TY  - JOUR
A1  - Sass, Andrea M.
A1  - Van Acker, Heleen
A1  - Förstner, Konrad U.
A1  - Van Nieuwerburgh, Filip
A1  - Deforce, Dieter
A1  - Vogel, Jörg
A1  - Coenye, Tom
T1  - Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
T2  - BMC Genomics
N2  - Background: Burkholderia 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. Methods: RNA 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. Results: Four 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. Conclusions: Mapping 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.
KW  - persistence
KW  - genomic islands
KW  - pathogen
KW  - identification
KW  - bacteria
KW  - small RNAs
KW  - translation initiation
KW  - cepedia complex
KW  - global gene expression
KW  - SEQ
KW  - resistance
KW  - burkholderia cenocepacia
KW  - biofilms
KW  - dRNA-Seq
KW  - transcription start site
KW  - antisense RNA
Y1  - 2015
UR  - https://opus.bibliothek.uni-wuerzburg.de/frontdoor/index/index/docId/13974
UR  - https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-139748
VL  - 16
IS  - 775
ER  -