Phylogenetic tree for A. vinelandii, all fully sequenced members of the Pseudomonas genus, and three outgroups. Accession numbers for the genomes used are given in Table S1 in the supplemental material. Bootstrap support for all branches was 100%.

Respiratory protection in Azotobacter vinelandii. (A) Illustration of A. vinelandii cell and the key proteins involved in respiratory protection. A number of alginate biosynthetic proteins are produced that direct the formation of an alginate coating around the cell, acting as a physical O₂ barrier (black lining). Respiratory proteins, including five terminal oxidases (dark blue), four NADH-ubiquinone oxidoreductases (light blue), two ATP synthases (orange), and other proteins involved in respiratory protection (lavender), provide the second line of defense against O₂. Proteins sensitive to O₂ exposure are shown in green boxes. Solid line arrows represent regulatory events for which experimental evidence exists. Dashed line arrows represent putative regulation on the basis of promoter binding regions. Regulatory proteins are depicted in gray. (B) Locations of respiratory and respiratory protection genes in the A. vinelandii genome. Proteins are color coded according to their role in respiration, respiratory protection, and nitrogen fixation. Genes whose protein products have been identified previously are represented by red dots. The genes identified in this work (represented by blue dots) encode the following proteins: cytochrome o oxidase (Avin11160 to Avin11180), Rnf2 complex (Avin19220 to Avin19270), Sdh complex (Avin29780 to Avin29810), Sha complex (Avin19530 to Avin19580), Nuo complex (Avin28440 to Avin28560), Nqr complex (Avin14590 to Avin14640), Rhd^Nif (Avin51050), Grx^Nif (Avin51060), cytochrome c oxidase (Avin00940 to Avin01020), chimeric soluble Ni-Fe hydrogenase (Avin04360 to Avin04410), Fdh (Avin03820), CODH (Avin04450 to Avin04490), ATP synthase 2 complex (Avin52150 to Avin52230), AlgB (Avin11120), AlgQ (Avin47550), AmrZ (Avin34410), AlgP (Avin47540), AlgW (Avin12950), MucP (Avin38920), Prc (Avin35170), AlyA1-3 (Avin13810, Avin23960, and Avin31810), AlgY (Avin49400), and the alginate lyase (Avin 46500).

Oxygen-sensitive protein-encoding genes in A. vinelandii and their genomic locations.