Ramakrishna Wusirika

Ramakrishna Wusirika



Associate Professor, Biological Sciences

Director, Biochemistry and Molecular Biology (BMB) Program

  • Ph.D. (1995), National Chemical Laboratory/ University of Pune, Pune, India

Research Description

Dr. Wusirika’s research group is presently working on the following projects.

Role of Heavy Metal Resistant Bacteria in Modulating Biochemical Pathways to Promote Plant Growth and Nutrient Uptake and their Application in Phytoremediation and Agriculture.  Marginal soils arise due to various industrial and agricultural practices reducing crop productivity. Deficiency of nitrogen, phosphorus and other macro and micronutrients in soils result in reduced plant biomass and significant loss of productivity. To meet increasing food and energy needs, development of novel technologies that enable cultivation of crops on marginal lands is essential.  We isolated Pseudomonas sp. TLC 6-6.5-4, a free-living multiple metal-resistant plant growth promoting bacteria (PGPB) from Torch Lake sediment contaminated with copper mine tailings, known as stamp sand. This strain promotes plant growth and copper uptake in maize by production of the plant hormone, indole-3-acetic acid (IAA) and siderophores as well as solubilization of phosphate. We characterized the PGPB and isolated two copper-sensitive mutants, CSM1 and CSM2, with transposon insertions in tryptophan synthase alpha subunit (trpA) and ATP-dependent Clp protease (clpA) genes, respectively. Proteomic analysis revealed that disruption of Clp protease gene up-regulated molecular chaperones and down-regulated the expression of enzymes related to tRNA modification, whereas metabolomic analysis showed that amino acid and oligosaccharide transporters that are part of ATP-binding cassette (ABC) transporters pathways were down-regulated.

We examined both PGPB-soil interaction and PGPB-maize interaction and showed that the mode of PGPB application has significant impact on these interactions. Four different methods of PGPB application exhibited significant improvement in biomass (2.5–7-fold) in comparison with control plants grown in marginal soil alone. The first two groups (G1 and G2) resulted in higher copper uptake (4-fold higher) by maize grown in soil with PGPB compared to control. PGPB improved soil health based on significant increase in activities of soil enzymes, invertase, dehydrogenase and catalase in soil with PGPB compared with marginal soil alone and marginal soil with maize. PGPB increased total chlorophyll content in maize leaves by 60% which suggests higher photosynthetic rates. The PGPB-soil interaction improved phosphorus uptake by maize and led to a significant decrease in organic bound copper in the marginal soil and a notable increase in exchangeable copper. PGPB addition increased both rhizospheric and non-rhizospheric soil bacteria.

Proteomic and metabolomic analysis was performed to identify candidate proteins and metabolites, which are likely to play a role in regulating biochemical, molecular and physiological responses of maize grown in marginal soils with PGPB. Metabolomic analysis of maize revealed that PGPB inoculation upregulated photosynthesis and hormone biosynthesis. Proteomic analysis identified upregulation of proteins related to plant development and stress response. Further, the activity of antioxidant enzymes and total phenolics decreased in plants grown in marginal soil suggesting alleviation of metal stress in presence of PGPB. The ability of PGPB to modulate interconnected biochemical pathways could be exploited to increase crop productivity in marginal soils, phytoremediation of metal contaminated soils and in organic agriculture.

Rice Callus Culture as an Anticancer Agent.  Plant natural products have been tested and used to control the progression of cancer. The major drawback of most anticancer drugs in the market is they also affect the growth and viability of normal cells. Callus is a mass of somatic undifferentiated plant cells that are totipotent.  Callus suspension culture is generated by growing callus in plant growth medium for three weeks when they release secondary metabolites.  Callus suspension cultures unlike plant parts offer the advantage of providing unlimited supply of compounds. Rice callus suspension culture showed promising results killing 83% colon cancer cells and 95% renal cancer cells, with little or no effect on normal cells (human lung fibroblasts).  Anticancer drugs such as paclitaxel (Taxol) and etoposide inhibited the growth of the two cancer cell lines as well as the human lung fibroblasts. Scanning electron microscopy (SEM) of the colon cancer cell line treated with rice callus culture showed reduced cell number, morphology and increased adhesiveness.

Genes and Metabolic Pathways Common to Abiotic (Drought) and Biotic (Bacteria) Stress Responses in Rice and Arabidopsis.  Crop productivity and survival are tightly linked to its environment which is being altered due to climate change threatening the food security of the world. According to the latest World Agricultural Supply and Demand Estimates (WASDE) report by United States Department of Agriculture (USDA), about 80% of agricultural land is experiencing drought. Plant stress response is a complex trait involving multiple genes that are regulated in several layers involving epigenomic, transcriptomic, proteomic and metabolomic factors. Reflecting the declining environmental conditions, plants are exposed simultaneously to multiple stresses resulting in enormous changes in the molecular landscape within the cell. Comprehensive understanding of the regulatory networks that modulate the dynamic adaptive changes in a plant responding to stress is critical to meet future energy needs. 

We performed bioinformatic and proteomic analysis to study differentially regulated genes (DRGs) under drought stress. DRGs were enriched with epigenetic features, namely, DNA methylation marks, microRNAs and show protein-protein interactions (PPIs) with other proteins encoded by DRGs, compared to a random gene set. Several DRGs that code for transcription factors are targeted by multiple (>5) microRNAs (miRNA). Metabolic pathway analysis revealed enrichment of pathways involved in synthesis of compounds that function as osmoprotectants and antioxidants in the cluster EU (genes upregulated under drought with either DNA methylation reads overlapping promoter region or genic region, miRNA target or ChromDB gene). We identified “master genes” coding for rice proteins including transcription factors which interact with a network of proteins significantly impacting drought response. 

Rice and Arabidopsis are model plant organisms representing monocots and dicots, respectively. Extensive biological knowledgebase and resources including complete genome sequence and highest number of microarray studies in the plant kingdom are available for these two genomes. Analysis of stress responsive genes within and between rice and Arabidopsis for different kinds of stresses would reveal a number of pivotal attributes spanning across the major plant division, angiosperms.

Research Interests

  • Plant Molecular Biology and Comparative Genomics
  • Plant Growth Promoting Metal Resistant Bacteria and their Role in Phytoremediation, Agriculture and Biofuels
  • Bioinformatic and Functional Analysis of Drought Responsive Genes
  • Role of Plant Natural Compounds as Anti-Cancer Agents
  • Bioinformatic and Functional Analysis of Plant Bidirectional promoters

Recent Publications

  • Rafi S, Ramakrishna W. (2012) Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PloS ONE 7:e49331. Read More
  • Li K, Pidatala RR, Ramakrishna W (2012) Mutational, proteomic and metabolomic analysis of a plant growth promoting copper-resistant Pseudomonas spp. FEMS Microbiol Lett 335: 140–148. Read More
  • Deshpande AD, Dhadi SR, Hager E, Ramakrishna W. (2012) Rice callus suspension cultures inhibit growth of two cancer cell lines. Phytotherapy Research 26: 1075–1081 Read More
  • Krom N, Ramakrishna, W. (2012) Retrotransposon insertions in rice gene pairs associated with reduced conservation of gene pairs in grass genomes. Genomics 99:308-314.
  • Dhadi SR, Deshpande A, Ramakrishna W. (2012) A novel non-wounding transient expression assay for cereals mediated by Agrobacterium tumefaciens. Plant Molecular Biology Reporter 30:36-45.
  • Li K, Ramakrishna W. (2011) Effect of multiple metal resistant bacteria from contaminated lake sediments on metal accumulation and plant growth. J. Hazardous Materials 189:531-539.
  • Xu Z, Rafi S, Ramakrishna W. (2011) Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters. Genome 54:629-638.
  • Krom N, Ramakrishna W. (2010) Conservation, rearrangement, and deletion of gene pairs during the evolution of four grass genomes. DNA Research 17:343-352.
  • Dhadi SR, Krom N, Ramakrishna W. (2009) Genome-wide comparative analysis of putative bidirectional promoters from rice, Arabidopsis and Populus. Gene 429:65-73.
  • Krom N, Ramakrishna, W. (2008) Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and Populus. Plant Physiology 147:1763-1773.
  • Krom N, Recla J, Ramakrishna W. (2008) Analysis of genes associated with retrotransposons in the rice genome. Genetica 134:297-310.
  • Xu Z, Ramakrishna W. (2008) Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. Gene 412:50-58.
  • Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J. (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640-1644.
  • Ramakrishna W, Deng Z, Ding CK, Handa AK, Ozminkowski RH Jr. (2003) A novel small heat shock protein gene, vis1, contributes to pectin depolymerization and juice viscosity in tomato fruit. Plant Physiology 131: 725-735.
  • Bennetzen JL, Ramakrishna W. (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Molecular Biology 48:821-827.
  • Ramakrishna W, Dubcovsky J, Park Y-J, Busso C, Emberton J, SanMiguel P, Bennetzen JL. (2002) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162:1389-1400.
  • Ramakrishna W, Emberton J, Ogden M, SanMiguel P, Bennetzen JL. (2002) Structural analysis of the maize Rp1 complex uncovers numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14:3213-3223.

Recent Funding

  • Rice Callus: A Side-Effect-Free Solution to Cancer. Superior Ideas. 5/2013-4/2014
  • Identification and Characterization of Bidirectional Promoters in the Rice Genome. USDA-NRI CSREES Plant Biology: Gene Function and Regulation. 7/2007-6/2010.
  • Development of Plant Based Products. Arch Personal Care Products. 8/2009-7/2010
  • Organization and Evolution of Disease Resistance Gene Clusters in Cereal Genomes. MTU Research Excellence Fund. 7/2004-12/2005.
  • NanoDrop Spectrophotometer for Molecular Biology and Biochemistry. MTU Century II Campaign Endowed Equipment (C2E2) Fund. 5/2004-5/2006.
  • Do bidirectional Promoters Exist in Rice and Maize? MTU Faculty Scholarship Grant. 7/2005-6/2006.