Transcriptome response to different carbon sources in Acetobacter aceti

Abstract

The draft genome sequence of Acetobacter aceti NBRC 14818 was determined by wholegenome shotgun sequencing and the transcriptome profile in cells exponentially grown on ethanol, acetate or glucose was analysed by using a DNA microarray. The genes for all enzymes that constitute the complete tricarboxylic acid (TCA) cycle and glyoxylate pathway were identified in the genome. The TCA cycle genes showed higher expression levels in A. aceti cells grown on acetate or glucose and the glyoxylate pathway genes were significantly induced by ethanol or acetate. Many SOS-response genes were upregulated in cells grown on ethanol, indicating that ethanol provoked damage of DNA and proteins. The superoxide dismutase and catalase genes showed high expression levels in culture on glucose, indicating that oxidation of glucose induced oxidative stress. A. aceti NBRC 14818 was found to have a highly branched respiratory chain. The genes for two type I and one type II NADH dehydrogenase were identified. The genes for one of the type I enzymes were highly expressed when cells were grown on acetate or glucose, but were significantly downregulated in culture on ethanol, probably because ubiquinones were directly reduced by pyrroloquinoline quinone-dependent alcohol dehydrogenase. Four sets of the genes for quinol oxidases, one bo 3 -type (BO3), one bd-type and two cyanide-insensitive-types (CIOs), were identified in the genome. The genes for BO3, which might have proton-pumping activity, were highly expressed under the conditions tested, but were downregulated in the glucose culture. In contrast, the genes for one of the CIOs were significantly upregulated in cells grown on glucose. The two CIOs, which are expected to have lower energy-coupling efficiency, seemed to have a higher contribution in glucose-grown cells. These results indicate that energy conservation efficiency is fine-tuned by changing the respiratory components according to the growth conditions in A. aceti cells.

The Key to Acetate: Metabolic Fluxes of Acetic Acid Bacteria under Cocoa Pulp Fermentation-Simulating Conditions

“…MDH, malate dehydrogenase. moles of ATP (22,52,53). Additionally, the glyoxylate shunt is missing in A. pasteurianus (21,40) and A. ghanensis (31).…”

“…At this point, it appears to be relevant to resolve the metabolic contribution of AAB in greater detail. The basic knowledge that we share indicates a unique metabolism among members of the genus Acetobacter, including a nonfunctional Embden-Meyerhof-Parnas (EMP) pathway and the generation of energy from the incomplete oxidation of ethanol into acetate (21,22). A few species are able to catabolize lactate (23-26).…”

Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

“…There are only 5 Alishewanella species with validly published names (1)(2)(3)(4)(5), 36 isolates from various environments, and 16S rRNA gene sequences of 27 uncultured Alishewanella strains, according to NCBI taxonomy. Their isolation sources include fermented foods, tidal flat sediments, plant leaf and root surfaces, soils, deserts in cold climates, sludge, permafrost soils, freshwater biofilms, metal tailings, guts of beetle larvae, lakes, wastewater, and heavy metal-resistant communities.…”

Transcriptome Analyses of Metabolic Enzymes in Thiosulfate- and Hydrogen-GrownHydrogenobacter thermophilusCells

“…Cells were collected by centrifugation for 10 min at 3;000 Â g. RNA was extracted from the cell pellet by a hot-phenol method, as described previously. 19) Microarray experiments and data analysis. A customized tiling array with a 4 Â 72 k format for H. thermophilus TK-6 was designed and manufactured by Roche NimbleGen (Basel, Switzerland) based on the genome sequence.…”

“…Double-stranded (ds)-cDNA synthesis and labeling were performed following the instructions in the NimbleGen arrays User's Guide for Gene Expression Analysis (Roche NimbleGen), as described previously. 19) A hybridization solution was prepared with a hybridization kit (Roche NimbleGen) following the protocol supplied by the manufacturer, and hybridization was performed using a NimbleGen hybridization system 4. Washing was carried out with a wash buffer kit (Roche NimbleGen) following the manufacturer's instructions, and the arrays were scanned with an MS 200 Microarray Scanner (Roche NimbleGen) with NimbleGen MS 200 v.1.0 software.…”