RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation.
BACKGROUND
The 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.


RESULTS
A 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.


CONCLUSIONS
The 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.
Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Norddeutsches Zentrum für Mikrobielle Genomforschung, Georg-August-Universität Göttingen, Grisebachstr, 8, D-37077 Göttingen, Germany. hlieseg@gwdg.de.
Sandra
S
Wiegand
Sascha
S
Dietrich
Robert
R
Hertel
Johannes
J
Bongaerts
Stefan
S
Evers
Sonja
S
Volland
Rolf
R
Daniel
Heiko
H
Liesegang
D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D001407:Bacillus / Q000235:genetics*; D001483:Base Sequence; D016000:Cluster Analysis; D005285:Fermentation / Q000235:genetics*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009876:Operon / Q000235:genetics; D010447:Peptide Hydrolases / Q000378:metabolism; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D020860:Subtilisin / Q000378:metabolism; D024363:Transcription Initiation Site; D059467:Transcriptome / Q000235:genetics
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D016372:RNA, Antisense; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D010447:Peptide Hydrolases; D020860:Subtilisin