Chemistry and Chemical Biology ETDs

Wang Min

Publication Date

2-1-2012

Abstract

My doctoral research began with the function assignment to two domains of fusion protein BT4699, from Bacteriodes thetaiotaomicron, BF1314 from Bacteriodes fragilis and PG1653 from Porphyromonas gingivalis. BT4699, however, is insoluble, so its orthologue BF1314 and PG1653 were prepared and studied. The fusion proteins consist of a domain that belong to a large family of phosphatases known as Haloacid Dehalogenase (HAD) superfamily, and a domain belong to the hotdog-fold thioesterase superfamily. The genes encoding the fusion proteins located at an operon that encoding enzymes involved in the menaquinone biosynthetic pathway. So we assumed that the thioesterase domain is connected to the biosynthesis of menaquinone, which sever as a crucial role in the anaerobic bacteria respiratory chain. While the HAD domain is involved in hydrolysis of pyrophosphate produced by MenA in the lower segment of the pathway. The thioesterase domain was predicted to catalyze the hydrolysis of 1,4-dihydroxyl-2-napthoyl-CoA (DHNA-CoA) to 1,4-dihydroxyl-2-napthoate (DHNA) as the precursor of menaquinone synthesis. To study the function of thioesterase domain, the putative substrate 1,4-dihydroxy naphthoyl-CoA was prepared by chemienzymatic strategy. The structure was confirmed by H NMR and mass spectrum. HPLC analysis indicated that DHNP-CoA is very unstable, which could be self-hydrolyzed within 16 hrs at pH=7.5. By using a combination of techniques like steady-state kinetics, HPLC, and NMR, the function of thioesterase domain of the fusion protein were investigated. Steady-state kinetics studies indicated that PG1653 has high activity over DHNP-CoA. HPLC and H-NMR proved the formation of hydrolyzed products. The high specificity of BF1314 and PG1653 over DHNP-CoA testified the function of thioesterase domain. The function of HAD domain is not that as we assumed. It didnt even show any activity towards pyrophosphate. PG1653 fusion protein did not have any phosphatase activity due to the mutation of Asp to Phe, which is a key catalytic residue of HAD phosphatase. The other fusion protein BF1314 just showed very weak activities towards a few phosphate substrates. Both truncated HAD domain and thioesterase domain were also prepared to investigate the function of HAD domain. Size exclusion chromatography was used to examine the effect of native structure on the functions of both HAD domain and thioesterase domain. The results indicated that the HAD domain may serve as an oligmerization domain that help the tetramerization of the thioesterase domain as an active thioesterase tetramer. The structure supportive role of the HAD domain disabled its phosphatase activity. The HAD domain homologue, BT3352, shares 47% identity with fusion protein BT4699. This high level of identity suggests that these two HADs are related by gene duplication. One gene copy must have fused with the thioesterase domain and took on a structural function that supports the thioesterase function while losing its catalytic function. The other copy may carry on the function of the original phosphatase. BT3352 exhibited good sugar phosphatase activities, and erythrose 4-phosphate turned out to be its physiological substrate. By comparing with its homologue yidA from E. coli, which may play a house keeping role in the galactonate degradation pathway, we hypothesized that BT3352 may also play house keeping role in likewise pathway. Bioinformatic analysis suggests that the 4 gene cluster might encode a partial β-oxidation pathway in Pseudomonas aeruginosa, which supported the pathway with seven other gene clusters. The target gene cluster contain two putative β-oxidation pathway enzymes, acyl-CoA dehydrogenase (PA5187), 3-hydroxy-acyl-CoA dehydrogenase (PA5188), a putative iron-containing alcohol dehydrogenase (PA5186) and a putative hotdog-fold thioesterase (PA5185). Substrate screen results indicated that PA5187 target C4-C15 fatty acyl-CoA, while PA5188 showed good activity towards C4-C10 and peak at 3-hydroxyhexanoyl-CoA. The hotdog-fold thioesterase exhibited narrow substrate specificities, which is good for C2-C4 acyl-CoA thioeters, and propionyl-CoA is the best substrate. Based on these results we conclude that This is a fatty acid oxidation pathway which augments the central fatty acid degradation pathway found in all bacteria. While the structure of the liganded PA5185 is needed to understand how it selects for the small substrates.

Language

English

Keywords

hotdog-fold thioesterase, Haloacid dehalogenase, menaquinone biosynthesis, beta oxidation pathway, acyl-CoA dehydrogenase, 3-hydroxyacyl-CoA dehydrogenase

Document Type

Dissertation

Degree Name

Chemistry and Chemical Biology

Level of Degree

Doctoral

Department Name

Department of Chemistry and Chemical Biology

First Committee Member (Chair)

Dunaway-Mariano, Debra

Second Committee Member

Allen, Karen N

Third Committee Member

Mariano, Patrick S

Fourth Committee Member

Wang, Wei

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