Abstract
Globins (Glbs) are proteins widely distributed in organisms. Three evolutionary families have been identified in Glbs: the M, S and T Glb families. The M Glbs include flavohemoglobins (fHbs) and single-domain Glbs (SDgbs); the S Glbs include globin-coupled sensors (GCSs), protoglobins and sensor single domain globins, and the T Glbs include truncated Glbs (tHbs). Structurally, the M and S Glbs exhibit 3/3-folding whereas the T Glbs exhibit 2/2-folding. Glbs are widespread in bacteria, including several rhizobial genomes. However, only few rhizobial Glbs have been characterized. Hence, we characterized Glbs from 62 rhizobial genomes using bioinformatics methods such as data mining in databases, sequence alignment, phenogram construction and protein modeling. Also, we analyzed soluble extracts from Bradyrhizobium japonicum USDA38 and USDA58 by (reduced + carbon monoxide (CO) minus reduced) differential spectroscopy. Database searching showed that only fhb, sdgb, gcs and thb genes exist in the rhizobia analyzed in this work. Promoter analysis revealed that apparently several rhizobial glb genes are not regulated by a -10 promoter but might be regulated by -35 and Fnr (fumarate-nitrate reduction regulator)-like promoters. Mapping analysis revealed that rhizobial fhbs and thbs are flanked by a variety of genes whereas several rhizobial sdgbs and gcss are flanked by genes coding for proteins involved in the metabolism of nitrates and nitrites and chemotaxis, respectively. Phenetic analysis showed that rhizobial Glbs segregate into the M, S and T Glb families, while structural analysis showed that predicted rhizobial SDgbs and fHbs and GCSs globin domain and tHbs fold into the 3/3- and 2/2-folding, respectively. Spectra from B. japonicum USDA38 and USDA58 soluble extracts exhibited peaks and troughs characteristic of bacterial and vertebrate Glbs thus indicating that putative Glbs are synthesized in B. japonicum USDA38 and USDA58.
Highlights
Globins (Glbs) are proteins widely distributed in organisms from the three kingdoms of life, i.e. in Archaea, Eubacteria and Eukarya[1]
We selected 62 out of the 96 rhizobial genomes reported by the above authors representing the major rhizobial genera, species and strains, which included α- and β-rhizobia
A total of 197 glb sequences were detected in the 62 rhizobial genomes, corresponding to 7 fhbs, 47 sdgbs, 40 gcss and 103 thbs (4 thbs class 1, 56 thbs class 2 and 43 thbs class 3)
Summary
Globins (Glbs) are proteins widely distributed in organisms from the three kingdoms of life, i.e. in Archaea, Eubacteria and Eukarya[1]. Glbs fold into a tertiary structure known as the globin fold. This protein folding consists of six to eight α-helices (designated with letters A to H) that form a hydrophobic pocket where a heme prosthetic group is located[2]. Two structural types of the globin fold have been identified in Glbs: the 2/2- and 3/3-fold. In the 2/2-Glbs, helices B and E overlap to helices G and H3 and in the 3/3-Glbs helices A, E and F overlap to helices B, G and H4,5. Three evolutionary families have been identified in Glbs[6,7]: the M, S and T Glb families. The M and S Glbs fold into the 3/3-fold whereas the T Glbs fold into the 2/2-fold
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