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John Moore, Megan Szekely, Karly Tarase, and Becky Velotta

Detailed Bioinformatics Analysis of the Oxidative Phosphorylation Pathway in Azotobacter vinelandii. John Moore, Megan Szekely, Karly Tarase, and Becky Velotta. Enzyme Name (Subunit). Gene Encoding E. coli Homolog. Gene Encoding A. vinelandii homolog. Polyphosphate kinase. ppk.

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John Moore, Megan Szekely, Karly Tarase, and Becky Velotta

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  1. Detailed Bioinformatics Analysis of the Oxidative Phosphorylation Pathway in Azotobacter vinelandii John Moore, Megan Szekely, Karly Tarase, and Becky Velotta Enzyme Name (Subunit) Gene Encoding E. coli Homolog Gene Encoding A. vinelandii homolog Polyphosphate kinase ppk Avin47440 Inorganic pyrophosphotase ppa Avin07940 ATP synthase, F1 sector, epsilon-subunit atpC Avin52150 ATP synthase, F1 sector, beta-subunit atpD Avin52160 ATP synthase, F1 sector, gamma-subunit atpG Avin52170 ATP synthase, F1 sector, alpha-subunit atpA Avin52180 ATP synthase, F1 sector, delta-subunit atpH Avin52190 ATP synthase, F0 sector, b-chain atpF Avin52200 Figure 1. Oxidative phosphorylation including membrane bound ATPsynthase in E.coli. The gene designations are as follows: 2.7.4.1 is ppk, Polyphosphate kinase; 3.6.1.1 is ppa, Inorganic pyrophosphotase; 3.6.3.14 is ATPsynthase including the F1 and F0 units. ATP synthase, F0 sector, c-chain atpE Avin52210 ATP synthase, F0 sector, a-chain atpB Avin52220 • As shown in Figure 1, there are 3 steps in the pathway. Each of the first two steps are catalyzed by single protein enzymes. The last step is catalyzed by the F1 unit composed of 5 different subunits and the F0 unit composed of 3 different subunits. All genes were found via BLAST in Azotobactervinelandii. • There are 10 Genes present within the Oxidative Phosphorylation Pathway and all were found in Azotobacter vinelandii. • Azotobacter vinelandii exhibits redundancy for two ATP synthase F1 sector subunits, alpha and beta. Avin19740 shows strong similarity (e-105) to the alpha subunit Avin52180. Avin19670 shows strong similarity (e-114 ) to the beta subunit Avin52160. Redundancy is seen for some F0 subunits, but with much less similarity. For example, Avin19720 is a ATP synthase F0 C subunit and 50% similar to Avin52210. Pseudomonas species do not show such redundancy. • Only one of our genes needed to have a start codon reassigned; Avin52200. • One operon was found with 9 ATP synthase genes involved; Avin52150, Avin52160, Avin52170, Avin52180, Avin52190, Avin52200, Avin52210, Avin52220, Avin52230. This operon also exists in Pseudomonas. • Our most interesting finding was another operon, Avin19660-Avin19750, that encodes another F-type ATP synthase distinct from the evolutionarily conserved F-type ATP synthase encoded by Avin52230-52150. This operon’s best hits are to Burkholderia species which are in a different group (Azotobacter and Pseudomonas are gamma-Proteobacteria while Burkholderia is in the beta-Proteobacteria). There is no evidence in the literature of another bacterial genome with two different F-type ATPase/ATP synthase operons. The operon that runs Avin19660-Avin19750 includes some redundant ATPsynthase genes, but 4/9 genes in the operon code for ATPase products. A project of the funded by the and the

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