NEW DIRECTION: Marine Microbial Research. Red deep sea crab contributes to the growing economy of Virginia and more specifically Hampton Roads Area. We partnered with Industry (Atlantic Red Crab Co.); Department of Marine and Environmental Sciences (MES), and J.Craig Venter Institute (JCVI) to conduct research in an area that is under-explored.
The objective of this new research initiative is to study the microbiome in the midgut (gutomics) of the red deep sea crab and in situ water samples with the potential to advance our understanding of microbial communities in an extreme environment and their contribution to ecological balance. The red deep sea crab’s, Chaceon quinquedens, ecological niche is within an environment characterized by extreme environmental conditions such as high pressure, low temperature, low dissolved oxygen, and high salinity. The microbiome at that depth and their association with red crabs might play an important role in key metabolic processes and fitness of the crabs. Globally, the composition of such microbial communities is extremely diverse and varies from geographic location and depth. It also is shaped by abiotic factors. Microbial communities living in such an extreme environment are composed of extremophiles such as halophiles, piezophiles and psychrophiles. Presently, the microbial diversity of the deep sea red crab and its surrounding environment has not been studied. We proposes to study the microbiome in the midgut (gutomics) of the red deep sea crab and in situ water samples. This will be achieved by 16S rDNA sequencing for identification of the taxonomic composition of microbial communities from both the midgut and in in situ water samples. The primary goal of this study is to generate several viable research projects that can be easily carried out by graduate and undergraduate students:
- Identify the taxonomic composition of microbial communities and to observe their relative abundance in the gut of the Chaceon sp. and in in situ water samples (on going project)
- To identify the cause of mortality in live holding tanks over a period of two weeks.
- To identify and characterize secondary metabolites present in the hemolymph of red deep sea crab.
- Understand the role of gut microbial species in shaping the immune system of red deep sea crab.
- Long term goal is to identify a microbial species whose abundance is sensitive to temperature with a potential to develop as a biosensor for climate change and man made unnatural disaster.
- Genetic diversity among red deep sea crabs (on going project)
EXPANDING PAST RESEARCH DIRECTION: Biomedical/ Malaria Parasite Biology
My research interest focuses on Plasmodium falciparum developmental biology. Unlike bacteria, Plasmodium cannot slow down or retard its growth in response to adverse environmental conditions: without transmission it does not survive. Plasmodium species confront dramatic temperature shifts as they moves from the vertebrate host to invertebrate mosquito. Changes in parasite protein synthesis apparatus correlate with, and are putatively an adaptation to, these transitions. It is well documented that P. falciparum has developmentally regulated ribosomal rRNA genes. These genes are differentially expressed during asexual blood stages (A-type), gametocytes (S1-type) and during development in the mosquito (S2-type). I am trying to understand: What molecules/pathways are involved in sensing the constantly changing thermal environment.
Development of new antimalarial drugs that targets novel sites to delay development of drug resistance.
Nocathiacins are thaizolyl peptide group of antibiotic and structurally related to thiostrepton. They have potent activity against a wide spectrum of multi drug resistant gram positive bacteria and inhibit protein synthesis. We evaluated the potential anti-malarial activity of two water soluble derivatives of nocathiacin (BMS461996 and BMS411886) against asexual blood stages of Plasmodium falciparum. The in vitro growth inhibition assay was done using three different laboratory strains of P. falciparum displaying varying degree of chloroquine (CQ) susceptibility. Our results indicates that, BMS461996 has potent anti-malarial activity and inhibits parasite growth with mean IC50 of 45.80 nM for P. falciparum 3D7 (CQ susceptible), 80.68 nM for P. falciparum Dd2 (intermediate CQ susceptibility) and 90.01 nM for P.falciparum K1 strain (multi drug resistant). Similar results at higher IC50 values were obtained with BMS411886. We also tested the effect of BMS491996 on gametocytes, our results shows that at a concentration of 1µM, gametocytes were deformed with a pyknotic nucleus and growth of stage I-III gametocytes appeared to be arrested. Our preliminary study shows significant potential for nocathiacin analogues to be developed as antimalarial drug candidates and warrants further investigation in animal model systems.
Protein arginine methylation: Emerging player in transcription, growth and developmental regulation of malaria parasite.
Research Interest: Malaria is one of the leading cause of death in tropical countries with socio economic problems. Approximately 219 million case reported worldwide and 660,000 died in endemic region with 90% death alone in African continent (WHO report, 2012). Climate change is already influencing the spread of vector borne diseases such as malaria, dengue, lyme diseases. Its been well established that epigenetic’s (i.e. methylation of DNA & histone proteins and chromatin remodeling) is influenced by surrounding environment. Previously we have identified a thermoregulated untranslated RNA (truRNA) whose transcription is modulated by temperature. Mass spec analysis of proteins interacting with truRNA revealed RGG/RSG motif, which is a potential methylation site. Post translational modification (PTM) especially methylation of arginine residue in RGG/RSG motif plays an important role in various cellular process such as RNA metabolism, formation of MRNP complexes, and developmental regulation of cell cycle. Methylation of arginine residue in proteins is carried out by a specialized protein arginine methyl transferases (PRMT). These proteins are highly conserved, homology search identified three protein arginine methyl transferase in Plasmodium falciparum i.e. PRMT1, PRMT 3 and PRMT5. The role of PRMTs in P. falciparum is not yet understood. We propose that three PRMTSs are developmentally regulated and PfPRMT5 plays an important role in optimizing cellular processes such as MRNP complex formation, RNA processing, RNA metabolism, developmental regulation of cell cycle in response to constantly changing environment. Our research on comparative proteome wide analysis of protein arginine methylation in response to temperature focuses on answering fundamental question “How parasite regulates its growth & adapts to its constantly changing environment as it completes its developmental cycle in Human host & mosquito vector?”.
- Sharma I, Lee MD (2019). Draft genome sequence of Cyclobacterium marinum strain Atlantic-IS, isolated from the Atlantic slope off the coast of Virginia, USA. Microbiol Resour Announc 8:e01089-19. https://doi.org/10.1128/MRA.01089-19.
- Sharma I, Sullivan M, McCutchan TF (2015) In vitro antimalarial activity of novel semisynthetic nocathiacin I antibiotics. Antimicrobial Agents Chemotherapy. 59(6):3174-49.
- Rawat DS, Sharma I, Jalah R, Lomash S, Kothekar V, Pasha ST and Sharma YD (2004). Identification, expression, modeled structure and serological characterization of Plasmodium vivax histone 2B. Gene. Aug ;337:25-35.
- Sharma A, Sharma I, Kogkasuriyachai D and Kumar N (2003). Structure of a gametocyte protein essential for sexual development in Plasmodium falciparum. Nature Structural Biology. Mar; 10(3):197-203.
- Sharma I and Sharma Y.D. (2001). Malarial mitochondrial genome: the 6 kb element. Indian J Malariol. 38:45-60. Review
- Sharma I, Aneja MK, Biswas S, Dev V, Ansari MA, Pasha ST and Sharma YD (2001). Allelic variation in Plasmodium falciparum cg2 gene and its unrelatedness with chloroquine resistance among Indian isolates. International Journal for Parasitology 31: 1669-1672.
- Sharma I, Rawat DS, Pasha ST, Biswas S and Sharma YD (2001). Complete nucleotide sequence of 6kb element and conserved cytochrome b gene sequences among Indian isolates of Plasmodium falciparum. International Journal for Parasitology 31:1107-1113.
- Sharma I, Pasha ST and Sharma YD (1998). Complete nucleotide sequence of the Plasmodium vivax 6 kb element. Molecular and Biochemical Parasitology. 97:259-263
- Sharma YD, Fakruddin JM, Bhutani N, Kaushik R, Raina OK and Sharma I (1997). Strain variation and gene hunting in malaria. Indian J. Clin. Biochem. 12(supp), 49 – 51
- Cuker B, Sharma I, Dorsey K,Stojilovic O, Smith N, Justice A. (2020) Pesticides bring the War on Nature to The Chesapeake Bay. Chapter 11, Diet for a Sustainable Ecosystem: The science for recovering the health of the Chesapeake Bay and its people Edited by Benjamin Cuker, Submitted to Springer Publishing Company, New York, USA.
- Sharma I and McCutchan TF. (2005) Plasmodium ribosome and Opportunities for Drug Intervention. Chapter 18, Molecular Approaches to Malaria Edited by Irwin W Sherman, ASM Press, Washington, DC, USA.