Abstract
BackgroundThe 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 α-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.ResultsSequencing 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).ConclusionsThis 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.
Highlights
The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm
Data generation and mapping statistics Bacteria need to adapt to their environment by sensing environmental parameters and activation of appropriate regulatory programs, which typically involve the
Detection of transcription start sites (TSSs) and revision of start codons The read mapping of all primary transcriptome libraries was used for the detection of TSSs by ReadXplorer [44]
Summary
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 α-proteobacterium Gluconobacter oxydans 621H is a Gram-negative acetic acid bacterium, which is used for a broad range of industrial applications requiring regioand stereoselective oxidations This is due to the ability to incompletely oxidize a great variety of carbohydrates in the periplasm and the release of resulting products into the medium. The Embden-Meyerhof-Parnas (EMP) pathway and the tricarboxylic acid (TCA) cycle are incomplete [9] Both the restricted ability to oxidize carbohydrates in the cytoplasm and the high activity of dehydrogenases in the periplasm as well as subsequent release of products into the medium result in a low final
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