ArticleRNA biology2016
Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism.
Article in RNA biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 62 citations in OpenAlex.
- Proteomic Analysis of Lactococcus lactis FM03 Under Prolonged Alkaline Stress.Environmental microbiology · 2026Article
- Small regulatory RNAs modulate lactococcal susceptibility to cell wall-targeting antimicrobials.Nucleic acids research · 2026Article
- Chromosomal and Plasmid-Based CRISPRi Platforms for Conditional Gene Silencing inInternational journal of molecular sciences · 2025Article
- Easy-Curing and pH-Regulated CRISPR-Cas9 Plasmids for Gene Editing and Plasmid Curing in Lactococcus cremoris.Microbial biotechnology · 2024Article
- Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection.Microbiology spectrum · 2024Article
- The growth-survival trade-off is hard-wired in the Lactococcus lactis gene regulation network.Environmental microbiology reports · 2022Article
- Riboswitch RSApplied and environmental microbiology · 2022Article
- Omics Approaches to Assess Flavor Development in Cheese.Foods (Basel, Switzerland) · 2022Review
- Insights into 6S RNA in lactic acid bacteria (LAB).BMC genomic data · 2021Article
- Deciphering the Regulation of the Mannitol Operon Paves the Way for Efficient Production of Mannitol in Lactococcus lactis.Applied and environmental microbiology · 2021Article
- Profiles of Small Regulatory RNAs at Different Growth Phases ofFrontiers in microbiology · 2021Article
- A computational system for identifying operons based on RNA-seq data.Methods (San Diego, Calif.) · 2020Review
- Structure of a Core Promoter in Bifidobacterium longum NCC2705.Journal of bacteriology · 2020Article
- The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities.mSystems · 2020Article
- A dual-chain assembly pathway generates the high structural diversity of cell-wall polysaccharides inThe Journal of biological chemistry · 2019Article
- Genetics of Lactococci.Microbiology spectrum · 2019Review
- The Primary Antisense Transcriptome ofGenes · 2019Article
- Article
- Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39.Nucleic acids research · 2018Article
- Antisense transcription in Pseudomonas aeruginosa.Microbiology (Reading, England) · 2018Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.