Gluconobacter oxydans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA35457 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR041180_1.fastq.gz | Fastqsanger.gz | |||
| DRR041180_2.fastq.gz | Fastqsanger.gz | |||
| SRR11458830_1.fastq.gz | Fastqsanger.gz | |||
| SRR11458830_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Acetic acid bacterium used in the food and pharmacuetical industries
| PRJNA13325 | ENA
Project description:The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this ?-proteobacterium has been characterized to some extent, yet little is known about its transcriptomes and related data. In this study, we applied two different RNAseq approaches. Primary transcriptomes enriched for 5'-ends of transcripts were sequenced to detect transcription start sites, which allow subsequent analysis of promoter motifs, ribosome binding sites, and 5´-UTRs. Whole transcriptomes were sequenced to identify expressed genes and operon structures.Sequencing of primary transcriptomes of G. oxydans revealed 2449 TSSs, which were classified according to their genomic context followed by identification of promoter and ribosome binding site motifs, analysis of 5´-UTRs including validation of predicted cis-regulatory elements and correction of start codons. 1144 (41%) of all genes were found to be expressed monocistronically, whereas 1634 genes were organized in 571 operons. Together, TSSs and whole transcriptome data were also used to identify novel intergenic (18), intragenic (328), and antisense transcripts (313).This study provides deep insights into the transcriptional landscapes of G. oxydans. The comprehensive transcriptome data, which we made publicly available, facilitate further analysis of promoters and other regulatory elements. This will support future approaches for rational strain development and targeted gene expression in G. oxydans. The corrections of start codons further improve the high quality genome reference and support future proteome analysis.
| S-EPMC5756330 | biostudies-literature
Project description:Gluconobacter oxydans Raw sequence reads
| PRJNA299470 | ENA
Project description:In this study we conducted genome-wide mRNA decay analysis to get further insights into the physiology of Gluconobacter oxydans.
2018-09-21 | GSE103428 | GEO
Project description:Gluconobacter oxydans is characterized by its ability to incompletely oxidize carbohydrates and alcohols. The high yields of its oxidation products and complete secretion into the medium make it important for industrial use. We report the finished genome sequence of Gluconobacter oxydans H24, an industrial strain with high l-sorbose productivity.
| S-EPMC3587919 | biostudies-literature
Project description:Gene expression in the obligatory aerobic acetic acid bacterium Gluconobacter oxydans was shown to respond to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed the function of a transcriptional regulator named GoxR, which belongs to the FNR family. Here, we aplied RNAseq to identify target genes of GoxR by comparing genes expression of a delta-goxR and its parental strain after 20 min of oxygen limitation.
2021-03-11 | GSE147810 | GEO
Project description:Gluconobacter oxydans is an important Gram-negative industrial microorganism that produces vitamin C and other products due to its efficient membrane-bound dehydrogenase system. Its incomplete oxidation system has many crucial industrial applications. However, it also leads to slow growth and low biomass, requiring further metabolic modification for balancing the cell growth and incomplete oxidation process. As a non-model strain, G. oxydans lacks efficient genome editing tools and cannot perform rapid multi-gene editing and complex metabolic network regulation. In the last 15 years, our laboratory attempted to deploy multiple CRISPR/Cas systems in different G. oxydans strains and found none of them as functional. In this study, Cpf1-based or dCpf1-based CRISPRi was constructed to explore the targeted binding ability of Cpf1, while Cpf1-FokI was deployed to study its nuclease activity. A study on Cpf1 found that the CRISPR/Cpf1 system could locate the target genes in G. oxydans but lacked the nuclease cleavage activity. Therefore, the CRISPR/Cpf1-FokI system based on FokI nuclease was constructed. Single-gene knockout with efficiency up to 100% and double-gene iterative editing were achieved in G. oxydans. Using this system, AcrVA6, the anti-CRISPR protein of G. oxydans was discovered for the first time, and efficient genome editing was realized.
| S-EPMC10980938 | biostudies-literature
Project description:Gastric and colorectal cancer are among the most frequently diagnosed malignancies of the gastrointestinal tract. Searching for methods of therapy that complements treatment or has a preventive effect is desirable. Bacterial metabolites safe for human health, which have postbiotic effect, are of interest recently. The study aimed to preliminary assessment of the safety, antimicrobial, and anti-cancer activity of cell-free metabolites of Gluconobacter oxydans strains isolated from Kombucha beverages as an example of the potential postbiotic activity of acetic acid bacteria (AAB). The study material consisted of five AAB strains of Kombucha origin and three human cell lines (gastric adenoma-AGS, colorectal adenoma-HT-29, and healthy cells derived from the endothelium of the human umbilical vein-HUVEC). Results of the study confirms the health safety and functional properties of selected AAB strains, including their potential postbiotic properties. The best potential anticancer activity of the AAB cell-free supernatants was demonstrated against AGS gastric adenoma cells. The conducted research proves the postbiotic potential of selected acetic acid bacteria, especially the KNS30 strain. KEY POINTS: •The beneficial and application properties of acetic acid bacteria are poorly studied. •Gluconobacter oxydans from Kombucha show a postbiotic activity. •The best anticancer activity of the G. oxydans showed against gastric adenoma.
| S-EPMC10756867 | biostudies-literature
Project description:BackgroundGluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variety of carbohydrates regio- and stereoselectively in the periplasm using membrane-bound dehydrogenases with accumulation of the products in the medium. As a consequence, only a small fraction of the carbon and energy source enters the cell, resulting in a low biomass yield. Additionally, central carbon metabolism is characterized by the absence of a functional glycolysis and absence of a functional tricarboxylic acid (TCA) cycle. Due to these features, G. oxydans is a highly interesting model organism. Here we analyzed global mRNA decay in G. oxydans to describe its characteristic features and to identify short-lived mRNAs representing potential bottlenecks in the metabolism for further growth improvement by metabolic engineering.ResultsUsing DNA microarrays we estimated the mRNA half-lives in G. oxydans. Overall, the mRNA half-lives ranged mainly from 3 min to 25 min with a global mean of 5.7 min. The transcripts encoding GroES and GroEL required for proper protein folding ranked at the top among transcripts exhibiting both long half-lives and high abundance. The F-type H+-ATP synthase transcripts involved in energy metabolism ranked among the transcripts with the shortest mRNA half-lives. RNAseq analysis revealed low expression levels for genes of the incomplete TCA cycle and also the mRNA half-lives of several of those were short and below the global mean. The mRNA decay analysis also revealed an apparent instability of full-length 23S rRNA. Further analysis of the ribosome-associated rRNA revealed a 23S rRNA fragmentation pattern exhibiting new cleavage regions in 23S rRNAs which were previously not known.ConclusionsThe very short mRNA half-lives of the H+-ATP synthase, which is likely responsible for the ATP-proton motive force interconversion in G. oxydans under many or most conditions, is notably in contrast to mRNA decay data from other bacteria. Together with the short mRNA half-lives and low expression of some other central metabolic genes it could limit intended improvements of G. oxydans' biomass yield by metabolic engineering. Also, further studies are needed to unravel the multistep process of the 23S rRNA fragmentation in G. oxydans.
| S-EPMC6191907 | biostudies-literature
Project description:Self-organized bacteria have been the subject of interest for a number of applications, including the construction of microbial fuel cells. In this paper, we describe the formation of a self-organized, three-dimensional network that is constructed using Gluconobacter oxydans B-1280 cells in a hydrogel consisting of poly(vinyl alcohol) (PVA) with N-vinyl pyrrolidone (VP) as a cross-linker, in which the bacterial cells are organized in a particular side-by-side alignment. We demonstrated that nonmotile G. oxydans cells are able to reorganize themselves, transforming and utilizing PVA-VP polymeric networks through the molecular interactions of bacterial extracellular polysaccharide (EPS) components such as acetan, cellulose, dextran, and levan. Molecular dynamics simulations of the G. oxydans EPS components interacting with the hydrogel polymeric network showed that the solvent-exposed loops of PVA-VP extended and engaged in bacterial self-encapsulation.
| S-EPMC6045399 | biostudies-literature