Laboratory of Genomic Instability and Diseases

Scholastic record: (https://scholar.google.co.in/citations?user=fef1gNUAAAAJ&hl=en)

• Scientist-F: (Since Jan. 2021) Institute of Life Sciences, Bhubaneswar, Odisha.
• Scientist-E: (Jan. 2016-Dec. 2020) Institute of Life Sciences, Bhubaneswar, Odisha.
• Scientist-D: (June 2011- Dec. 2015) Institute of Life Sciences, Bhubaneswar, Odisha.
• Research Scientist: (2009-2011) Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas.
• Post-Doctoral Fellow: (2003-2009) Sealy center for Molecular Sciences, UTMB, Galveston, Texas.
• Ph. D. (1997-2003) Dept. of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

Patent filed/granted:

        (1) PCT/IN2021/051070

        (2) Indian Patent Application No.: 202231013971 (CNA94)

        (3) Indian Patent Application No.: 202231043203 (CNA25)

Fellowships and Awards

• Stood first class first in B.Sc.
• Stood first class first in M. Sc.
• Awarded the fellowship of the Indian Institute of Science, Bangalore, India.
• Senior research fellowship from CSIR (Council of scientific and Industrial Research), Govt. of India.
• Attended “Young Investigator Meeting-2010, Kolkata”.

Journals Academic Editor

Genomic Instability and Diseases

Research Summary:

Replication of DNA strands during each cell division is a prerequisite and critical for proper functioning of any genome. It necessitates faithful duplication of the genetic content and ensures genome stability by preventing faulty DNA synthesis that could render spontaneous mutation, genome rearrangement, and DNA breaks. DNA polymerases (Pol) are the enzymes required for DNA synthesis virtually in all the DNA transaction pathways, and any abnormalities in Pol function has been shown to be associated with cell death, tumorigenesis, resistance to chemotherapeutics, and development of an array of complex diseases in humans. In microorganisms, genome instability is also linked to virulence and multidrug resistance. We focus on the mechanism of eukaryotic DNA replication and use both yeasts and human cells as our model systems. Genetic and biochemical studies in S. cerevisiae have indicated that the highly accurate and processive genomic DNA replication is carried out by the coordinated action of Polα-primase, Polδ and Polε (Biochemical Society Trans. 2020 and Current Genetics 2020). PCNA (the eukaryotic clamp loader) is an essential homotrimeric ring protein plays a critical role in orchestrating the assembly of replisome complex,  recruiting DNA polymerases, and factors involved in DNA damage response, chromatin assembly and remodeling, and cell cycle control. Each of the PCNA-binding partners harbors a dedicated region called PCNA-interacting protein (PIP) motif. PIPs in all three subunits contribute to processive DNA synthesis by Polδ, and mutational inactivation of all three PIP motifs abrogates its ability to synthesize DNA with PCNA (PNAS, 2011). In human, unlike in yeast, Polδ is a pentameric holoenzyme consisting of p125, p50, p68, and dimeric p12 subunits. An amino-terminal dimerization and a carboxyl terminal PIP motifs in p12 have been mapped, and dimerization of p12 is critical for its interaction with PCNA (LSA, 2019). Although PCNA is a structurally conserved protein, complementation analyses suggest it to be highly species specific (BMC-Micro. 2015 and FEBS letters 2021). By using structural and mutational analyses, we find that the IDCL and J loop structures of PCNA are unique and responsible for cross-species incompatibility, therefore these regions may be targeted to develop species-specific inhibitors (JBC(a)-2021). DNA replication does not proceed smoothly, as it encounters both DNA lesions and non-B form of DNA structures that must be by-passed to prevent collapsing of replication fork. Trans-lesion DNA synthesis (TLS) polymerases are highly sophisticated enzymes can bypass certain lesions in DNA. DNA polymerase eta (Polη) is one such enzymes required for efficient bypass of UV- induced cyclobutane pyrimidine dimers in the genome.  Additionally, Polη also possess non-TLS activities such as serum induced morphogenesis, amphotericin B drug resistance and virulence in pathogenic yeast Candida albicans (Molecular Micro.- 2018, Cellular Micro. 2019, and Current Genetics 2019). Further, we identify three distinct group of Polηs from species across kingdom based on their modes of PCNA interaction (JBC (b)-2021). Candida albicans survives as a commensal fungus in the gastrointestinal tract, and its excessive growth causing infections in immune-suppressed individuals is widely accepted. However, our recent data suggests a mutualism between the host and C. albicans. Dietary C. albicans does not cause any noticeable infections, rather it colonizes in the gut to modulate microbiome dynamics which in turn negates the high-fat diet induced uncontrolled body weight gain, metabolic hormonal imbalances, and inflammatory responses. Interestingly, adding C. albicans to a non-obesogenic diet stimulates the appetite regulated hormones and helped the mice gain healthy body weight (biorxiv-2022/M.Spectrum 2022). In its pathogenic state, C. albicans causes fatal systemic infections and are associated with a higher rate of morbidity and mortality, and represent major healthcare problems. Currently, chemotherapy is the sole available option for combating fungal diseases and no vaccine has been developed yet for human use (FCIM-2022). We have generated several genetically engineered knockout strains of C. albicans and also identified few of those strains to be attenuated. Two of such isolates (CNA94-Indian Patent Application No.: 202231013971 and CNA24- Indian Patent Application No.: 202231043203) have also been patented to explore further as a whole cell vaccine against fungal and other cross-species infections.

Genomic Instability and Disease

Peer reviewed publications:

1. N. Acharya, L. Prakash, and S. Prakash (2022) Yeast 9-1-1 complex acts as a sliding clamp for DNA synthesis by DNA polymerase ε. Journal of Biological Chemistry, Nov 13., doi.org/10.1016/j.jbc.2022.102727.
2. D. Peroumal, S. R. Sahu, P. Kumari, B. G. Utkalaja, and Narottam Acharya (2022) Commensal fungus Candida albicans maintains a long-term mutualistic relationship with the host to modulate gut microbiota and metabolism. Microbiology Spectrum, doi: 10.1128/spectrum.02462-22. 
3. S. R. Sahu, S. Bose, M. Singh, P. Kumari, A. Dutta, B. G. Utkalaja, S. K. Patel, and Narottam Acharya (2022) Vaccines against Candidiasis: Status, Challenges and Emerging opportunity. Front. Cell. Infect. Microbiol., doi: 10.3389/fcimb.2022.1002406.
4. K. Manohar, P. Khandagale, S. K. Patel, J. K. Sahu, and Narottam Acharya (2021) The ubiquitin-binding domain of DNA polymerase eta directly binds to the DNA clamp PCNA and regulates translesion DNA synthesis. Journal of Biological Chemistry,Dec 17:101506. doi: 10.1016/j.jbc.2021.101506.
5. P. Kumari, R. Sundaram, K. Manohar, D. Vasudevan and Narottam Acharya (2021) Interdomain connecting loop and J loop structures determine cross-species compatibility of PCNA. Journal of Biological Chemistry, Jul;297(1):100911. doi: 10.1016/j.jbc.2021.100911.
6. R. Sundaram, K. Manohar, S. K. Patel, Narottam Acharya and Dileep Vasudevan (2021) Structural analyses of PCNA from the fungal pathogen Candida albicans. FEBS Letters, May;595(9):1328-1349. doi: 10.1002/1873-3468.
7. Narottam Acharya, S. K. Patel, S. R. Sahu, and P. Kumari (2020) “PIPs” in DNA polymerase – PCNA interaction affairs. Biochem. Soci. Trans. Nov 16:BST20200678. doi: 10.1042/BST20200678.
8. S. Bose, S. Aggarwal, D. V. Singh and Narottam Acharya (2020) Extracellular vesicles: An emerging platform in gram-positive bacteria. Microbial cell, Vol. 7, No. 12, pp. 312 – 322; doi: 10.15698/mic2020.12.737.
9. P. Khandagale, S. Thakur and Narottam Acharya (2020) Identification of PCNA interacting protein motifs in human DNA polymerase delta, Bioscience Reports, 40 (4). (doi.org/10.1042/BSR20200602)
10. Narottam Acharya, P. Khandagale, S. Thakur, J. K. Sahu and B. G. Utakalaja (2020) Quaternary structural diversity in Eukaryotic DNA Polymerases: Monomeric to Multimeric form. Current Genetics, Aug; 66 (4):635-655. doi: 10.1007/s00294-020-01071-1.
11. D. Peroumal, K. Manohar, S. K. Patel, P. Kumari, S. R. Sahu and Narottam Acharya (2019) Virulence and pathogenicity of a Candida albicans mutant with reduced filamentation. Cellular Microbiology, 21 (12) doi.org/10.1111/cmi.13103).
12. P. Khandagale, D. Peroumal, K. Manohar and Narottam Acharya (2019) Human DNA polymerase delta is a pentameric holoenzyme with a dimeric p12 subunit. Life Science Alliance, Vol. 2, No., 2. (doi.org/10.26508/lsa.201900323)
13. Narottam Acharya, K. Manohar, D. Peroumal, P. Khandagale, S. K. Patel, S. R. Sahu, and P. Kumari (2019) Multifaceted activities of DNA Polymerase eta: Beyond translesion DNA synthesis. Curr. Genetics, 65(3), 649-656. (doi.org/10.1007/s00294-018-0918-5).
14. N. Jingde, R. Ray, S. Sinha,  K. Rana, S. K. Singh,  P. Khandagale, Narottam Acharya and V. Rai (2018) Cysteine mediated disulfide bond formation in RAGE V domain facilitates its functionally relevant dimerization. Biochimie, 154, 55-61.
15. K. Manohar, D. Peroumal and Narottam Acharya (2018) TLS dependent and independent functions of DNA polymerase eta (Polh/ Rad30) from Pathogenic Yeast Candida albicans. Molecular Microbiology, 110 (5), 707-727.
16. S. Satpati, K. Manohar, Narottam Acharya, Anshuman Dixit.  (2017) Comparative molecular dynamics studies of heterozygous open reading frames of DNA polymerase eta (η) in pathogenic yeast Candida albicans. Scientific Reports, 7:41087. doi: 10.1038/srep41087. 
17. K. Manohar and Narottam Acharya (2015) Characterization of Proliferating Cell Nuclear Antigen (PCNA) from Pathogenic Yeast Candida albicans and its functional analyses in S. cerevisiae. BMC-Microbiology, 15:257.
18. Yoon J.H⁺., Acharya N., Jeseong P., Debashree Basu, Prakash S. and Prakash L. (2014) Identification of two functional PCNA binding domains in human DNA polymerase κ (+ joint first author). Genes to Cells., 19(7):594-601.
19. Acharya N., Kalssen R., Johnson R.E., Prakash L. and Prakash S. (2011) PCNA binding domains in all three subunits of yeast DNA polymerase δ modulate its function in DNA replication. Proc Natl Acad Sci USA., Nov.1; 108(44):17927-17932.
20. Acharya N., Yoon J.H., Hutwitz J., Prakash L. and Prakash S. (2010) DNA polymerase eta lacking the ubiquitin-binding domain promotes replicative lesion bypass in human cells (⁺ joint first author). Proc Natl Acad Sci USA., Jun 8; 107(23):10401-10405.
21. Acharya N., Johnson R.E., Pagès V., Prakash L. and Prakash S. (2009) Yeast Rev1 protein promotes complex formation of DNA polymerase zeta with Pol32 subunit of DNA polymerase delta. Proc Natl Acad Sci USA., Jun 16; 106(24):9631-9636.
22. Acharya N., Yoon J.H., Gali H., Unk I., Haracska L., Johnson R.E., Hutwitz J., Prakash L. and Prakash S. (2008) Roles of PCNA-binding and ubiquitin-binding domains in human DNA polymerase eta in translesion DNA synthesis. Proc Natl Acad Sci USA., Nov 18; 105 (46):17724-17729.
23. Pagès V., Bresson A., Acharya N., Prakash L. Fuchs R.P. and Prakash S. (2008) Requirement of Rad5 for DNA polymerase zeta-dependent translesion synthesis in Saccharomyces cerevisiae. Genetics, 2008 Sep; 180(1):73-82.
24. Acharya N., Haracska L., Prakash S. and Prakash L. (2007) Complex formation of yeast Rev1 with DNA polymerase {eta}. Mol Cell Biol., Dec; 27 (23):8401-8408.
25. Acharya N., Brahma A., Haracska L., Prakash S. and Prakash L. (2007) Mutations in the Ubiquitin Binding UBZ Motif of DNA Polymerase {eta} Do Not Impair Its Function in Translesion Synthesis during Replication. Mol Cell Biol., Oct; 27(20):7266-7272.
26. Acharya N., Johnson R.E., Prakash S. and Prakash L. (2006) Complex formation with Rev1 enhances the proficiency of Saccharomyces cerevisiae DNA polymerase zeta for mismatch extension and for extension opposite from DNA lesions. Mol. Cell Biol., Dec. 26 (24), 9555-9563.
27. Acharya N., Haracska L., Johnson R.E., Unk I., Prakash S. and Prakash L. (2005) Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain. Mol. Cell Biol., Nov. 25 (21), 9734-9740.
28. Haracska L., Acharya N., Unk I., Johnson R.E., Hurwitz J., Prakash L. and Prakash S. (2005) A single domain in human DNA polymerase iota mediates interaction with PCNA: implications for translesion DNA synthesis. Mol. Cell Biol., Feb. 25 (3), 1183-1190
29. Acharya N, Talawar R. K., Purnapatre K, Varshney U. (2004) Use of sequence microdivergence in mycobacterial ortholog to analyze contributions of the water-activating loop histidine of Escherichia coli uracil-DNA glycosylase in reactant binding and catalysis. Biochem. Biophys. Res. Commun., 320(3), 893-899.
30. Acharya, N., Talawar R. K., Saikrishnan, K., Vijayan, M and Varshney, U. (2003) Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition. Nucleic Acids Res., 31(24), 7216-7226.
31. Acharya, N., Kumar P. and Varshney, U. (2003) Complexes of Uracil-DNA glycosylase inhibitor protein, Ugi, with Mycobacterium smegmatis and Mycobacterium tuberculosis uracil-DNA glycosylases. Microbiology 149, 1647-1658.
32. Saikrishnan, K., Jeyakanthan, Venkatesh, J., Acharya, N., Purnapatre, K., Sekar, K., Varshney, U. and Vijayan, M. (2003) Structure of Mycobacterium tuberculosis single stranded DNA binding protein. Variability in quaternary structure and its implications. J. Mol. Biol., 331, 385-393.
33. Acharya, N., Roy, S., and Varshney, U. (2002) Mutational analysis of the uracil DNA glycosylase inhibitor protein and its interaction with Escherichia coli uracil DNA glycosylase. J. Mol. Biol., 321 (4), 579-590.
34. Acharya, N., and Varshney, U. (2002) Biochemical properties of single stranded DNA binding protein from Mycobacterium smegmatis, a fast growing mycobacterium and its physical and functional interaction with uracil DNA glycosylases. J. Mol. Biol., 318 (5), 1251-1264.
35. Handa, P.⁺, Acharya, N.⁺, and Varshney, U. (2002) Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and substrate. (+ joint first author) Nucleic Acids Res, 30(14), 3086-3095.
36. Handa, P., Acharya, N., Talwar R. K., Roy, S., and Varshney, U. (2002) Contrasting effects of mutating active site residues, aspartic acid 64 and histidine 187 of Escherichia coli uracil-DNA glycosylase on uracil excision and interaction with an inhibitor protein. Indian J. Biochem. Biophys., 29, 312-317.
37. Saikrishnan, K., Jeyakanthan, Venkatesh, J., Acharya, N., Purnapatre, K., Sekar, K., Varshney, U. and Vijayan, M. (2002) Crystallization and preliminary X-ray studies on the single stranded DNA binding protein from Mycobacterium tuberculosis. Acta Crystallogr D Biol Crystallogr, 58, 327-329.
38. Handa, P., Acharya, N. and Varshney, U. (2001) Chimeras between single stranded DNA binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C-terminal domains interact with uracil-DNA glycosylases. J. Biol. Chem. 276, 16992-16997.
39. Handa, P., Acharya, N., Thanedar, S., Purnapatre, K. and Varshney, U. (2000) Distinct properties of single stranded DNA binding protein from Mycobacterium tuberculosis and its functional characterization in Escherichia coli. Nucleic Acids Res. 28, 3823-3829.
40. Sadhale, P., Sharma, N., Beena, P, Katoch, A., Acharya, N., and Singh, S. K. (1998) Modulation of polymerase II composition: a possible mode of transcriptional regulation of stress response in eukaryotes. J. Biosci. 23, 331-335.
44. Book chapter
45. Narottam Acharya, Kodavati Manohar, Shreenath Nayak, Avishek Chatterjee and Amrita Dalei (2106) DNA Polymerase: A putative drug target against Candidiasis. Frontiers in Life Sciences, Excel Indian Publishers, New Delhi, India. Pp. 12-23

Laboratory of Genomic Instability and Diseases

Ph.D. students: 

Satya Ranjan Sahu (UGC-JRF): Mutasome complex and candidiasis

Swagata Bose (ILS-SRF): Polymicrobial interaction and C. albicans pathogenesis 

Bhabasha Gyanadeep Utkalaja (UGC-SRF):  DNA polymerase epsilon of  C. albicans

Jugal Kishore Sahu (CSIR-SRF): Human DNA polymerase theta

Ipsita Subhadarsini (CSIR- SRF): TLS DNA Polymerases and Chemo-resistance

Sushree Subhashree Parida (DBT-JRF): Cell fate without TLS  DNA Polymerase

……………………………………………………………………………………………………………………………..

Post-Doctoral Fellow:

Shweta Thakur, Ph. D. (DBT/Project-RA): Architecture of Human DNA Polymerase delta

Abinash Dutta, Ph. D.  (DBT/Project-RA) Therapeutics against Candida infection

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 Lab. Technician:

Sitendra Prasad Panda

………………………………………………………………………………………………………………………………

Our Graduates:

 Kodavati Manohar, Ph. D.  (Graduated from the Laboratory in the year 2018) Thesis entitled  “Characterization of DNA polymerase eta ( (Polη/Rad30) from pathogenic yeast Candida albicans: Role in genome stability, morphogenesis and multidrug resistance”

( Currently Pursuing Post-doctoral training at Houston Methodist, USA)

 Prashant R. Khandagale, Ph. D.  (Graduated from the Laboratory in the year 2019) Thesis entitled “Targeting of human DNA polymerase delta to the replication machinery”.

(Currently Pursuing Post-doctoral training at NIH)

Premlata Kumari, Ph.D. (Graduated from the Laboratory in the year 2022) Ph. D. Thesis “DNA-protein crosslink repair in pathogenic yeast C. albicans”

Shraddheya Kumar Patel, Ph.D. (Graduated from the Laboratory in the year 2022) Thesis entitled ” Deciphering the role of Pol 32, the non-essential subunit of DNA polymerase delta in Candida albicans pathogenesis”

Our Alumni

Manish Singh, Ph.D. (DBT Project RA- 2012 (April-Nov.)

Doureradjou Peroumal, Ph. D. (CISR/DBT-RA- 2016-March 2021)

Amrita Dalei (Lab. Technician – 2013-2018)

Shreenath Nayak, Ph.D. (DBT-RA; from the year 2013-2016)

Jawed Alam, Ph.D. (CSIR-RA)

Avishek Chatterji

Ritayu Chakraborty

Short-term Fellows (2-6 months):

Manoj Kumar (IAS Fellow – 2019, Anna University Regional Campus Coimbatore)

Aishi Satpathy (M. Sc. Dissertation-2019, Central University of Tamil Nadu)

Rituparna Moharana (M. Sc. Dissertation-2019, S & O University)

Mousumi Sajjan (Summer project-2018,OUAT, BBSR)

Riya Gupta (IAS Fellow 2017,M. Tech. Biotechnology, Meerut Institute of Engineering and Technology )

Ravi Kumar (IAS Fellow 2016, NIT, Durgapur) 

M. Suresh (IAS Fellow 2015)

Also see

Genomic Instability and Diseases

Ongoing sponsored Research Projects:

1. “Fidelity and processivity of variants of human DNA polymerase delta (Polδ): Implications in DNA double-strand break repair and carcinogenesis”. Funded by DBT (Feb. 2021-2024)
2. “Evaluation of pathogenic potential of various DNA polymerase knock out strains of Candida albicans: Implications in development of live attenuated anti-fungal vaccine” Funded by DBT (Jan. 2021-2024)
3. “DNA-Protein crosslink repair in pathogenic yeast Candida albicans” Funded by SERB (2022-2025)

Completed sponsored Research Projects:

1. Characterization of pol3-t mutant of yeast DNA polymerase δ and its role in mutagenesis. Funded by CSIR (2014-2017)
2. Understanding the role of DNA polymerase eta dependent trans-lesion DNA synthesis in pathogenicity of Candida albicans. Funded by DBT (2016-2019)
3. Deciphering the role of DNA polymerase delta dependent mutagenesis in   morphogenesis, multidrug resistance and fungal pathogenesis of C. albicans. Funded by SERB (2016-2019)

Lab. in News

https://vigyanprasar.gov.in/isw/Study-paves-way-for-a-new-approach-to-fight-infections.html

https://thefederal.com/science/indian-researchers-find-new-way-to-fight-infections-with-protein/

We are looking for motivated students (CSIR/DBT/ICMR Fellowship is mandatory) for pursuing Ph.D. in the laboratory.