Comparative Genomics of <i>Acetobacterpasteurianus</i> Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu

<div><p><i>Acetobacter pasteurianus</i>, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of <i><a href="http://dx.doi.org/10.1601/nm.10550" target="_blank">A. pasteurianus</a></i> Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among <i><a href="http://dx.doi.org/10.1601/nm.10550" target="_blank">A. pasteurianus</a></i> strains revealed that <i>A</i>. <i>pasteurianus</i> Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in <i><a href="http://dx.doi.org/10.1601/nm.10550" target="_blank">A. pasteurianus</a></i> to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in <i>Acetobacter</i> species and guiding industrial strain breeding for vinegar fermentation processes.</p></div

Comparative genomic analysis between <i>A</i>. <i>pasteurianus</i> Ab3 and other strains belonging to acetic acid bacteria.

<p>A: alignment of the genomes from <i>A</i>. <i>pasteurianus</i> Ab3 and 386B using MAUVE. The identically colored boxes, known as locally collinear blocks, represent homologous regions in the two sequences. The vertical lines connect the LCBs point with homologous regions between the two-genome sequences. The numbers represent the position of nucleotides. B: whole genome alignment among strain Ab3 and other strains belonging to genus <i>Gluconobacter</i> and <i>Komagataeibacter</i> using the Ab3 genome as the reference. Ab3: <i>A</i>. <i>pasteurianus</i> Ab3; 386B: <i>A</i>. <i>pasteurianus</i> 386B; 3283–01: <i>A</i>. <i>pasteurianus</i> IFO 3283–01; 3283–03: <i>A</i>. <i>pasteurianus</i> IFO 3283–03; E25: <i>K</i>. <i>xylinus</i> E25; 621H: <i>G</i>. <i>oxydans</i> 621H.</p

Comparison of sequenced genomes of <i>Acetobacter</i> strains.

<p>Comparison of sequenced genomes of <i>Acetobacter</i> strains.</p

The genes encoding TCS in the genome sequence of <i>A</i>. <i>pasteurianus</i> Ab3.

<p>The genes encoding TCS in the genome sequence of <i>A</i>. <i>pasteurianus</i> Ab3.</p

The putative TA system superfamily in the chromosome of acetic acid bacteria.

<p>The putative TA system superfamily in the chromosome of acetic acid bacteria.</p

The analysis of transporters in the genome of <i>A</i>. <i>pasteurianus</i> Ab3 compared with <i>A</i>. <i>pasteurianus</i> 386B.

<p>The analysis of transporters in the genome of <i>A</i>. <i>pasteurianus</i> Ab3 compared with <i>A</i>. <i>pasteurianus</i> 386B.</p

Morphology of <i>A</i>. <i>pasteurianus</i> Ab3 taken by scanning electron microscopy.

<p>Morphology of <i>A</i>. <i>pasteurianus</i> Ab3 taken by scanning electron microscopy.</p

Representation of the comparative analysis of the TAs in the plasmid sequences among acetic acid bacteria using the sequence of Ab3 as a reference.

<p>The available plasmid sequences that deposited in the NCBI GenBank database involved in each strain were extracted and analyzed using Local BLAST (Blastn). Whether the TAs of Ab3 appear in other selected strains was judged according to the fact if the relative genes in other strains displayed the orthologous segments with a query coverage of 30% and identity of 60%. The distribution of the TAs between different strains were identified and illustrated in a 3D graph. X, Y and Z-axis, respectively, denote TA superfamily, organism and the number of genes.</p

The phylogenetic tree highlights the position of <i>Acetobacterpasteurianus</i> Ab3 relative to other strains of <i>Acetobacter</i>, <i>Gluconacetobacter</i>, <i>Gluconobacter</i> and <i>Komagataeibacter</i>.

<p>The phylogenetic tree was built using 16S rRNA gene sequences aligned by CLUSTALW. Phylogenetic inferences were made using the Neighbor-joining method of the MEGA 6.0 software.</p

The unique genes in the genome sequence of <i>A</i>. <i>pasteurianus</i> Ab3 compared to strain 386B.

<p>The genes were categorized according to the COG annotation.</p