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BMC Evolutionary Biology

, 12:147

Genome evolution and evolutionary systems biology

Abstract

BackgroundShort chain dehydrogenases-reductases SDR are NADPH-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities.
The SDR196C family http:-www.sdr-enzymes.org groups bacterial sorbitol dehydrogenases SDH, which are of great industrial interest.
In this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence conserved blocks, a new and a more accurate classification is proposed.

ResultsThe distribution of the 66 bacterial SDH species analyzed was limited to Gram-negative bacteria.
Six different bacterial families were found, encompassing α-, β- and γ-proteobacteria.
This broad distribution in terms of bacteria and niches agrees with that of SDR, which are found in all forms of life.
A cluster analysis of sorbitol dehydrogenase revealed different types of gene organization, although with a common pattern in which the SDH gene is surrounded by sugar ABC transporter proteins, another SDR, a kinase, and several gene regulators.

According to the obtained trees, six different lineages and three sublineages can be discerned.
The phylogenetic analysis also suggested two different origins for SDH in β-proteobacteria and four origins for γ-proteobacteria.

Finally, this subdivision was further confirmed by the differences observed in the sequence of the conserved blocks described for SDR and some specific blocks of SDH, and by a functional divergence analysis, which made it possible to establish new consensus sequences and specific fingerprints for the lineages and sub lineages.

ConclusionSDH distribution agrees with that observed for SDR, indicating the importance of the polyol metabolism, as an alternative source of carbon and energy.
The phylogenetic analysis pointed to six clearly defined lineages and three sub lineages, and great variability in the origin of this gene, despite its well conserved 3D structure.
This suggests that SDH are very old and emerged early during the evolution.
This study also opens up a new and more accurate classification of SDR196C family, introducing two numbers at the end of the family name, which indicate the lineage and the sublineage of each member, i.e, SDR196C6.3.

AbbreviationsSDRShort-chain dehydrogenase-reductases

SDHSorbitol dehydrogenases

ABCATP-binding cassette

MDRMedium-chain dehydrogenase-reductases

AKRAldo-keto reductases

HADHaloacid dehalogenases

MDHMannitol dehydrogenases

MLMaximum likelihood

BYBayesian analysis

NJNeighbor joining.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2148-12-147 contains supplementary material, which is available to authorized users.

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Author: Agustín Sola-Carvajal - María I García-García - Francisco García-Carmona - Álvaro Sánchez-Ferrer

Source: https://link.springer.com/



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