacterial pathogen. Mortality from tuberculosis was estimated at 1.5 million deaths worldwide in 2013. Development of new TB drugs is needed to not only to shorten the medication period but also to treat multi-drug resistant and extensively drug-resistant TB. Mycobacterium tuberculosis (Mtb) grows slowly and only multiplies once or twice per day. Therefore, conventional drug screening takes more than 3 weeks. Additionally, a biosafety level-3 (BSL-3) facility is required. Thus, we developed a new screening method to identify TB drug candidates by utilizing luciferase-expressing recombinant Mycobacterium bovis bacillus Calmette-Guéren (rBCG). Using this method, we identified several candidates in 4 days in a non-BSL-3 facility. We screened 10,080 individual crude extracts derived from Actinomyces and Streptomyces and identified 137 extracts which possessed suppressive activity to the luciferase of rBCG. Among them, 41 compounds inhibited the growth of both Mtb H37Rv and the extensively drug-resistant Mtb (XDR-Mtb) strains. We purified the active substance of the 1904–1 extract, which possessed strong activity toward rBCG, Mtb H37Rv, and XDR-Mtb but was harmless to the host eukaryotic cells. The MIC of this substance was 0.13 μg/ml, 0.5 μg/ml, and 2.0–7.5 μg/ml against rBCG, H37Rv, and 2 XDR-strains, respectively. Its efficacy was specific to acid-fast bacterium except for the Mycobacterium avium intracellular complex. Mass spectrometry and nuclear magnetic resonance analyses revealed that the active substance of 1904–1 was cyclomarin A. To confirm the mode of action of the 1904-1-derived compound, resistant BCG clones were used. Whole genome DNA sequence analysis showed that these clones contained a mutation in the clpc gene which encodes caseinolytic protein, an essential component of an ATP-dependent proteinase, and the likely target of the active substance of 1904–1. Our method provides a rapid and convenient screen to identify an anti-mycobacterial drug.
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Affiliation(s)
- Yuriko Ozeki
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- * E-mail:
| | - Masayuki Igarashi
- Department of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Matsumi Doe
- Graduate School of Sciences, Osaka City University, Osaka, Japan
| | - Aki Tamaru
- Bacteriology Division, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Naoko Kinoshita
- Department of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Yoshitoshi Ogura
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Tomotada Iwamoto
- Department of Microbiology, Kobe Institute of Health, Kobe, Japan
| | - Ryuichi Sawa
- Department of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Maya Umekita
- Department of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Shymaa Enany
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Mayuko Osada-Oka
- Food Hygiene and Environmental Health Division of Applied Life Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Tetsuya Hayashi
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Mamiko Niki
- Department of Bacteriology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaki Hatano
- Department of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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Host ICAMs play a role in cell invasion by Mycobacterium tuberculosis and Plasmodium falciparum. Nat Commun 2015; 6:6049. [PMID: 25586702 DOI: 10.1038/ncomms7049] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/05/2014] [Indexed: 12/19/2022] Open
Abstract
Intercellular adhesion molecules (ICAMs) belong to the immunoglobulin superfamily and participate in diverse cellular processes including host-pathogen interactions. ICAM-1 is expressed on various cell types including macrophages, whereas ICAM-4 is restricted to red blood cells. Here we report the identification of an 11-kDa synthetic protein, M5, that binds to human ICAM-1 and ICAM-4, as shown by in vitro interaction studies, surface plasmon resonance and immunolocalization. M5 greatly inhibits the invasion of macrophages and erythrocytes by Mycobacterium tuberculosis and Plasmodium falciparum, respectively. Pharmacological and siRNA-mediated inhibition of ICAM-1 expression also results in reduced M. tuberculosis invasion of macrophages. ICAM-4 binds to P. falciparum merozoites, and the addition of recombinant ICAM-4 to parasite cultures blocks invasion of erythrocytes by newly released merozoites. Our results indicate that ICAM-1 and ICAM-4 play roles in host cell invasion by M. tuberculosis and P. falciparum, respectively, either as receptors or as crucial accessory molecules.
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Samuchiwal SK, Tousif S, Singh DK, Kumar A, Ghosh A, Bhalla K, Prakash P, Kumar S, Trivedi AC, Bhattacharyya M, Das G, Ranganathan A. A novel peptide interferes with Mycobacterium tuberculosis virulence and survival. FEBS Open Bio 2014; 4:735-40. [PMID: 25349777 PMCID: PMC4208091 DOI: 10.1016/j.fob.2014.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/22/2014] [Accepted: 08/01/2014] [Indexed: 11/16/2022] Open
Abstract
The novel peptide SL3 is a strong binder of the virulence-determining protein ESAT-6. SL3 caused debilitating effects on mycobacterial growth and morphology. SL3 led to accelerated clearance of M.tb and lowered immune response in a pre-clinical mouse model. Microarray analysis of the mutant strain demonstrated a wide-scale transcriptional disruption caused by SL3 in M.tb.
Tuberculosis (TB) is a huge global burden, with new and resistant strains emerging at an alarming rate, necessitating an urgent need for a new class of drug candidates. Here, we report that SL3, a novel 33-amino acid peptide, causes debilitating effects on mycobacterial morphology. Treatment with SL3 drastically inhibits the growth of Mycobacterium tuberculosis in vitro as well as in a pre-clinical mouse model for M.tb infection. Microarray analysis of SL3-expressing strain demonstrates wide-scale transcriptional disruption in M.tb. We therefore believe that SL3 and similar peptides may herald a new approach towards discovering new molecules for TB therapy.
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Affiliation(s)
- Sachin Kumar Samuchiwal
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sultan Tousif
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India ; Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, India ; School of Laboratory Medicine, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Dhiraj Kumar Singh
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Arun Kumar
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anamika Ghosh
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kuhulika Bhalla
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prem Prakash
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sushil Kumar
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Maitree Bhattacharyya
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, India
| | - Gobardhan Das
- School of Laboratory Medicine, College of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Anand Ranganathan
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, India
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HupB, a nucleoid-associated protein of Mycobacterium tuberculosis, is modified by serine/threonine protein kinases in vivo. J Bacteriol 2014; 196:2646-57. [PMID: 24816602 DOI: 10.1128/jb.01625-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HU, a widely conserved bacterial histone-like protein, regulates many genes, including those involved in stress response and virulence. Whereas ample data are available on HU-DNA communication, the knowledge on how HU perceives a signal and transmit it to DNA remains limited. In this study, we identify HupB, the HU homolog of the human pathogen Mycobacterium tuberculosis, as a component of serine/threonine protein kinase (STPK) signaling. HupB is extracted in its native state from the exponentially growing cells of M. tuberculosis H37Ra and is shown to be phosphorylated on both serine and threonine residues. The STPKs capable of modifying HupB are determined in vitro and the residues modified by the STPKs are identified for both in vivo and the in vitro proteins through mass spectrometry. Of the identified phosphosites, Thr(65) and Thr(74) in the DNA-embracing β-strand of the N-terminal domain of HupB (N-HupB) are shown to be crucial for its interaction with DNA. In addition, Arg(55) is also identified as an important residue for N-HupB-DNA interaction. N-HupB is shown to have a diminished interaction with DNA after phosphorylation. Furthermore, hupB is shown to be maximally expressed during the stationary phase in M. tuberculosis H37Ra, while HupB kinases were found to be constitutively expressed (PknE and PknF) or most abundant during the exponential phase (PknB). In conclusion, HupB, a DNA-binding protein, with an ability to modulate chromatin structure is proposed to work in a growth-phase-dependent manner through its phosphorylation carried out by the mycobacterial STPKs.
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Expression of the ARPC4 subunit of human Arp2/3 severely affects mycobacterium tuberculosis growth and suppresses immunogenic response in murine macrophages. PLoS One 2013; 8:e69949. [PMID: 23894563 PMCID: PMC3718739 DOI: 10.1371/journal.pone.0069949] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/13/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The search for molecules against Mycobacterium tuberculosis is urgent. The mechanisms facilitating the intra-macrophage survival of Mycobacterium tuberculosis are as yet not entirely understood. However, there is evidence showing the involvement of host cell cytoskeleton in every step of establishment and persistence of mycobacterial infection. METHODOLOGY/PRINCIPAL FINDINGS Here we show that expression of ARPC4, a subunit of the Actin related protein 2/3 (Arp2/3) protein complex, severely affects the pathogen's growth. TEM studies display shedding of the mycobacterial outer-coat. Furthermore, in infected macrophages, mycobacteria expressing ARPC4 were cleared off at a much faster rate, and were unable to mount a pro-inflammatory cytokine response. The translocation of ARPC4-expressing mycobacteria to the lysosome of the infected macrophage was also impaired. Additionally, the ARPC4 subunit was shown to interact with Rv1626, an essential secretory mycobacterial protein. Real-time PCR analysis showed that upon expression of ARPC4 in mycobacteria, Rv1626 expression is downregulated as much as six-fold. Rv1626 was found to also interact with mammalian cytoskeleton protein, Arp2/3, and enhance the rate of actin polymerization. CONCLUSIONS/SIGNIFICANCE With crystal structures for Rv1626 and ARPC4 subunit already known, our finding lays out the effect of a novel molecule on mycobacteria, and represents a viable starting point for developing potent peptidomimetics.
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Kumar K, Tharad M, Ganapathy S, Ram G, Narayan A, Khan JA, Pratap R, Ghosh A, Samuchiwal SK, Kumar S, Bhalla K, Gupta D, Natarajan K, Singh Y, Ranganathan A. Phenylalanine-rich peptides potently bind ESAT6, a virulence determinant of Mycobacterium tuberculosis, and concurrently affect the pathogen's growth. PLoS One 2009; 4:e7615. [PMID: 19901982 PMCID: PMC2768790 DOI: 10.1371/journal.pone.0007615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 10/07/2009] [Indexed: 11/22/2022] Open
Abstract
Background The secretory proteins of Mycobacterium tuberculosis (M. tuberculosis) have been known to be involved in the virulence, pathogenesis as well as proliferation of the pathogen. Among this set, many proteins have been hypothesized to play a critical role at the genesis of the onset of infection, the primary site of which is invariably the human lung. Methodology/Principal Findings During our efforts to isolate potential binding partners of key secretory proteins of M. tuberculosis from a human lung protein library, we isolated peptides that strongly bound the virulence determinant protein Esat6. All peptides were less than fifty amino acids in length and the binding was confirmed by in vivo as well as in vitro studies. Curiously, we found all three binders to be unusually rich in phenylalanine, with one of the three peptides a short fragment of the human cytochrome c oxidase-3 (Cox-3). The most accessible of the three binders, named Hcl1, was shown also to bind to the Mycobacterium smegmatis (M. smegmatis) Esat6 homologue. Expression of hcl1 in M. tuberculosis H37Rv led to considerable reduction in growth. Microarray analysis showed that Hcl1 affects a host of key cellular pathways in M. tuberculosis. In a macrophage infection model, the sets expressing hcl1 were shown to clear off M. tuberculosis in much greater numbers than those infected macrophages wherein the M. tuberculosis was not expressing the peptide. Transmission electron microscopy studies of hcl1 expressing M. tuberculosis showed prominent expulsion of cellular material into the matrix, hinting at cell wall damage. Conclusions/Significance While the debilitating effects of Hcl1 on M. tuberculosis are unrelated and not because of the peptide's binding to Esat6–as the latter is not an essential protein of M. tuberculosis–nonetheless, further studies with this peptide, as well as a closer inspection of the microarray data may shed important light on the suitability of such small phenylalanine-rich peptides as potential drug-like molecules against this pathogen.
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Affiliation(s)
- Krishan Kumar
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Megha Tharad
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Swetha Ganapathy
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Geeta Ram
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Azeet Narayan
- Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Rana Pratap
- School of Life Sciences, Jawahar Lal Nehru University, New Delhi, India
| | - Anamika Ghosh
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sachin Kumar Samuchiwal
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sushil Kumar
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kuhulika Bhalla
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Deepti Gupta
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Krishnamurthy Natarajan
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Yogendra Singh
- Institute of Genomics and Integrative Biology, Delhi, India
| | - Anand Ranganathan
- Recombinant Gene Products Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- * E-mail:
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