Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity.

Fh Sant’Anna,Tg Sokolova,Ft Robb,Av Lebedinsky,Jm Gonzalez

doi:10.1186/s12864-015-1955-9

Abstract

BackgroundThe Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms.MethodsAverage nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneus genomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms.ResultsThe three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases.ConclusionsGenomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1955-9) contains supplementary material, which is available to authorized users.

Highlights

The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products
Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production
The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, these organisms constitute a remarkable resource of enzymes with biotechnological potential

Summary

Introduction

The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. Thermophilic bacteria possess diverse adaptations in order to thrive under high temperatures [1, 2] These organisms are sources of potentially useful thermostable proteins, which is promising because of the increasing biotechnological interest in highly thermostable enzymes [3]. Caldanaerobacter subterraneus includes fermentative thermophilic bacteria with relatively low genomic GC content (under 40 %) able to grow on carbohydrate substrates with acetate L-alanine, H2, and CO2 as the main products that have been isolated from a variety of hot environments [8,9,10,11]. Yonseiensis has been published [14], which can contribute to the understanding of the evolution of the metabolic features in this species relative to its sibling strains These genomes constitute helpful resources for cloning and expression of novel enzymes of biotechnological importance These genomes constitute helpful resources for cloning and expression of novel enzymes of biotechnological importance (e.g. [1, 2, 15])

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