ArticleBMC genomics2015
Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 40 citations in OpenAlex.
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- Rationally designed pooled CRISPRi-seq uncovers an inhibitor of bacterial peptidyl-tRNA hydrolase.Cell reports · 2024Article
- Non-coding regulatory sRNAs from bacteria of the Burkholderia cepacia complex.Applied microbiology and biotechnology · 2024Review
- Identification of Burkholderia cenocepacia non-coding RNAs expressed during Caenorhabditis elegans infection.Applied microbiology and biotechnology · 2023Article
- The Small RNA NcS25 Regulates Biological Amine-Transporting Outer Membrane Porin BCAL3473 in Burkholderia cenocepacia.mSphere · 2023Article
- Pellicle Biofilm Formation inJournal of bacteriology · 2022Article
- Promoter Architecture Differences amongmSystems · 2021Article
- Improved Dynamic Range of a Rhamnose-Inducible Promoter for Gene Expression inApplied and environmental microbiology · 2021Article
- Complete Genome Sequence of Burkholderia cenocepacia Phage Magia.Microbiology resource announcements · 2021Article
- A majority ofProceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Transcriptomic Landscape ofGenes · 2020Article
- Article
- In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1.BMC genomics · 2020Article
- Low iron-induced small RNA BrrF regulates central metabolism and oxidative stress responses in Burkholderia cenocepacia.PloS one · 2020Article
- The role of small proteins inBiofilm · 2019Article
- Various Evolutionary Trajectories Lead to Loss of the Tobramycin-Potentiating Activity of the Quorum-Sensing Inhibitor Baicalin Hydrate inAntimicrobial agents and chemotherapy · 2019Article
- Defining the Transcriptional and Post-transcriptional Landscapes ofFrontiers in microbiology · 2019Article
- Competitive Fitness of Essential Gene Knockdowns Reveals a Broad-Spectrum Antibacterial Inhibitor of the Cell Division Protein FtsZ.Antimicrobial agents and chemotherapy · 2018Article
- Small Noncoding Regulatory RNAs fromInternational journal of molecular sciences · 2018Review
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBurkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale.
methodsRNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes.
resultsFour thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered.
conclusionsMapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.
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