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首页> 美国卫生研究院文献>other >A bioinformatics insight to rhizobial globins: gene identification and mapping polypeptide sequence and phenetic analysis and protein modeling.
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A bioinformatics insight to rhizobial globins: gene identification and mapping polypeptide sequence and phenetic analysis and protein modeling.

机译：根瘤菌球蛋白的生物信息学见解：基因鉴定和作图多肽序列和物候分析以及蛋白质建模。

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摘要

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.
机译：球蛋白（Glbs）是广泛分布于生物体中的蛋白质。在Glbs中鉴定了三个进化家族：M，S和T Glb家族。 M Glbs包括黄素血球蛋白（fHbs）和单域Glbs（SDgbs）； S Glbs包括球蛋白偶联传感器（GCS），原球蛋白和传感器单域球蛋白，T Glbs包括截短的Glbs（tHbs）。在结构上，M和S Glbs显示3/3折叠，而T Glbs显示2/2折叠。 Glbs广泛存在于细菌中，包括几个根瘤菌基因组。但是，只有很少的根瘤菌Glbs被鉴定。因此，我们使用生物信息学方法（例如数据库中的数据挖掘，序列比对，表型构建和蛋白质建模）从62个根瘤菌基因组中鉴定了Glbs。另外，我们通过（还原+一氧化碳（CO）减去还原）差示光谱分析了日本根瘤菌USDA38和USDA58的可溶性提取物。数据库搜索显示，在这项工作中分析的根瘤菌中仅存在fhb，sdgb，gcs和thb基因。启动子分析表明，显然有几个根瘤菌glb基因不受-10启动子调控，但可能受-35和Fnr（富马酸酯-硝酸盐还原调节剂）样启动子调控。映射分析显示，根瘤菌fhbs和thbs旁有多种基因，而一些根瘤菌sdgbs和gcss旁有编码涉及硝酸盐和亚硝酸盐代谢和趋化性的蛋白质的基因。物性分析表明，根瘤菌的Glbs分为M，S和T Glb家族，而结构分析表明，预测的根瘤菌的SDgbs，fHbs和GCSs的球蛋白结构域和tHbs分别折叠为3/3和2/2折叠。来自日本芽孢杆菌USDA38和USDA58可溶性提取物的光谱显示出细菌和脊椎动物Glbs的峰和谷特征，因此表明推定的Glbs在日本芽孢杆菌USDA38和USDA58中合成。

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