Divya Prakash | Chemistry and Biochemistry| SIU

Home
Southern Illinois University

CONTACT

SIU.EDU

College of Agriculture, Life and Physical Sciences

Divya Prakash

Assistant Professor

Phone: 618-453-6481
Fax: 618-453-6408
email: divya.prakash@siu.edu 

 

We employ an interdisciplinary approach to examine processes that have a significant impact on the global carbon cycle, alternative energy, and biomedicine. We use tools from chemistry, biochemistry, microbiology, molecular biology, spectroscopy (EPR, Mӧssbauer), and biophysics to develop a molecular understanding of the proteins involved in electron transport coupled with energy conservation and stress response in anaerobic microbes. Our lab focuses on understanding the microbial metabolism of methane formation and oxidation which includes advance understanding of the role and mechanism of only two known [4Fe-4S] constituting disulfide reductases: heterodisulfide reductases (HDR) and ferredoxin disulfide reductases (FDR), which are important for energy conservation and oxidative stress in methanogens, respectively. In addition, we are interested in understanding the metabolism of gut-associated methanogens since the host-associated microbial studies have focused on bacterial, fungal, or viral communities, but the archaeal component has often been neglected, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. We aim to investigate the role of gut-associated methanogenic archaea to combat atherosclerosis and other trimethylamine-associated diseases.

  1. Microbial metabolism of methane formation and oxidation: In addition to being a potent greenhouse gas, methane is also a cheap, renewable fuel that has great potential for manufacturing value-added chemicals. Acetate-utilizing methane-producing anaerobes (acetotrophic methanogens) account for two-thirds of the methane produced in anaerobic microbial food chains converting complex renewable biomass to methane (biomethanation). Although much is known regarding one-carbon transformations leading from the methyl group of acetate to methane, there is a rudimentary understanding of electron transport processes coupled to energy conservation and oxidative stress. The mechanism of energy conservation and oxidative stress in acetotrophic methanogens needs to be studied in order to gain a deeper understanding of acetate metabolism and harness energy from methane. Overall, the understanding of energy conservation and stress response in methanogens will lead to better methods for modulating biological methane production. Our aim is to advance understanding by determining the role and mechanism of only two known [4Fe-4S] constituting disulfide reductases: heterodisulfide reductases (HDR) and ferredoxin disulfide reductases (FDR), which are important for energy conservation and oxidative stress in methanogens, respectively.

    (i). Heterodisulfide reductases (Hdr): We aim to advance an understanding by employing biochemical, biophysical, and molecular approaches to determine the mechanism of heterodisulfide reductases essential for energy conservation in methanogens. The project will investigate two heterodisulfide reductase complexes (HdrED and HdrA2B2C2), essential for acetotrophic growth of the model acetotroph Methanosarcina acetivorans and homologs essential in other diverse methanogenic pathways. All catalyze reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB), yielding HS-CoM and HSCoB. HdrA2B2C2 is an electron bifurcating complex representing a new mechanism of energy conservation. The genomes of diverse species in the domains Bacteria and Archaea are annotated with genes encoding homologs which suggests roles in diverse energy-conserving metabolisms including the anaerobic oxidation of CH4.

    (ii). Mechanistic and physiological role of ferredoxin: disulfide reductase: Thioredoxins and thioredoxin reductases (TrxR) are important group of enzymes responding to oxidative stress in all domains of life. Acetotrophic methanogens, M. acetivorans produces the Fdx:disulfide reductase (FDR), and a homolog Archael Ferreodxin: Thioredoxin Reductase (AFTR). Both FDR and AFTR are upregulated during extracellular electron transfer suggesting a role in respiratory metabolism and methane oxidation. Although FDR and AFTR are widely distributed in organisms from the domain Archaea and Bacteria, substantially less is understood of the biochemistry and physiology. The extensively characterized plant-type Fdx:thioredoxin reductase (FTR) and FDRs (FDR and AFTR) belong to a distinct class of disulfide reductases that contain a non-canonical CPC*XnCPCXnCY/HC* [4Fe4S] motif for which the ‘asterisked’ cysteines form the redox-active disulfide, and the remaining cysteines ligate the unusual [4Fe4S] cluster. Not reported for either FTR or FDR, reduction of AFTR yields a transient [4Fe-4S]1+ cluster with features attributed to an S=7/2 spin state that accompany a classical S=1/2 signal of the [4Fe-4S]1+ cluster. We propose to further investigate the catalytic mechanism that includes this unprecedented S=7/2 intermediate. Overall, the findings will provide a more in-depth understanding of oxidative stress in methanogens and the broader field of anaerobes.

  2. Therapeutic effectiveness of gut-associated methanogens in the prevention of atherosclerosis: Understanding the metabolism of anaerobic gut microbes at the molecular level is essential, as the metabolic functions of these microbes shape the gut environment and influence human health. We aim to investigate the role of gut-associated methanogenic archaea to combat atherosclerosis and other trimethylamine-associated diseases. Trimethylamine (TMA) produced by gut microbiota from dietary ingredients is further oxidized into trimethylamine- oxide (TMAO) in the liver and contributes towards atherosclerosis and other clinical effects. Therefore, prevention of these diseases could rely on lowering the TMA level by human gut-associated TMA-utilizing methane-producing anaerobes ('archaebiotics') that convert TMA into non-reactive methane. We are working to elucidate the bioenergetics and oxidative stress response of archaebiotics. Further, we will employ these findings to encapsulate archaebiotics into nanoparticles to develop nanoarchaebiotics similar to nanoprobiotics for efficient delivery into the gut. Finally, we will determine the effect of nanoarchaebiotics on Apolipoprotein E knockout mice (a human atherosclerosis model). We will also look for other potential collaborators working on TMA-associated disease, including the human model, to understand the role of methanogens in combating cardiovascular-related disease.

Education 

M.Sc. (Biotechnology), Goa University, India, 2007
M. Phil. (Enviromental Sciences/Raditation Biology), Jawaharlal Nehru University, India, 2009
Ph.D. (Chemistry & Biochemistry), Auburn University, 2014
Postdoctoral Scholar, Pennsylvania State University, 2015-2017
Assistant Research Professor, Pennsylvania State University, 2017-2022

Selected Publications

  1. Divya Prakash, Xiong Jin, Shikha S Chauhan, Karim A. Walters, Neela H. Yennawar, John H. Golbeck, Yisong Guo, and James G. Ferry “Characterization of the archetype from group 4 of the FTR-like ferredoxin: thioredoxin reductase family replete with homologs from methanogenic Archaea.” ( Under review in iSciences).
  2. Divya Prakash, Prashanti R. Iyer, Suharti Suharti, Karim A. Walters, John H. Golbeck, Katsuhiko S. Murakami, and James G. Ferry. (2019) “Structure and Function of Flavodoxin from the Domain Archaea Stabilizing an Anionic Semiquinone”. Natl. Acad. Sci. U.S.A, 116 (51) 25917-25922.
  3. Divya Prakash, Shikha Chauhan, James G. Ferry. (2019). “Life on the Thermodynamic Edge: Respiratory Growth of an Acetotrophic Methanogen”. Science Advances 5: eaaw9059.
  4. Prakash, D*., Chauhan, S., & Behari, J. (2019). “Therapeutic effectiveness of Hydroxyapatite Nanoparticles and Pulsed Electromagnetic Field in Osteoporosis and Cancer”. Journal Of Advances In Biotechnology, 8, 1058-107 (Corresponding author)
  5. Prakash, D., Walters, K. A., Martinie, R. J., Mc Carver, A. C., Kumar, A. K., Lessner, D. J., Krebs, C., Golbeck, J. H., and Ferry, J. G. (2018). “Toward a mechanistic and physiological understanding of a ferredoxin: disulfide reductase from the domains Archaea and Bacteria”. Journal of Biological Chemistry 293, 9198-9209.
  6. Evert Duin, Tristan Wagner, Seigo Shima, Divya Prakash, Bryan Cronin, David R. Yáñez-Ruiz, Stephane Duval, Robert Rümbeli, René T. Stemmler, Rudolf Kurt Thauer, and Maik Kindermann. (2016). “Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol”. Proc. Natl. Acad. Sci. U.S.A, 113 (22), 6172–6177.
  7. Deepa Yenugudhati, Divya Prakash, Adepu Kumar, R. Siva Sai Kumar, Neela H. Yennawar, Hemant P. Yennawar, and James G. Ferry. (2016). “Structural and Biochemical Characterization of Methanoredoxin from Methanosarcina acetivorans, a Glutaredoxin-Like Enzyme with Coenzyme M-Dependent Protein Disulfide Reductase Activity”. Biochemistry, 55 (2), 313–321.
  8. Yifeng Wei, Bin Li, Divya Prakash, James G. Ferry, Sean J. Elliott, and JoAnne Stubbe. (2015). “A Ferredoxin Disulfide Reductase Delivers Electrons to the Methanosarcina barkeri Class III Ribonucleotide Reductase”. Biochemistry, 54 (47), pp 7019–7028.
  9. Divya Prakash, Yonnie Yu, Sang-Jin Suh, Evert C Duin (2014). “Elucidating the process of activation of Methyl-Coenzyme M Reductase”. Journal of Bacteriology, 196 (13), 2491-98.
  10. Prakash Divya, J (2009). “Synergistic role of hydroxyapatite nanoparticles and pulsed electromagnetic field therapy to prevent bone loss in rats following exposure to simulated microgravity”. International Journal of Nanomedicine 4, 133-144.