title: Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism.
abstract: RNA sequencing has revolutionized genome-wide transcriptome analyses, and the identification of non-coding regulatory RNAs in bacteria has thus increased concurrently. Here we reveal the transcriptome map of the lactic acid bacterial paradigm Lactococcus lactis MG1363 by employing differential RNA sequencing (dRNA-seq) and a combination of manual and automated transcriptome mining. This resulted in a high-resolution genome annotation of L. lactis and the identification of 60 cis-encoded antisense RNAs (asRNAs), 186 trans-encoded putative regulatory RNAs (sRNAs) and 134 novel small ORFs. Based on the putative targets of asRNAs, a novel classification is proposed. Several transcription factor DNA binding motifs were identified in the promoter sequences of (a)sRNAs, providing insight in the interplay between lactococcal regulatory RNAs and transcription factors. The presence and lengths of 14 putative sRNAs were experimentally confirmed by differential Northern hybridization, including the abundant RNA 6S that is differentially expressed depending on the available carbon source. For another sRNA, LLMGnc_147, functional analysis revealed that it is involved in carbon uptake and metabolism. L. lactis contains 13% leaderless mRNAs (lmRNAs) that, from an analysis of overrepresentation in GO classes, seem predominantly involved in nucleotide metabolism and DNA/RNA binding. Moreover, an A-rich sequence motif immediately following the start codon was uncovered, which could provide novel insight in the translation of lmRNAs. Altogether, this first experimental genome-wide assessment of the transcriptome landscape of L. lactis and subsequent sRNA studies provide an extensive basis for the investigation of regulatory RNAs in L. lactis and related lactococcal species.
authors.affiliation: a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.|b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands.
authors.forename: Sjoerd B
authors.initials: SB
authors.lastname: van der Meulen
authors.affiliation: a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.|b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands.
authors.forename: Anne
authors.initials: A
authors.lastname: de Jong
authors.affiliation: a Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Groningen , The Netherlands.|b Top Institute Food and Nutrition (TIFN) , Wageningen , The Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: Kok
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites; D002244:Carbon / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D013294:Lactococcus lactis / Q000235:genetics* / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D014157:Transcription Factors; D002244:Carbon
keywords: 6S; dRNA-seq; lactic acid bacteria; small regulatory RNA; transcriptome