Dr. Ramakrishna Wusirika
Assistant Professor

Ph.D., University of Pune, 1995

Research Area: Plant Molecular Biology and Comparative Genomics; Bioinformatics; Evolutionary and Functional Analysis of Plant Genes, Promoters, and Transposable Elements; Organization and Evolution of Cereal Disease Resistance Genes.

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

(1) Comparative analysis of regulation of genes associated with retrotransposons in indica and japonica rice.
A large proportion of complex plant genomes are composed of transposable elements (TEs), which play an important role in gene and genome evolution.  We identified genes with retrotransposon insertions from rice (Oryza sativa).  Phylogenetic conservation and fixation of sequenced genes with retrotransposon insertions in rice is being investigated in cultivated and wild rice species belonging to the genus Oryza.  The ability of retrotransposons to regulate gene expression by insertion in genes or their promoters is being investigated by studying expression patterns in indica and japonica rices as well as their F1 hybrids.  Effect of epigenetic modifications in regulating retrotransposon mediated gene expression is also being evaluated.     

(2) Identification and characterization of bidirectional promoters in rice, Arabidopsis, and Populus genomes using a comparative genomic approach.
Bidirectional promoters regulate two adjacent divergent genes arranged in a head-to-head manner in opposite orientations.  We are investigating the presence of bidirectional promoters in rice, Arabidopsis, and Populus.  Putative bidirectional promoters from rice, Arabidopsis, and Populus genomes were identified using bioinformatic approaches.  Some of these putative bidirectional promoters including those present between divergent genes with conserved order and orientation between Arabidopsis and rice are being tested for their ability to drive the expression of the reporter genes egfp and rfp in forward and reverse orientations, respectively.  In addition, deletion constructs are being made for selected promoters to identify regions in the promoter that contribute to their bidirectional nature.  Tissue specific expression patterns of reporter genes driven by the full-length and truncated promoters will be studied in transgenic plants. 

(3) Molecular characterization and phylogenetic analysis of copper resistant microorganisms from mine tailings. 
The purpose of this study is to identify copper resistant microorganisms which can be used in bioremediation.  We are in the process of identifying microbes from Torch Lake cores with different copper levels by sequencing rpoD gene encoding sigma unit of RNA polymerase and gyrB gene encoding β-subunit of DNA gyrase.  This comparative approach has identified different Pseudomonas species from different cores.  Once the phylogenetic position of these organisms is established, the mechanism of copper resistance will be investigated. 
   

Publications

• Analysis of genes associated with retrotransposons in the rice genome. N Krom, J Recla, W Ramakrishna Genetica (2008) doi: 10.1007/s10709-007-9237-3.
• Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. Z Xu, W Ramakrishna. Gene (2008) doi: 10.1016/j.gene.2008.01.012.
• Differential expansion and expression of - and -tubulin gene families in Populus. RV Oakley, Y-S Wang, W Ramakrishna, SA Harding and C-J Tsai. Plant Physiol (2007) 145: 961-973.
•  Fine mapping of the Pc locus of Sorghum bicolor, a gene controlling the reaction to a fungal pathogen and its host-selective toxin. E Nagy, T-C Lee, W Ramakrishna, Z Xu, P Klein, P SanMiguel, C-P Cheng, J Li, K Devos, K Schertz, L Dunkle and J Bennetzen. Theor Appl Genet (2007) 114: 961-970.
• Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings. M Gorantla, P Babu, VL Reddy, A Reddy, R Wusirika, JL Bennetzen and AR Reddy. J Exp Botany (2007) 58: 253-265.
• Consistent over-estimation of gene number in complex plant genomes. JL Bennetzen, C Coleman, R Liu, J Ma and W Ramakrishna. Curr Opin Plant Biology (2004) 7: 732-736.
• Close split of sorghum and maize genome progenitors. Z Swigoňová, J Lai, J Ma, W Ramakrishna, V Llaca, JL Bennetzen and J Messing. Genome Res (2004) 14: 1916–1923.
• Gene loss and movement in the maize genome. J Lai, J Ma, Z Swigonová, W Ramakrishna, E Linton, V Llaca, B Tanyolac, Y-J Park, O-Y Jeong, J L Bennetzen and J Messing. Genome Res (2004) 14: 1924-1931.
• The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. L.Yan, A Loukoianov, A Blechl, G Tranquilli, W Ramakrishna, P SanMiguel, JL Bennetzen, V Echenique and J Dubcovsky. Science (2004) 303: 1640-1644.
• A novel small heat shock protein gene, vis1, contributes to pectin depolymerization and juice viscosity in tomato fruit. W Ramakrishna, Z Deng, C-K Ding, AK Handa and RH Ozminkowski Jr. Plant Physiol (2003) 131: 725-735.
• Genomic colinearity as a tool for plant gene isolation. W Ramakrishna and JL Beneetzen. Chapter in the book, "Plant Functional Genomics: Methods & Protocols" (2003) Humana Press, Ed. Grotewold, E, Vol. 236: 109-121.
• Structural analysis of the maize Rp1 complex uncovers numerous sites and unexpected mechanisms of local rearrangement. W Ramakrishna, P SanMiguel, J Emberton, M Ogden and JL Bennetzen. Plant Cell (2002) 14: 3213-3223.
• Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal denomes. W Ramakrishna, J Dubcovsky, Y-J Park, C Busso, J Emberton, P SanMiguel and JL Bennetzen. Genetics (2002) 162: 1389-1400.
• Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex. W Ramakrishna, P SanMiguel, J Emberton, M Ogden, J Messing and JL Bennetzen. Plant Physiol (2002) 130: 1728-1738.
• Exceptional haplotype variation in maize JL Bennetzen and W Ramakrishna. Proc Natl Acad Sci USA (2002) 99: 9093-9095.
• Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. JL Bennetzen and W Ramakrishna. Plant Mol Biol (2002) 48: 821-827.
• Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes. L Yan, V Echenique, C Busso, W Ramakrishna, P SanMiguel, JL Bennetzen, S Harrington and J Dubcovsky. Mol Genet Genomics (2002) 268: 488-499.
• Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. W Ramakrishna et al., Comparative and Functional Genomics (2002) 3: 165-166.
• The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. M Stam, C Belele, W Ramakrishna, JE Dorweiler, JL Bennetzen and VL Chandler. Genetics (2002) 162: 917-930.
• Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22). AR Reddy, W Ramakrishna, A Chandra Sekhar, N Ithai, P Ravindra Babu, MF Bonaldo, MB Soares and JL Bennetzen. Genome (2002) 45: 204-211.
• Genomic sequencing reveals gene content, genomic organization and recombination relationships in barley. N Rostoks, Y-J Park, W Ramakrishna, J Ma, A Druka, BA Shiloff, PJ SanMiguel, Z Jiang, R Brueggeman, D Sandhu, K Gill, JL Bennetzen and A Kleinhofs.  Functional and Integrative Genomics (2002) 2: 51-59.
• Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am. P SanMiguel, W Ramakrishna, JL Bennetzen, CS Busso and J Dubcovsky. Functional and Integrative Genomics (2002) 2: 70-80.
• Comparative sequence analysis of colinear barley and rice bacterial artifical chromosomes. J Dubcovsky, W Ramakrishna, P SanMiguel, CS Busso, L Yan, BA Shiloff and JL Bennetzen. Plant Physiol (2001) 125: 1342-1353.
• Potential of (GATA)4 microsatellites from rice for inter- and intra- specific variability studies. AP Davierwala, W Ramakrishna, KV Chowdari, PK Ranjekar and VSGupta. BMC Evol Biol (2001) 1: 7.
• Sequence variations at a complex microsatellite locus in rice and its conservation in cereals. AP Davierwala, W Ramakrishna, PK Ranjekar and VS Gupta. Theor Appl Genet (2000) 101: 1291-1298.
• Microsatellite (GATA)4 reveals sex specific differences in Papaya. AS Parasnis, W Ramakrishna, KV Chowdari, VS Gupta and PK Ranjekar. Theor Appl Genet (1999) 99: 1047-1052.
• Phylogenetic classification and molecular evolution of knotted1 homeobox genes. AD Deshpande, W Ramakrishna, GP Mulay, VS Gupta and PK Ranjekar. Theor Appl Genet (1999) 99: 203-209.
• Differential methylation of microsatellite and minisatellite loci in rice. W Ramakrishna, VS Gupta and PK Ranjekar. Cereal Res Comm (1999) 27: 365-371.
• Expansion of a (GA) dinucleotide at a microsatellite locus associated with domestication in rice. W Ramakrishna, AP Davierwala, VS Gupta and PK Ranjekar. Biochemical Genet (1998) 97: 135-140.
• Idendification of minor DNA variations in rice somoclonal variants. KV Chowdari, W Ramakrishna, SA Tamhankar, RR Hendre, VS Gupta, NA Sahasrabudhe and PK Ranjekar. Plant Cell Rep (1998) 18: 55-58.
• DNA fingerprinting of Indian isolates of Xanthomonas oryzae pv. oryzae. MD Rajebhonsle, KV Chowdari, W Ramakrishna, S Tamhankar, VS Gupta, SS Gnanamanickam and PK Ranjekar. Theor Appl Genet (1997) 95: 103-111.
• DNA fingerprinting to detect variation in rice using hypervariable DNA sequences. W Ramakrishna, KV Chowdari, MD Lagu, VS Gupta and PK Ranjekar. Theor Appl Genet (1995) 90: 1000-1006.
• DNA fingerprinting detects genetic variability in the pearl millet downy mildew pathogen (Sclerospora graminicola) using simple sequence repeats. JG Sastry, W Ramakrishna, S Sivaramakrishnan, RP Thakur, VS Gupta and PK Ranjekar. Theor Appl Genet (1995) 91: 856-861.                                                                        
• DNA fingerprinting in rice with oligonucleotide probes specific for simple repetitive DNA sequences. W Ramakrishna, MD Lagu, VS Gupta and PK Ranjekar. Theor Appl Genet (1994) 88: 402-406.
• (CAC)5 detects DNA fingerprints and sequences homologous to gene transcripts in rice. VS Gupta, W Ramakrishna, SR Rawat and PK Ranjekar. Biochemical Genet (1994) 32: 1-8.

Lab Personnel
Graduate Students (Ph.D.)
Zijun Xu
Nicholas Krom
Surendar Reddy Dhadi
Kefeng Li  

Undergraduate Students
Megan McQuillan
Nari Kang

Teaching
BL5030/BL4030 - Molecular Biology (Fall)
BL4840 - Molecular Biology Techniques (Fall)
BL4500 - Discussions in Bioinformatics (Spring)
BL2310/BL4000 - Molecular Biology Computational Laboratory (Spring)

Research Funding
Identification and Characterization of Bidirectional Promoters in the Rice Genome: A Pilot Scale Study.
USDA-NRI CSREES Plant Biology: Gene Function and Regulation ($100,000) 7/2007-6/2009.

Organization and Evolution of Disease Resistance Gene Clusters in Cereal Genomes.
MTU Research Excellence Fund ($40,000) 7/2004-12/2005.

NanoDrop Spectrophotometer for Molecular Biology and Biochemistry.
MTU Century II Campaign Endowed Equipment (C2E2) Fund ($3,135) 5/2004-5/2006

Do bidirectional Promoters Exist in Rice and Maize?
MTU Faculty Scholarship Grant ($3,000) 7/2005-6/2006