Abstract
BackgroundThe production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. Regulatory events within the process result in a dynamic change of the transcriptional activity of the genome. This complex network of genes is orchestrated by proteins as well as regulatory RNA elements. Here we present an RNA-Seq based study considering selected phases of an industry-oriented fermentation of Bacillus licheniformis.ResultsA detailed analysis of 20 strand-specific RNA-Seq datasets revealed a multitude of transcriptionally active genomic regions. 3314 RNA features encoded by such active loci have been identified and sorted into ten functional classes. The identified sequences include the expected RNA features like housekeeping sRNAs, metabolic riboswitches and RNA switches well known from studies on Bacillus subtilis as well as a multitude of completely new candidates for regulatory RNAs. An unexpectedly high number of 855 RNA features are encoded antisense to annotated protein and RNA genes, in addition to 461 independently transcribed small RNAs. These antisense transcripts contain molecules with a remarkable size range variation from 38 to 6348 base pairs in length. The genome of the type strain B. licheniformis DSM13 was completely reannotated using data obtained from RNA-Seq analyses and from public databases.ConclusionThe hereby generated data-sets represent a solid amount of knowledge on the dynamic transcriptional activities during the investigated fermentation stages. The identified regulatory elements enable research on the understanding and the optimization of crucial metabolic activities during a productive fermentation of Bacillus licheniformis strains.
Highlights
The production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter
Upon formation of secondary structures, trans-encoded Non-coding RNA (ncRNA) interact with their target RNAs by imperfect base pairing, which is triggered by the binding of a seed region of at least six contiguous nucleotides [15,16]
A second class of regulatory ncRNAs is encoded in cis, which means that these ncRNAs are transcribed from the antisense strand of protein-coding genes [18]
Summary
The production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. A second class of regulatory ncRNAs is encoded in cis, which means that these ncRNAs are transcribed from the antisense strand of protein-coding genes [18] They are complementary in full-length and can form RNA duplexes with the mRNA of the targeted genes [19]. A second class of RNA-based regulators encompasses cisregulatory elements, mainly present at the 5′ untranslated region (5′UTR) of mRNA transcripts, e.g. riboswitches, T-boxes or thermosensors [23] Whereas both 5′ as well as 3’untranslated regions can bear signals for the initiation and termination of translation [24,25], respectively, 5′UTRs have the ability to fine-tune translation by cis-regulatory elements. They can be prone to RNA-binding proteins or antisense
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