Complete genome and gene expression analyses ofAsaia bogorensisreveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen

Abstract

Asaia bogorensis, a member of acetic acid bacteria (AAB), is an aerobic bacterium isolated from flowers and fruits, as well as an opportunistic pathogen that causes human peritonitis and bacteraemia. Here, we determined the complete genomic sequence of the As. bogorensis type strain NBRC 16594, and conducted comparative analyses of gene expression under different conditions of co-culture with mammalian cells and standard AAB culture. The genome of As. bogorensis contained 2,758 protein-coding genes within a circular chromosome of 3,198,265 bp. There were two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases: cyoABCD-1 and cyoABCD-2. The cyoABCD-1 operon was phylogenetically common to AAB genomes, whereas the cyoABCD-2 operon belonged to a lineage distinctive from the cyoABCD-1 operon. Interestingly, cyoABCD-1 was less expressed under co-culture conditions than under the AAB culture conditions, whereas the converse was true for cyoABCD-2. Asaia bogorensis shared pathogenesis-related genes with another pathogenic AAB, Granulibacter bethesdensis, including a gene coding pathogen-specific large bacterial adhesin and additional genes for the inhibition of oxidation and antibiotic resistance. Expression alteration of the respiratory chain and unique hypothetical genes may be key traits that enable the bacterium to survive under the co-culture conditions.

Whole genomic DNA sequencing and comparative genomic analysis ofArthrospira platensis: high genome plasticity and genetic diversity

“… 6 GC skew analysis to anchor potential origin and terminator for chromosome replication did not show obvious skew shift. This is different from those bacteria whose chromosomal replication origin and terminator could be clearly identified, 9 , 25 but is similar to other cyanobacterial genomes, suggesting the occurrence of potential chromosomal rearrangements, sequence duplications and lateral gene transfer (LGT) events, 26 because the bias of nucleotide compositions between leading and lagging strands were disrupted. In addition, mapping Illumina short reads back to the genome resulted in 99.6% of the total reads uniquely aligned to the assembly and 98.4% paired-end reads represented correct orientation and distance, which was indicative of the high credibility of the assembled genome.…”

Identification of Carotenoids and Isoprenoid Quinones from Asaia lannensis and Asaia bogorensis

“…In studies conducted by Kawaii et al (2015) it was found that bacterium Asaia bogorensis has an operon with genes that were homologous to rhodopsin and beta-carotene 15,15′-monooxygenase—participating in the synthesis of phytofluene and neurosporene ( Appendix A Figure A2 ) [ 20 ]. Our results showed that tested strains of A. bogorensis did not accumulate the first compound, but can produce neurosporene.…”

“…It was noted that in the case of Escherichia coli , low oxygen concentrations increase the level of menaquinones, and therefore, reduce the amount of ubiquinones [ 42 ]. On the other hand, Kawai et al (2015), in the study on Asaia bogorensis , found that A. bogorensis , like Escherichia coli , contains cyd genes (encoding cytochrome d oxidase), whose expression is upgraded under oxygen limited conditions [ 20 ]. The presence of MC-7 and MC-8, as well as expression of cyd genes, is important, due to the fact that Asaia lannensis and Asaia bogorensis contaminate functional beverages containing low levels of oxygen.…”

“…Bolded pink lines with purple markers are ubiquinone-10 and menaquinone.

Figure A2 Genes encoding carotenoids identified for Asaia bogorensis (marked in green) by Kawaii et al (2015) [ 20 ]. Adapted from Kawaii et al (2015) using KEEG mapper.

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“… Genes encoding carotenoids identified for Asaia bogorensis (marked in green) by Kawaii et al (2015) [ 20 ]. Adapted from Kawaii et al (2015) using KEEG mapper.…”