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Detailed Bioinformatics Analysis of the Oxidative
Phosphorylation Pathway in Azotobacter vinelandii
John Moore, Megan Szekely, Karly Tarase, and Becky Velotta
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.
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
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 Azotobacter
vinelandii.
 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 Ftype 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 betaProteobacteria). 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.
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