Complete Genome Sequencing and Comparative Genomic Analysis of the Thermotolerant Acetic Acid Bacterium, <i>Acetobacter pasteurianus</i> SKU1108, Provide a New Insight into Thermotolerance

Abstract

Acetobacter pasteurianus SKU1108 is a typical thermotolerant acetic acid bacterium. In this study, the complete genome sequence of the SKU1108 strain was elucidated, and information on genomic modifications due to the thermal adaptation of SKU1108 was updated. In order to obtain a clearer understanding of the genetic background responsible for thermotolerance, the SKU1108 genome was compared with those of two closely related complete genome strains, thermotolerant A. pasteurianus 386B and mesophilic A. pasteurianus NBRC 3283. All 24 “thermotolerant genes” required for growth at higher temperatures in the thermotolerant Acetobacter tropicalis SKU1100 strain were conserved in all three strains. However, these thermotolerant genes accumulated amino acid mutations. Some biased mutations, particularly those that occurred in xanthine dehydrogenase XdhA, may be related to thermotolerance. By aligning whole genome sequences, we identified ten SKU1108 strain-specific regions, three of which were conserved in the genomes of the two thermotolerant A. pasteurianus strains. One of the regions contained a unique paralog of the thermotolerant gene xdhA, which may also be responsible for conferring thermotolerance. Thus, comparative genomics of complete genome sequences may provide novel insights into the phenotypes of these thermotolerant strains.

Comparative Genomic Analysis of Closely Related Acetobacter pasteurianus Strains Provides Evidence of Horizontal Gene Transfer and Reveals Factors Necessary for Thermotolerance

“…The diluted samples (7 l) were dotted onto plates of YPGD medium and then incubated at 30, 37, and 39°C. pCM62 is a broad-host-range vector, and pCM83 is pCM62 harboring the nhaK2 gene of NBRC 3283. and 386B strains (15). Thus, xdhABC and paralogous genes may also be responsible for the thermotolerance in these strains.…”

“…The comparative genomics approach has the capability of identifying candidate genes responsible for the phenotypic difference present among closely related species. By using such approaches, we have identified some genes important for thermotolerance in AAB (14,15). In this study, we performed a comparative genomic analysis of 22 closely related A. pasteurianus strains to better understand the genetic background underpinning their phenotypes, and we found that there are some horizontal gene transfer (HGT) events and gene mutations that are responsible for the thermotolerant phenotype.…”

“…Identification of genes associated with thermotolerance and related to respiratory chains. Twenty-four known thermotolerant genes conserved in the 22 AAB genomes were searched by BLASTP with an E value cutoff of 10 Ϫ5 and a sequence overlap (query and subject) of Ն70% using the genes conserved in SKU1108 as queries (15). Genes related to the respiratory chains were also searched against the 22 AAB genomes.…”

“…Genes related to the respiratory chains were also searched against the 22 AAB genomes. Sequence alignment and a phylogenetic tree of each protein-coding sequence set was constructed as previously reported (15). Undetected or incomplete genes were searched using TBLASTN with an E value cutoff of 10 Ϫ5 against the 22 AAB genome sequences.…”