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Chem Biol Interact. 2019 Mar 9;304:83-87. doi: 10.1016/j.cbi.2019.03.006. [Epub ahead of print]

Aldehyde dehydrogenase diversity in bacteria of the Pseudomonas genus.

Author information

1
Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, 04510, México; Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada. Electronic address: hriveros@unam.mx.
2
Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, 04510, México.
3
Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada.
4
Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, CdMx, 04510, México.

Abstract

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.

KEYWORDS:

ALDH classification; Phylogenetic analysis; Protein evolution

PMID:
30862475
DOI:
10.1016/j.cbi.2019.03.006

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