- Director of Alumni Relations
- Research area(s): Biochemistry of Methanogenic Archaea
Ph.D., Microbiology, University of Iowa, 1993
M.S., Microbiology, University of Iowa, 1987
B. Tech., Biochemical Engineering and Food Technology, Jadavpur, University of 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
- Visiting Scientist (2001), Senior Research Scientist (1995 - 2000), and Research Associate (1993 - 1995), Department of Microbiology, University of Illinois
- Biochemical Engineer (1982 - 1983), Assistant Engineer (1980 – 1982), and Management Trainee (1978 - 1980), Hindustan Antibiotics Ltd., Pimpri, Pune, India
BCHM 4124: Laboratory Problems in Biochemistry and Molecular Biology
BCHM 5004: Seminar in Biochemistry
BCHM 5014: Biochemical Research Rotations (co-taught)
GBCB 5004: Seminar in Genetics, Bioinformatics, and Computational Biology (co-taught)
SYSB 2025: Intro to Systems Biology (Teaching Team Member)
Current Advising and Research Training
Two PhD students
Three undergraduate students: BCHM4994 - 2; BCHM 2974 - 1
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 the 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 a 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 widespread in the extant living systems. This exploration has been funded by 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 plants and animals. Some of the notable examples of Trx-controlled systems are photosynthesis in plant and cell death and aging in humans. 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 greenhouse-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 humans. 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 a 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 a 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 an 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.
Publications (total 44 peer-reviewed, 1 book chapter and 1 non-peer reviewed as marked with*; **Undergraduate Student; *** Graduate Student):
Susanti, D., Frazier, M.C. and B. Mukhopadhyay. 2019. A genetic system for Methanocaldococcus jannaschii, an evolutionary deeply rooted hyperthermophilic methanarchaeon. Front Microbiol 10:1256. https://www.frontiersin.org/articles/10.3389/fmicb.2019.01256/full
Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. 2018. Yu, H., Susanti, D., McGlynn, S.E., Skennerton, C.T., Chourey, K. Iyer, R., Scheller, S., Tavormina, P.L., Hettich, R.L., Mukhopadhyay, B., and Orphan, V.J. Front Microbiol. 9:2917. https://www.frontiersin.org/articles/10.3389/fmicb.2018.02917/full
Purwantini, E., Loganathan, U., Mukhopadhyay, B. 2018. Coenzyme F420-Dependent Glucose-6-Phosphate Dehydrogenase-Coupled Polyglutamylation of Coenzyme F420 in Mycobacteria. Purwantini E, Loganathan U, and B. Mukhopadhyay. J Bacteriol. 200:e00375-18. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6222201/
Tn2008-Driven Carbapenem-Resistance in Acinetobacter baumannii Isolates from a Period of Increased Incidence of Infections in a Southwest Virginia Hospital..Rao, J., Susanti, D., Childress, J.C., Mitkos, M.C., Brima, J.K., Baffoe-Bonnie, A.W., Pearce, S.N., Grgurich, D., Fernandez-Cotarelo, M.J., Kerkering, T.M., Mukhopadhyay, B. 2018. J. Glob. Antimicrob. Resist.12:79-87. https://www.sciencedirect.com/science/article/pii/S2213716517301650?via%3Dihub
Susanti, D., Loganathan, U., Compton, A., and B. Mukhopadhyay. 2017. A Reexamination of Thioredoxin Reductase from Thermoplasma acidophilum, a Thermoacidophilic Euryarchaeon, Identifies It as an NADH-Dependent Enzyme. ACS Omega 2: 4180–4187. https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/28884159/
Caudill, M.T. Budnick, J.A, Sheehan, L.M., Lehman, C.R., Endang, E., Mukhopadhyay, B. and C.C. Caswell. 2017. Proline utilization system is required for infection by the pathogenic α-proteobacterium Brucella abortus. Microbiology doi: 10.1099/mic.0.000490. https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/28691659/
**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. http://genomea.asm.org/content/5/17/e00235-17.full
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. http://genomea.asm.org/content/5/15/e00078-17.full?sid=18fae9f9-d9b6-414c-9bc1-ded099032dd4
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. http://www.jbc.org.ezproxy.lib.vt.edu/content/291/44/23084.full
Purwantini, E., Daniels, L., and B. Mukhopadhyay. 2016. F420H2 is required for phthiocerol dimycocerosates synthesis in mycobacteria. J. Bacteriol. 198:2020-8. http://jb.asm.org.ezproxy.lib.vt.edu/content/198/15/2020.full
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
**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) . http://www.pnas.org/cgi/doi/10.1073/pnas.1324240111.
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). http://link.springer.com/article/10.1007%2Fs00425-012-1803-y/fulltext.html
***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. http://jb.asm.org/content/194/20/5703.long
***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. http://www.pnas.org/content/107/33/14573.full
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. http://www.pnas.org/content/106/15/6333.full
***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. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000653
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.. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005797
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.. http://www.biomedcentral.com/1471-2164/10/145
**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. http://mic.sgmjournals.org/content/155/1/69.long
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. http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2008.06702.x/full
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. http://jb.asm.org/content/190/8/2957.long
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. http://aem.asm.org/content/74/11/3591.long
**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.. http://aem.asm.org/content/74/11/3591.long
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. http://jb.asm.org/content/189/20/7392.long
*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.. http://www.jbc.org/content/281/51/39262.long
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.. http://aem.asm.org/content/72/12/7785.long
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.. http://aem.asm.org/content/72/10/6833.long
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.. http://www.jbc.org/content/280/46/38776.long
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. http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04514.x/full
**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. http://jb.asm.org/content/186/15/5129.long
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. http://link.springer.com/article/10.1016%2Fj.jasms.2004.04.031
*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. http://genome.cshlp.org/content/12/4/532.long
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. http://jb.asm.org/content/183/12/3804.long
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.. http://www.jbc.org/content/276/19/16137.long
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. http://www.pnas.org/content/97/21/11522.long
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.. http://link.springer.com/article/10.1007%2Fs002030000225
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. http://www.sciencedirect.com/science/article/pii/S0304416500000647
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. http://aem.asm.org/content/65/11/5059.long
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.
2014 - Outstanding Dissertation Advisor, STEM Area, Virginia Tech
2013 - Virginia Tech International Faculty Development Program Fellow (Singapore, Indonesia)
NSF REU: Microbiology in the Post-genome Era (2009-2015)
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 the Southern Piedmont Agricultural Research and Extension Center
Changes in Rumen Microflora Populations Influenced by Genetics and Endophyte Type in Cows Grazing -a collaboration with the Southern Piedmont Agricultural Research and Extension Center (SPAREC) and Shenandoah Valley Agricultural Research and Extension Center (SVAREC)
Specialty Chief Editor (2017-Present), Specialty Assistant Chief Editor (2016-2017), Frontiers in Microbiology, section Microbial Physiology and Metabolism
Member, Editorial Review Board, Archaea, 2003-2009 & 2010-2017.