The public genome data base identifies about 44 potential aminotransferase-like enzymes that are present in the genome of the model organism Arabidopsis thaliana. Aminotransferases are ubiquitous enzymes that catalyze the transfer of an amino group from a donor that is usually an amino acid to an acceptor that is usually a 2-keto acid. These enzymes are involved in numerous anabolic and catabolic pathways including; amino acid metabolism, vitamin metabolism, and secondary metabolism, among others. Determination of the functional and biochemical proprties of these enzymes becomes important to understanding basic plant biology including plant growth and development. Because aminotransferases are ubiquitous also in other organisms, this study will provide insights into the role of these enzymes in other organisms.

Broader impacts This project will provide research mentoring and training opportunities for undergraduate students enrolled in the biology related programs at the Rochester Institute of Technology. This training is particular critical to mold future scientists, policymakers and informed citizens. The students are frequently from demographic groups that are under-represented in the STEM disciplines, most notably African American, Latino and Native American students.

Project Report

The grant was awarded to investigate and elucidate a subset of enzymes involved in the amino acid metabolism in plants. Specifically, the project investigated the aminotransferase class of enzymes. We were able to elucidate and characterize a novel alanine and beta-alanine aminotransferase that we think is involved in stress response in the model plant Arabidopsis thaliana. In addition, we were able to elucidate the function of a novel tyrosine aminotransferase and its role in plant defense response to biotic stress through the up-regulation of secondary metabolites through the phenylpropanoid pathway. Regarding the broader impacts, the grant supported 8 undergraduate research students who were able to perform research under the direction of the PI. The PI initiated an outreach program to high schools in the Rochester NY area to liaise with high school science teacher regarding incorporation of plant biology into the science curriculum. In addition, the research was showcased at the annual RIT imagine festival where students presented the research to lay public. Publication supported by the grant Asterisks denote undergraduate student researcher from the PI's lab Triassi, AJ*,Wheatley, MS*, Savka, MA, Gan, HG, Dobson, RCJ, Hudson, AO. (2014) L,L-diaminopimelate aminotransferase (DapL): A putative target for the development of narrow –spectrum antibacterial compounds. Front. Microbiol 5:509. doi: 10.3389/fmicb.2014.00509. Babbitt, GA, Alawad, MA, Schulze, KV, Hudson, AO. (2014). Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucl. Acids Res doi:10.1093/nar/gku811. Gan, HY, Gan, HM, Savka, MA, Triassi, AJ*, Wheatley, MS*, Smart, LB, Fabio, ES, Hudson, AO. Whole genome sequences of thirteen endophytic bacteria isolated from shrub willow (Salix) grown in Geneva, New York. (2014) Genome Announc. 2(3):e00288-14.doi:10.1128/genomeA.00288-14. Oliver, MR, Crowther, JM, Leeman, MM*, Kessans, SA, North, RA, Donovan KA, Griffin, MDW, Suzuki, H, Hudson, AO, Kassanmascheff, M, Dobson, RCJ. (2014) The purification, crystallization and preliminary X-ray diffraction analysis of two isoforms of meso-diaminopimelate decarboxylase from Arabidopsis thaliana. Acta Cryst (F70) 663-668. Gan, HM, Triassi, AJ*, Wheatley, MS*, Savka, MA, Hudson, AO. (2014) High quality whole genome sequences of three strains of Enterobacter sp. Isolated from Jamaican Dioscorea cayenensis (Yellow Yam). Genome Announc: 13;2(2) doi:10.1128/genomeA.00170-14. Mckinnie, SM, Rodriquez-Lopex, EM, Vederas, JC, Crowther, JM, Suzuki, H, Dobson, RC, Leustek, T, Triassi, AJ*, Wheatley, MS*, Hudson, AO. (2014) Differential response of orthologous L,L-diaminopimelate aminotransferase (DapL) to enzyme inhibitory antibiotic lead compounds. Bioorganic and Medicinal Chemistry. 22 (1) 523-530. Gan, HM, Hudson, AO, Rahman, A, Chan KG and Savka MA.(2013) Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: Insights into host interactions, marine adaptation and bioremediation. BMC Genomics: 14:431 doi:10.1186/1471-2164-14-431. McGroty, SE*, Pattaniyil, DT*, Patin, D, Blanot, D, Ravichandran, AC, Suzuki, H, Dobson RCJ, Savka, MA and Hudson, AO. (2013) Biochemical Characterization of UDP-N-acetylmuramoyl-l-alanyl-d-glutamyl:meso-2,6 diaminopimelate ligase (MurE) from Verrucomicrobium spinosum DSM 4136T PLoS ONE 8(6): e66458.doi:10.1371/journal.pone.0066458. North, R*, Kessans, S*, Atkinson, S*, Suzuki, H, Watson, A, Burgess, B, Angley, L, Hudson, AO, Varsani, A, Griffin, M, Fairbanks, A, Dobson, RCJ. (2013). Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetyl neuraminate lyase from methicillin resistant Staphylococcus aureus. Acta Cryst (F69) 306-312. Gan, HM, McGroty, SE*, Chew, TH, Chan, KG, Buckley, LJ, Savka, MA, Hudson, AO. (2012). Whole genome sequence of Enterobacter sp. SST3, an endophyte isolated from Jamaica sugarcane (Saccharum sp) stalk tissue. Journal of Bacteriol.194: 5981-5982. Nachar, VR*, Savka, FC*, McGroty, SE*, Donovan, KA*, North, RA*, Dobson, RC, Buckley, LJ, Hudson, AO (2012). Genomic and biochemical analysis of the diaminopimelate and lysine biosynthesis pathway in Verrucomicrobium spinosum: Identification and partial characterization of L,L-diaminopimelate aminotransferase and UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-meso-diaminopimelate igase. Front. Microbio. 3:183.doi:10.3389/fmicb.2012.00183. Bulman,Z*, Le,P, Hudson, AO, Savka, MA (2011). A novel property of propolis (bee glue): Anti-pathogenic activity by inhibition of N-acyl-homoserine lactone mediated signaling in bacteria. Journal of Ethanopharmacology. 138. 788-797. Dobson, RCJ, Giron, I*, Hudson, AO (2011) L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii: A Target for Algaecide Development. PLoS ONE 6(5): e20439. doi:10.1371/journal.pone.0020439. Hudson, AO, Giron, I*, Dobson, R. (2011) Crystallization and preliminary X-ray diffraction analysis of l,l-diaminopimelate aminotransferase (DapL) from Chlamydomonas reinhardtii. Acta Cryst (F67) 140-143.

National Science Foundation (NSF)
Division of Molecular and Cellular Biosciences (MCB)
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Susanne von Bodman
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Rochester Institute of Tech
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