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RESEARCH PROJECTS

1.    Amino acid metabolism

My laboratory is primarily interested in amino acid metabolism. More specifically, we are interested in the aminotransferase class of enzyme. Aminotransferases or transaminases (EC 2.6.1.x) are ubiquitous enzymes that are involved in amino acid biosynthesis, vitamin metabolism, carbon and nitrogen assimilation, secondary metabolism etc. They catalyze reversible reactions by transferring an amino group from a donor to an acceptor. The amino donor is usually an amino acid and the amino acceptor is usually a 2-oxo-acid. In the model organism Arabidopsis thaliana, there are 44 annotated aminotransferases many of which are uncharacterized. Using biochemical and bio-informatical approaches, my lab is interested in elucidating the function of the remaining aminotransferase enzymes that are deemed putative from organisms such as; plants, bacteria and algae.

A picture of organisms used in the lab
Various organisms used in the Hudson lab
Arabidopsis chromosomes
The relative map positions of aminotranferase-like genes distributed on the 5 chromosomes of Arabidopsis thaliana

A GIF of the transamination process
Source

Transamination interconverts pairs of amino acids and keto acids. During transamination, the amino group of an amino acid is transferred to a keto acid, this produces a new keto acid while from the original keto acid, a new amino acid is formed. The enzyme employs a ping-pong (double displacement)(see cartoon above) mechanism facilitated by the co-factor pyridoxal phosphate (PLP) which is bound to a conserved lysine residue in the active site of the enzyme.

2.    Structural analyses of enzymes involved in amino acid metabolism/
Characterization of a putative target for antibiotic development

with Dr. Renwick C.J. Dobson - University of Canterbury, New Zealand

Some of the enzymes involved in the metabolism of amino acids are putative or validated antibiotic targets based on the fact these amino acids are essential for bacterial growth and the anabolic pathways are absent in animals particularly humans. The Hudson lab is currently collaborating with the lab of Dr. Renwick Dobson from the University of Canterbury to elucidate the 3-dimensional structure of enzymes involved in amino acid metabolism.

DAPL protein structure
The dimeric structure of diaminopimelat aminotransferase from the alga C. reinhardtii solved by the Hudson and Dobson groups


V. spinosum diaminopimelate aminotransferase
Homology model of V. spinosum diaminopimelate aminotransferase

Meso-diaminopimelate ligase
Homology model of meso-diaminopimelate ligase (MurEVs).(a) The homology model of MurEVs highlighting domains A (grey), B (violet) and C (pink). (b) Shows the structure model of MurEVs bound to UDP-MurNAc-tripeptide (UMT) product (yellow). (c) Active site residue hypothesized to bind to UMT product is shown in red. The structure has been rotated 90 degrees on the right panel for the better viewing of the binding pocket. (d) Cross eye stereo view showing the interaction between amino acid residues of the binding site and UMT product.

3.    Identification of Bacterial Endophytes/Epiphytes

A collaborative project with Dr. Michael Savka (GSOLS) to identify and assess the role(s) of endophytic and epiphytic bacteria from plants such as sugarcane, grape  etc is under way.

Sugarcane endophytes
Isolation and identification of bacterial endophytes from sugarcane using 16S V3 rDNA analysis
Recently, the genomes of 19 plant associated bacteria fromw sugarcane, yam and willow were sequenced and annotated in collaboration with Dr. Han Ming Gan (Monash University, Malaysia).

Research Opportunities

I am always interested in having enthusiastic and passionate students in my laboratory if there are openings. Students in my laboratory will be exposed to a variety of techniques from many disciplines including; biochemistry, molecular biology, enzymology, microbiology, plant biology/pathology, evolutionary biology, structural biology among others. Email me at aohsbi@rit.edu to inquire about research opportunities.

Acknowledgements

I would like to thank the National Institutes of Health (NIH), the National Science Foundation (NSF), The RIT College of Science (COS), The Thomas H. Gosnell School of Life Sciences (GSOLS), The RIT Office of the Vice President for Research (OVPR), Sweetwater Energy and Natcore Technology for financial support. I would also like to thank all of the wonderful collaborators and students throughout the years.