RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentationReport as inadecuate




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BMC Genomics

, 14:667

Prokaryote microbial genomics

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.

KeywordsdRNA-Seq RNA-based regulation UTR ncRNA sRNA Antisense RNA Subtilisin Transcription start site Operon prediction Reannotation Abbreviations°CDegrees Celsius

μLMicroliter

AAdenine

asRNAAntisense RNA

bpBase pairs

CCytosine

cDNAComplementary DNA

dRNA-SeqDifferential RNA sequencing

gGram

gGravitational constant

GGuanine

hHours

LLiter

lnNatural logarithm

MbMegabase pairs

minMinute

mLMilliliter

mMMillimolar

mRNAMessenger RNA

ncRNANon-coding RNA

NPKMNucleotide activity per kilobase of exon model per million mapped reads

ntNucleotides

ODOptical density

ORFOpen reading frame

PCRPolymerase chain reaction

RNA-SeqRNA sequencing

rpmRevolutions per minute

rRNARibosomal RNA

TThymine

TAPTobacco Acid Pyrophosphatase

TEXTerminator™ 5′-Phosphate-Dependent Exonuclease

tmRNATransfer-messenger RNA

tRNATransfer RNA

TSSTranscription start sites

UTRUntranslated region

VVolt

v-vVolume per volume

w-vWeight per volume.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-667 contains supplementary material, which is available to authorized users.

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