Fernandes de Brito, Luciana; Irla, Marta; Kalinowski, Jörn; Wendisch, Volker F.: Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. In: BMC Genomics. Jg.18 H. 1. 2017
Inhalt
- Methods
- Cultivation of P. riograndensis SBR5 in different conditions
- RNA isolation and preparation of cDNA libraries for sequencing
- Mapping sequenced reads onto the genome of P. riograndensis SBR5
- Determination of transcription start sites (TSS) based on 5′-end enriched library
- Determination of 5′ UTR length and identification of cis-regulatory elements in 5′ UTRs of P. riograndensis SBR5 genes
- Detection of conserved ribosomal biding site (RBS) and promoter motifs sequences
- Determination of most abundant genes transcribed in P. riograndensis SBR5
- Identification of operon structures in P. riograndensis SBR5
- Strains, plasmid construction and primers
- Fluorescence-activated cell scanning analysis
- Results
- Cultivation of P. riograndensis SBR5 under various growth conditions
- RNA-seq experiment of P. riograndensis SBR5
- Identification of transcription start sites (TSS) based on the mapped 5′-end enriched data
- Distribution of 5′ UTR length in P. riograndensis SBR5
- Identification of consensus promoter motif sequences in P. riograndensis SBR5
- Identification of RBS (ribosome binding site) and TLS (translation start site) consensus sequences in P. riograndensis SBR5
- Identification of cis-regulatory elements in 5′ UTRs of P. riograndensis SBR5 genes
- A TPP riboswitch influences gfpUV expression in P. riograndensis SBR5
- Identification and characterization of novel transcripts
- Gene expression ranked according to transcript abundances
- Identification of operon structures in P. riograndensis SBR5
- Discussion
- Conclusions
- Additional files
- Abbreviations
- Funding
- Availability data and materials
- Authors’ contributions
- Ethics approval and consent to participate
- Consent for publication
- Competing interests
- Publisher’s Note
- Author details
- References