Biswarup Mukhopadhyay

Courses Taught

BCHM 4115: General Biochemistry (Summer 2021)

BCHM 4124: Laboratory Problems in Biochemistry and Molecular Biology

BCHM 5004: Seminar in Biochemistry

BCHM 5014: Biochemical Research Rotations (co-taught) (2016-19)

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

Three PhD students
Five undergraduate students: BCHM 4994

Research

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/

References:

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. .

5.    Purwantini, E., and L. Daniels. 1998. Molecular analysis of the gene encoding F₄₂₀-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. Journal of bacteriology 180:2212-2219.

6.    Purwantini, E., and L. Daniels. 1996. Purification of a novel coenzyme F₄₂₀-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. Journal of bacteriology 178:2861-2866.

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.

9.    Purwantini, E., and B. Mukhopadhyay. 2013. Rv0132c of Mycobacterium tuberculosis Encodes a Coenzyme F420-Dependent Hydroxymycolic Acid Dehydrogenase. PloS one 8:e81985.

10.  Susanti, D., and B. Mukhopadhyay. 2012. An intertwined evolutionary history of methanogenic archaea and sulfate reduction. PloS one 7:e45313.

Dr. Mukhopadhyay's PubMed Site

Dr. Mukhopadhyay's Google Scholar Site

Selected publications (total: 66 peer-reviewed; 2 editorially reviewed; 2 currently under peer review; three non-peer reviewed. *, graduate student; underlined, undergraduate student; **, co-mentored graduate student)

Heryakusuma C*, Susanti D, Yu H, Li Z, Purwantini E, Hettich RL, Orphan VJ, Mukhopadhyay B. 2022. A Reduced F_420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon. J Bacteriol 204:e0007822. https://doi.org/10.1128/jb.00078-22.

Khairunisa BH*, Susanti D, Loganathan U, Teutsch CD, Campbell BT, Fiske D, Wilkinson CA, Aylward FO, Mukhopadhyay B. 2022. Dominant remodelling of cattle rumen microbiome by Schedonorus arundinaceus (tall fescue) KY-31 carrying a fungal endophyte. Access Microbiol 4:000322. https://doi.org/10.1099/acmi.0.000322.

Das JK, Heryakusuma C*, Susanti D, Choudhury PP, Mukhopadhyay B. 2022. Reduced protein sequence patterns in identifying key structural elements of dissimilatory sulfite reductase homologs. Comput Biol Chem 98:107691. https://doi.org/10.1016/j.compbiolchem.2022.107691.

Banavar A, Amirkolaei SK, Duscher L, Khairunisa BH*, Mukhopadhyay B, Schwarz M, Urick S, Ovissipour R. 2022. Nutritional Evaluation of Black Soldier Fly Frass as an Ingredient in Florida Pompano (Trachinotus carolinus L.) Diets. Animals 12:2407. https://doi.org/10.3390/ani12182407

Heryakusuma C*, Johnson EF, Purwantini E, Mukhopadhyay B. 2022. Nitrite reductase activity in F₄₂₀-dependent sulfite reductase (Fsr) from Methanocaldococcus jannaschii. (in review) https://doi.org/10.1099/acmi.0.000482.v1.

Khairunisa BH*, Loganathan U, Ogejo JA, Mukhopadhyay B. 2022. Nitrogen Transformation Processes in Manure Microbiomes of Earthen Pit and Concrete Storages on Commercial Dairy Farms. (in review) https://doi.org/10.21203/rs.3.rs-1969129/v1.

Phan HD, Norris AS, Du C, Stachowski K, Khairunisa BH*, Sidharthan V, Mukhopadhyay B, Foster MP, Wysocki VH, Gopalan V. 2022. Elucidation of structure-function relationships in Methanocaldococcus jannaschii RNase P, a multi-subunit catalytic ribonucleoprotein. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac595.

Velander P, Wu L, Hildreth SB, Vogelaar NJ, Mukhopadhyay B, Helm RF, Zhang S, Xu B. 2022. Catechol-Containing Compounds are a Broad Class of Protein Aggregation Inhibitors: Redox State is a Key Determinant of the Inhibitory Activities. Pharmacol Res https://doi.org/10.1016/j.phrs.2022.106409.

Mukhopadhyay B, Dodsworth JA, Whitman WB. 2022. Genus Methanocaldococcus, p 1-14. In Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB (ed), Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc., in association with Bergey's Manual Trust. https://doi.org/10.1002/9781118960608.gbm00500.pub2

Mukhopadhyay B, Dodsworth JA, Whitman WB. 2022. Genus Methanotorris. In Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB (ed), Bergey's Manual of Systematics of Archaea and Bacteria (in press). John Wiley & Sons, Inc., in association with Bergey's Manual Trust.

Brown CL**, Garner E, Jospin G, Coil DA, Schwake DO, Eisen JA, Mukhopadhyay B, Pruden AJ. 2020. Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus. PLoS One 15:e0223033. https://doi.org/10.1371/journal.pone.0223033.

Susanti D, Frazier MC, Mukhopadhyay B. 2019. A Genetic System for Methanocaldococcus jannaschii: An Evolutionary Deeply Rooted Hyperthermophilic Methanarchaeon. Frontiers in Microbiology 10:1256. https://doi.org/10.3389/fmicb.2019.01256.

Purwantini E, Loganathan U, Mukhopadhyay B. 2018. Coenzyme F₄₂₀-Dependent Glucose-6-Phosphate Dehydrogenase-Coupled Polyglutamylation of Coenzyme F₄₂₀ in Mycobacteria. J Bacteriol 200:00375-18. https://doi.org/10.1128/JB.00375-18.

Yu H, Susanti D, McGlynn SE, Skennerton CT, Chourey K, Iyer R, Scheller S, Tavormina PL, Hettich RL, Mukhopadhyay B, Orphan VJ. 2018. Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. Front Microbiol 9:2917. https://doi.org/10.3389/fmicb.2018.02917.

Purwantini E, Daniels L, Mukhopadhyay B. 2016. F₄₂₀H₂ Is Required for Phthiocerol Dimycocerosate Synthesis in Mycobacteria. J Bacteriol 198:2020-8. https://doi.org/10.1128/JB.01035-15.

Susanti D, Loganathan U*, Mukhopadhyay B. 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. https://doi.org/10.1074/jbc.M116.750208.

Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. 2014. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol 5:634. https://doi.org/10.3389/fmicb.2014.00634.

Susanti D*, Wong JH, Vensel WH, Loganathan U*, DeSantis R, Schmitz RA, Balsera M, Buchanan BB, Mukhopadhyay B. 2014. Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii. Proc Natl Acad Sci U S A 111:2608-13. https://doi.org/10.1073/pnas.1324240111.

Purwantini E, Mukhopadhyay B. 2013. Rv0132c of Mycobacterium tuberculosis Encodes a Coenzyme F₄₂₀-Dependent Hydroxymycolic Acid Dehydrogenase. PLoS One 8:e81985. https://doi.org/10.1371/journal.pone.0081985.

Susanti D*, Johnson EF, Rodriguez JR*, Anderson I, Perevalova AA, Kyrpides N, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Mavrommatis K, Peters L, Land ML, Hauser L, Gopalan V, Chan PP, Lowe TM, Atomi H, Bonch-Osmolovskaya EA, Woyke T, Mukhopadhyay B. 2012. Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia. J Bacteriol 194:5703-4. https://doi.org/10.1128/JB.01314-12.

Susanti D*, Mukhopadhyay B. 2012. An intertwined evolutionary history of methanogenic archaea and sulfate reduction. PLoS One 7:e45313. https://doi.org/10.1371/journal.pone.0045313.

Dharmarajan L*, Kraszewski JL*, Mukhopadhyay B, Dunten PW. 2011. Structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate. Proteins 79:1820-9. https://doi.org/10.1002/prot.23006.

Cho IM, Lai LB, Susanti D*, Mukhopadhyay B, Gopalan V. 2010. Ribosomal protein L7Ae is a subunit of archaeal RNase P. Proc Natl Acad Sci U S A 107:14573-8. https://doi.org/10.1073/pnas.1005556107.

Anderson I, Ulrich LE, Lupa B, Susanti D*, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L*, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J, Kyrpides N. 2009. Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One 4:e5797. https://doi.org/10.1371/journal.pone.0005797.

Purwantini E, Mukhopadhyay B. 2009. Conversion of NO₂ to NO by reduced coenzyme F₄₂₀ protects mycobacteria from nitrosative damage. Proc Natl Acad Sci U S A 106:6333-8. https://doi.org/0812883106

Dharmarajan L*, Case CL, Dunten P, Mukhopadhyay B. 2008. Tyr²³⁵ of human cytosolic phosphoenolpyruvate carboxykinase influencing catalysis through an anion-quadrupole interaction with phosphoenolpyruvate carboxylate. FEBS Journal 275:5810-9. https://doi.org/10.1111/j.1742-4658.2008.06702.x

Johnson EF, Mukhopadhyay B. 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. https://doi.org/10.1128/AEM.00098-08

Case CL, Concar EM, Boswell KL, Mukhopadhyay B. 2006. Roles of Asp⁷⁵, Asp⁷⁸, and Glu⁸³ of GTP-dependent phosphoenolpyruvate carboxykinase from Mycobacterium smegmatis. J Biol Chem 281:39262-72. https://doi.org/10.1074/jbc.M602591200

Lai H, Kraszewski J*, Purwantini E, Mukhopadhyay B. 2006. Identification of pyruvate carboxylase genes in Pseudomonas aeruginosa PAO1 and development of a P. aeruginosa-based overexpression system for a₄- and a₄b₄-type pyruvate carboxylases. Appl Environ Microbiol 72:7785-92. https://doi.org/10.1128/AEM.01564-06.

Johnson EF, Mukhopadhyay B. 2005. A new type of sulfite reductase, a novel coenzyme F₄₂₀-dependent enzyme, from the methanarchaeon Methanocaldococcus jannaschii. J Biol Chem 280:38776-86. https://doi.org/10.1074/jbc.M503492200.

Patel HM, Kraszewski JL, Mukhopadhyay B. 2004. The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure. J Bacteriol 186:5129-37. https://doi.org/10.1128/JB.186.15.5129-5137.2004

2022-23 - Center for Advanced Innovation in Agriculture (CAIA) Faculty Fellow

2014 - Outstanding Dissertation Advisor, STEM Area, Virginia Tech

2013 - Virginia Tech International Faculty Development Program Fellow (Singapore, Indonesia)

Education Outreach

NSF REU: Microbiology in the Post-genome Era (2009-2015)
http://microbiologyreu-ret.vbi.vt.edu/

http://microbiologyreu-ret.vbi.vt.edu/

Current Projects

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

Extension Collaboration

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)

Editorial Service

Specialty Chief Editor (2017-Present), Specialty Assistant Chief Editor (2016-2017), Frontiers in Microbiology, section Microbial Physiology and Metabolism

https://www.frontiersin.org/journals/microbiology/sections/microbial-physiology-and
metabolism

Member, Editorial Review Board, Archaea, 2003-2009 & 2010-2017.