Ph.D., Microbiology, University of Iowa, 1993
M.S., Microbiology, University of Iowa, 1987
B. Tech., Biochemical Engineering and Food Technology, Jadavpur University, Calcutta, 1978
B.S. (Honors), Chemistry, University of Calcutta
July 2017 - present - Professor, Department of Biochemistry, Virginia Tech, Blacksburg
July 2012 – June 2017 - Associate Professor, Department of Biochemistry, Virginia Tech, Blacksburg
July 2012 – present – Adjunct Associate Professor, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg
September 2009 – 2012 –Associate Professor, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg
September 2001 – 2009 –Assistant Professor, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg
2001–2001 - Visiting Scientist (2001), Senior Research Scientist (1995-2000), and Research Associate (1993-1995), Department of Microbiology, University of Illinois
1978-83 - Biochemical Engineer (1982-1983), Assistant Engineer (1980–1982), and Management Trainee (1978-1980), Hindustan Antibiotics Ltd., Pimpri, Pune, India
Selected Major Awards
2014 Outstanding Dissertation Advisor, STEM Area, Virginia Tech
2013 Virginia Tech International Faculty Development Program Fellow (Singapore, Indonesia)
BCHM 4124 - Laboratory Problems in Biochemistry and Molecular Biology (2013-14)
Methanogenic Archaea – Hydrothermal Vent – Early Earth- Evolution of Redox Metabolism – Bioenergy Production - Redox Metabolism of Mycobacteria
Evolution of heme-based systems:
Methane forming strictly anaerobic archaea, called methanogens, were generally considered incapable of metabolizing sulfite and devoid of the respective enzyme called sulfite reductase. These organisms perform one of the most ancient metabolisms of Earth, hydrogen dependent methanogenesis (4H2 + CO2 à CH4 + 2H2O). In 2005-2012 period our laboratory showed that the methanogens that live in deep-sea volcanoes or hydrothermal vents indeed metabolize sulfite and for this purpose they employ a special enzyme called F420-dependent sulfite reductase (Fsr) (2-4, 10). The conditions in the hydrothermal vents mimic some aspects of early Earth. The data indicated that Fsr was probably built in methanogens from certain ancient parts. Starting from these clues we have carried a bioinformatics based search and found that small heme-containing proteins of variety of structures representing the essential core of sulfite reductases, is almost universally present in the methanogens, although only rarely a methanogen exhibits sulfite reductase activity (10). We named these proteins dissimilatory sulfite reductase type protein or Dsr-LP. It is likely that Dsr-LP carries out a function that was essential to living cells on early Earth. The structural characteristics of the DsrLPs taken together provide a scheme for the evolution of heme-containing sulfite reductases in bacteria, plant and animal. Current research in the laboratory hints to the possibility of new heme-based
metabolism that began with DsrLPs and could be wide spread in the extant living systems. This exploration has been funded by the NASA.
Evolution of thioredoxin based redox control systems:
Thioredoxin or Trx has been known as a master controller of critical metabolisms in a wide variety of living cells and the associated systems have been studied in detail in plant and animal. Some the notable examples of Trx-controlled systems are photosynthesis in plant and cell death and aging in human. The Trx systems have not been studied much in the anaerobic microorganisms some of whom are most ancient inhabitants of Earth. Our recent bioinformatics and experimental studies indicate that two branches of the Trx system, one being dependent on a nicotinamide coenzyme (NTR) and the other on iron-containing proteins called ferredoxins (FTR), arose independently. We found that FTR is likely an invention of the ancient bacteria and NTR seemed to have been developed by the early archaea, including methanogens (1) (our unpublished data). In both cases, the likely early utilities of the Trx systems have been in the control of carbon dioxide fixation and defense against oxidative damage. The latter aspect became an important metabolism as oxygen appeared on Earth and the original inhabitants, which were accustomed to living without oxygen, had to deal with oxidative stress. Since the Trx system is an integral part of the cellular redox-control, the new information resulting from our research would have applicability in the production of biofuel and mitigation of green house-gas (methane) emission and provide new leads for research on plant and animal metabolism. This research has been supported by a grant from the NSF and involves the following collaborators: Bob. B. Buchanan, University of California, Berkeley, CA; Ruth Schmitz-Streit, Christian-Albrechts-Universität Kiel, Kiel, Germany; Mónica Balsera, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Salamanca, Spain; Peter Schürmann, Laboratoire de Biologie Moléculaire et Cellulaire, Rue Emile Argand 11, Neuchâtel, Switzerland;
Development of therapeutics and vaccine for tuberculosis:
In this research we are collaborators of Endang Purwantini of the Department of Biochemistry, Virginia Tech. Coenzyme F420 is an essential component of the methanogenic archaea and rarely found in bacteria and absent in human. Mycobacteria, which includes Mycobacterium tuberculosis, the causative agent of tuberculosis or TB, are the rare group of bacteria that carry F420 (5-7). The ongoing research by us and others indicates that it plays could play critical role in TB pathogenesis. We have shown in M. tuberculosis could use the reduced form of coenzyme F420 to neutralize nitrosative stress imposed by the human host and this process could act as a sensor for the immunological competence of the host (8). More recently, we have found that some of the coenzyme F420-dependent proteins help to build the resilient cell wall of M. tuberculosis, and they could occur on the cell surface (9). Consequently, these proteins are attractive targets for the development of TB vaccines and drugs. To capitalize on this opportunity we have developed collaboration with the PT Bio Farma, an Indonesian company producing international quality vaccines that are used worldwide, including the USA. The research on mycobacteria has been funded by a NIH grant
The Gene Ontology Describes Microbial Biofuel Production: This project has been funded by the US Department of Energy Systems Biology Knowledgebase (KBase) program and led by us, Brett M. Tyler, Oregon State University, and Joao C. Setubal, Universidade de São Paulo, Brazil. The key team members are Endang Purwantini and Trudy Torto-Alalibo of the Virginia Tech. http://mengo.bioinformatics.vt.edu/
1. Balsera, M., E. Uberegui, D. Susanti, R. A. Schmitz, B. Mukhopadhyay, P. Schurmann, and B. B. Buchanan. 2013. Ferredoxin:thioredoxin reductase (FTR) links the regulation of oxygenic photosynthesis to deeply rooted bacteria. Planta 237:619-635.
2. Johnson, E. F., and B. Mukhopadhyay. 2008. Coenzyme F420-dependent sulfite reductase-enabled sulfite detoxification and use of sulfite as a sole sulfur source by Methanococcus maripaludis. Applied and environmental microbiology 74:3591-3595.
3. Johnson, E. F., and B. Mukhopadhyay. 2005. A new type of sulfite reductase, a novel coenzyme F420-dependent enzyme, from the methanarchaeon Methanocaldococcus jannaschii. The Journal of biological chemistry 280:38776-38786.
4. Johnson, E. F., and B. Mukhopadhyay. 2007. A novel coenzyme F420-dependent sulfite reductase and a small size sulfite reductase in methanogenic archaea. In C. Dahl and C. G. Friedrich (ed.), Proceedings of the International Symposium on Microbial Sulfur Metabolism. Springer, New York, N.Y. .
7. Purwantini, E., T. P. Gillis, and L. Daniels. 1997. Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea. FEMS Microbiol Lett 146:129-134.
8. Purwantini, E., and B. Mukhopadhyay. 2009. Conversion of NO2 to NO by reduced coenzyme F420 protects mycobacteria from nitrosative damage. Proceedings of the National Academy of Sciences of the United States of America 106:6333-6338.
NSF REU: Microbiology in the Post-genome Era (2009-current)
Collaboration with Dr. Brian Campbell, Southern Piedmont Agricultural Research and Extension Center: Rumen Microbial Processes Guiding Forage Utilization By Steers in a Rotational Grazing System: a metagenomics investigation
Rumen Microbial Processes Guiding Forage Utilization By Steers in a Rotational Grazing System: a metagenomics investigation – a collaboration with Dr. Brian Campbell, Southern Piedmont Agricultural Research and Extension Center
**Efendi Y.S., Susanti D., Tritama E., ***Pasier M.L., Niwan Putri G.N., Raharso S., Iskandar, Aditiawati P., Giri-Rachman E.A., Mukhopadhyay B., and E. Purwantini. 2017. Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine. Genome Announc. 5:e00235-17.
Susanti D., Johnson E.F., Lapidus A., Han J., Reddy T.B., Mukherjee S., Pillay M., Perevalova A.A., Ivanova N.N., Woyke T., Kyrpides N.C., B. Mukhopadhyay. 2017. Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533T, a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia. Genome Announc. 5: e00078-17
Susanti, D., Loganathan, U., and B. Mukhopadhyay. 2016. A novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD: A Tool for Redox Regulation in an Anaerobe. J. Biol. Chem. 291:23084-23100. IM
Purwantini, E., Daniels, L., and B. Mukhopadhyay. 2016. F420H2 is required for phthiocerol dimycocerosates synthesis in mycobacteria. J. Bacteriol. 198:2020-8.
Qian***, Y., Otsuka, Y., Sonoki, T., Mukhopadhyay, B., Nakamura, M., Jellison, J., and B. Goodell. 2016. Engineered Microbial Production of 2-Pyrone- 4,6-Dicarboxylic Acid from Lignin Residues for Use as an Industrial Platform Chemical. BioResources. 11: 6097-6109.
Perevalova, A.A., Kulvanov, I.V., Bidzhieva, S. Kh., Mukhopadhyay, B., Bonch-Osmolovskaya, E. A., and A. V. Lebedinsky. 2015. Reclassification of Desulfurococcus mobilis as a synonym of Desulfurococcus mucosus, Desulfurococcus fermentans and Desulfurococcus kamchatkensis as synonyms of Desulfurococcus amylolyticus, and emendation of D. mucosus and D. amylolyticus species descriptions. Int. J. System. Evol. Microbiol. 66:514-7.
Susanti, D., Johnson, E. F., Lapidus, A., Han, J., Reddy, T.B.K, Pillay, M., Ivanova, N. N., Markowitz, V. M., Woyke, T., Kyrpides, N. C., and B. Mukhopadhyay. 2015. Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. Stand Genomic Sci 11:3.
Purwantini, E., Torto-Alalibo, T., Lomax, J., Setubal, J.C., Tyler, B.M. and B. Mukhopadhyay. 2014. Genetic resources for methane production from biomass described with the Gene Ontology. Front. Microbiol. 5:634
Torto-Alalibo, T., E. Purwantini, E., Lomax, J., Setubal, J.C., Mukhopadhyay, B., and B.M. Tyler. 2014. Genetic resources for advanced biofuel production described with the Gene Ontology. Front. Microbiol. 5:528
Publications (total 44 peer-reviewed, 1 book chapter and 1 non-peer reviewed as marked with*; **Undergraduate Student; *** Graduate Student):
**Susanti, D., Wong, J. H., Vensel, W.H., Loganathan, U., **DeSantis, R., Schmitz, R.A., Balsera, M., Buchanan, B.B., and B. Mukhopadhyay. 2014. Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii. Proc. Natl. Acad. Sci. U. S. A. (In Press)
Purwantini, E., and B. Mukhopadhyay. 2013. Rv0132c of Mycobacterium tuberculosis Encodes a Coenzyme F420-dependent Hydroxymycolic Acid Dehydrogenase PLoS ONE 8: e81985.
Balsera, M., Uberegui, E., ***Susanti, D., Schmitz, R.A., Mukhopadhyay, B., Schürmann, P., and B.B. Buchanan. 2013. Ferredoxin:thioredoxin reductase (FTR) links the regulation of oxygenic photosynthesis to deeply rooted bacteria. Planta. 237:619-35. (Cover Article)
***Susanti, D., E. F. Johnson, ***J. R. Rodriguez, I. Anderson, A. A. Perevalova, N. Kyrpides, S. Lucas, J. Han, A. Lapidus, J.-F. Cheng, L. Goodwin, S. Pitluck, K. Mavromatis, L. Peters, M. L. Land, L. Hauser, G. Gopalan, P. P. Chan, T. M. Lowe, H. Atomi, E. A. Bonch-Osmolovskaya, T. Woyke, and B. Mukhopadhyay. 2012. Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia. Journal of Bacteriology. 194:5703–5704
***Susanti D, and B. Mukhopadhyay. 2012. An intertwined evolutionary history of methanogenic archaea and sulfate reduction. PLoS One. 7:e45313.
***Dharmarajan, L., J.L. Kraszewski, B. Mukhopadhyay and P.W. Dunten. 2011. Structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate. PROTEINS: Structure, Function and Bioinformatics. 79:1820-1829
Cho, I-M., L. Lai, ***D. Susanti, B. Mukhopadhyay, and V.Gopalan. 2010. Ribosomal protein L7Ae is a bona fide subunit of archaeal RNase P. Proc. Natl. Acad. Sci. U. S. A. 107:14573-14578
Purwantini, E., and B. Mukhopadhyay. 2009. Conversion of NO2 to NO by Reduced Coenzyme F420 protectsmycobacteria from nitrosative damage. Proc. Natl. Acad. Sci. U. S. A. 106:6333-6338
***Dharmarajan, L., ***J.L. Kraszewski, B. Mukhopadhyay and P. W. Dunten. 2009. Expression, purification, and crystallization of an archaeal-type phosphoenolpyruvate carboxylase. Acta Crystallographica Section F. 65:1193-1196.
Kwang-Hyung Kim, K-H., S.D. Willger, S.-W. Park, S. Puttikamonkul, N. Grah, Y. Cho, B. Mukhopadhyay, R.A. Cramer Jr and C.B. Lawrence. 2009. TmpL, a transmembrane protein is required for intracellular redox homeostasis and virulence in a plant and an animal fungal pathogen. PLoS Pathogens 5:e1000653.
Anderson I, L.E. Ulrich, B. Lupa, ***D. Susanti, I. Porat, S.D. Hooper, A. Lykidis, M. Sieprawska-Lupa, ***L. Dharmarajan, E. Goltsman, A. Lapidus, E. Saunders, C. Han, M. Land, S. Lucas, B. Mukhopadhyay, W.B. Whitman, C. Woese, J. Bristow, and N. Kyrpides. 2009. Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One. 4:e5797.
Anderson, I.J., L. ***Dharmarajan, ***J. Rodriguez, S. Hooper, I. Porat, L.E. Ulrich, J.G. Elkins, K. Mavromatis, H. Sun, M. Land, A. Lapidus, S. Lucas, K. Barry, H. Huber, I.B. Zhulin, W. B. Whitman, B. Mukhopadhyay, C. Woese, J. Bristow, and N. Kyrpides. 2009. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics. 10:145.
**Case, C.L., J.R. Rodriguez and B. Mukhopadhyay. 2009. Characterization of a NADH oxidase of the flavin-dependent disulfide reductase family from Methanocaldococcus jannaschii. Microbiology. 155:69-79
Dharmarajan L., C. L. Case**, P. Dunten and B. Mukhopadhyay. 2008. Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influencing catalysis through an anion-quadrupole interaction with phosphoenolpyruvate. FEBS J. 275:5810-9
Anderson, I.J., *** J.Rodriguez, ***D.Susanti, I.Porat, C.Reich, L.E.Ulrich, J.G.Elkins, K.Mavromatis, A.Lykidis, E.Kim, L.S.Thompson, M.Nolan, M.Land, A.Copeland, A.Lapidus, S.Lucas, C.Detter, I.B.Zhulin, G.J.Olsen, W.Whitman, B.Mukhopadhyay, J.Bristow, and N.Kyrpides. 2008. Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol. 190:2957-65
Johnson, E. F. and B. Mukhopadhyay. 2008. Coenzyme F420-dependent sulfite reductase-enabled sulfite detoxification and use of sulfite as a sole sulfur source by Methanococcus maripaludis. Appl Environ Microbiol. 74:3591-5
**Case, C. L., and B. Mukhopadhyay. 2007. Kinetic characterization of recombinant human cytosolic phosphoenolpyruvate carboxykinase with and without a His10-tag. Biochim. Biophys. Acta 1770:1576-1584.
Staples, C. R., S. Lahiri, J. Raymond, **L. Von Herbulis, B. Mukhophadhyay, and R. E. Blankenship. 2007. The expression and association of group IV nitrogenase NifD And NifH homologs in the non-nitrogen fixing archaeon Methanocaldococcus jannaschii. J. Bacteriol. 89:7392-8
*Johnson, E. F. and B. Mukhopadhyay. 2007. A novel coenzyme F420-dependent sulfite reductase and a small size sulfite reductase in methanogenic archaea. In C. Dahl and C. G. Friedrich (eds.), Proceedings of the International symposium on Microbial Sulfur Metabolism. Springer, New York, N.Y.
**Case, C.L., **Concar, E.M., **Boswell, K.L., and Mukhopadhyay, B. 2006. Roles of Asp75, Asp78, and Glu83 of GTP-dependent phosphoenolpyruvate carboxykinase from Mycobacterium smegmatis. J Biol Chem 281:39262-39272.
Lai, H., ***J. L. Kraszewski, E. Purwantini, and B. Mukhopadhyay. 2006. Identification of the pyruvate carboxylase genes in Pseudomonas aeruginosa PA01 and development of a P. aeruginosa-based over-expression system for α4- and α4β4-type pyruvate carboxylases. Appl Environ Microbiol 72:7785-7792.
Seleem, M.N., Ali, M., Boyle, S.M., Mukhopadhyay, B., Witonsky, S.G., Schurig, G.G., and Sriranganathan, N. 2006. Establishment of gene expression system in Ochrobactrum anthropi. Appl. Environ Microbiol. 72:6833-6836.
Johnson, E.F. and B. Mukhopadhyay. 2005. A new type of sulfite reductase - a novel coenzyme F420-dependent enzyme from the methanarchaeon Methanocaldococcus jannaschii. J. Biol. Chem. 280:38776-86.
Guss, A.M., Mukhopadhyay, B., Zhang, J.K. and Metcalf, W.W. 2005. Genetic analysis of mch mutants in two Methanosarcina species demonstrates multiple roles for the methanopterin-dependent C-1 oxidation/reduction pathway and differences in H2 metabolism between closely related species. Mol. Microbiol. 55, 1671-1680.
**Patel, H.M., **J.L. Kraszewski, and B. Mukhopadhyay. 2004. The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure. J. Bacteriol. 186:5129-5137
Patrie, S.M., J. P. Charlebois, D. Whipple, N. L. Kelleher, C.L. Hendrickson J.P. Quinn, A. G. Marshall, and B. Mukhopadhyay. 2004. Construction of a Hybrid Quadrupole/Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Versatile MS/MS Above 10 kDa. J. Am. Soc. Mass Spect. 15:1099-1118.
*McInerney, T., E.J. Johnson, B. Mukhopadhyay, and A. Borthwick. 2003. Analysing 2-D gels at High Throughput, Data mining with Progenesis Discovery Informatics Tool. Genetic Engineering News. 23:31-32,36
Galagan, J. E., et al. 2002. The genome of M. acetivorans reveal extensive metabolic and physiological diversity. Genome Res. 21: 532-542.
Mukhopadhyay, B., E. Purwantini, C. L. Kreder, and R. S. Wolfe. 2001. Oxaloacetate synthesis in the methanarchaeon Methanosarcina barkeri: pyruvate genes and a putative E. coli-type bifunctional botin protein ligase gene (bpl/birA) exhibit a unique gene organization. J. Bacteriol. 183:3804-3810.
Mukhopadhyay, B., **E. M. Concar, and R. S. Wolfe. 2001. A GTP-dependent vertebrate-type phosphoenolpyruvate carboxykinase from Mycobacterium smegmatis. J. Biol. Chem. 276:16137-45.
Mukhopadhyay, B., E. F. Johnson, and R. S. Wolfe. 2000. A novel pH2 control on the expression of flagella in the hyperthermophilic strictly hydrogenotrophic methanarchaeaon Methanococcus jannaschii. Proc. Natl. Acad. Sci. U. S. A. 97:11522-11527.
Mukhopadhyay, B., **V. J. Patel, and R. S. Wolfe. 2000. A stable archaeal pyruvate carboxylase from the hyperthermophile Methanococcus jannaschii. Arch. Microbiol. 174:406-414.
Mukhopadhyay, B., and E. Purwantini. 2000. Pyruvate carboxylase from Mycobacterium smegmatis: stabilization, rapid purification, molecular and biochemical characterization and regulation of the cellular level. Biochim Biophys Acta 1475:191-206.
Mukhopadhyay, B., E. F. Johnson, and R. S. Wolfe. 1999. Reactor-scale cultivation of the hyperthermophilic methanarchaeon Methanococcus jannaschii to high cell densities. Appl. Environ. Microbiol. 65:5059-5065.
Mukhopadhyay, B., E. F. Johnson, and **M. Ascano, Jr. 1999. Conditions for vigorous growth on sulfide and reactor-scale cultivation protocols for the thermophilic green sulfur bacterium Chlorobium tepidum. Appl. Environ. Microbiol. 65:301-306.
Mukhopadhyay, B., S. F. Stoddard, and R. S. Wolfe. 1998. Purification, regulation, and molecular genetic and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain ∆H. J. Biol. Chem. 273: 5155-5166.
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