Aldehyde dehydrogenase diversity in bacteria of the Pseudomonas genus
Aldehyde dehydrogenase diversity in bacteria of the Pseudomonas genus
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DOI：
10.1016/j.cbi.2019.03.006
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发表时间：
2019-05-01
影响因子：
5.1
通讯作者：
Munoz-Glares, Rosario A.
中科院分区：
文献类型：
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作者：
Riveros-Rosas, Hector;Julian-Sanchez, Adriana;Munoz-Glares, Rosario A.
乙醛脱氢酶（ALDHs）是最古老的蛋白质超家族之一，广泛分布于生命的三大领域。它们的成员已在动物和植物中被广泛研究，在不同的ALDH蛋白家族中被分类，并且它们参与各种各样的代谢途径已被记录。遗憾的是，迄今为止尚未进行包含来自细菌的ALDH的系统研究。在细菌中，假单胞菌属占据许多生态位，并且是已知种类最多的最复杂的细菌属之一。基于这些原因，我们选择假单胞菌作为范例来分析细菌中ALDH的多样性。为此，从NCBI的RefSeq基因组数据库中检索完整的假单胞菌基因组序列和注释。258株假单胞菌属于46个不同的种，沿着有23个没有种名称。这些假单胞菌的基因组包含3，315至6，825个注释的蛋白质编码基因。在选定的假单胞菌中发现了总共6，510个ALDH序列，每个菌株的平均ALDH编码基因为24个（相比之下，人类仅拥有19个不同的ALDH基因座）。假单胞菌saudiphocaensis具有最低数量的aldh基因（9），而假产碱假单胞菌KF 707 NBRC110670具有最大数量的aldh基因（49）。假单胞菌中的ALDH可分为42个蛋白质家族，其中14个家族占优势，占所有ALDH的76%。考虑到所有菌株都含有ALDH 4、ALDH 5、ALDH 6、ALDH 14、ALDH 18和ALDH 27家族的成员，我们认为这些家族是假单胞菌核心基因组的一部分。
Aldehyde dehydrogenases (ALDHs) comprise one of the most ancient protein superfamilies widely distributed in the three domains of life. Their members have been extensively studied in animals and plants, sorted out in different ALDH protein families and their participation in a broad variety of metabolic pathways has been documented. Paradoxically, no systematic studies comprising ALDHs from bacteria have been performed so far. Among bacteria, the genus Pseudomonas occupies numerous ecological niches, and is one of the most complex bacterial genera with the largest number of known species. For these reasons, we selected Pseudomonas as a paradigm to analyze the diversity of ALDHs in bacteria. With this aim, complete Pseudomonas genome sequences and annotations were retrieved from NCBI's RefSeq genome database. The 258 Pseudomonas strains belong to 46 different species, along with 23 with no species designation. The genomes of these Pseudomonas contain from 3,315 to 6,825 annotated protein coding genes. A total of 6,510 ALDH sequences were found in the selected Pseudomonas, with a median of 24 ALDH-coding genes per strain (by comparison humans possess only 19 different ALDH loci). Pseudomonas saudiphocaensis possesses the lowest number of aldh genes (9), while Pseudomonas pseudoalcaligenes KF707 NBRC110670 possesses the maximum number of aldh genes (49). The ALDHs found in Pseudomonas can be sorted out into 42 protein families, with a predominance of 14 families, which contained 76% of all ALDHs found. In this regard, it is important to note that many Pseudomonas genomes have multiple aldh genes coding for proteins belonging to the same family. Given that all strains contained members of families ALDH4, ALDH5, ALDH6, ALDH14, ALDH18 and ALDH27, we consider these families to be part of the core Pseudomonas genome.