Irla, Marta; Neshat, Armin; Brautaset, Trygve; Rückert, Christian; Kalinowski, Jörn; Wendisch, Volker F.: Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted [...]. In: BMC Genomics. Jg.16 H. 1. 2015
Inhalt
- Background
- Methods
- Cultivation of B. methanolicus MGA3 in different growth media
- Total RNA isolation
- Preparation of two different cDNA libraries for high-throughput sequencing
- Mapping of the generated RNA-seq data to reference sequences
- Determination of putative transcription start sites using 5′-ends of enriched primary transcripts
- Identification of operon structures using whole transcriptome cDNA library RNA-seq data
- Detection of conserved sequence motifs in Bacillus methanolicus MGA3
- Calculation of transcript abundances in Bacillus methanolicus MGA3
- Results
- Cultivations of B. methanolicus MGA3 under different conditions for analysis of the primary and whole transcriptome
- Sequencing of cDNA libraries and mapping to the B. methanolicus MGA3 reference sequences
- Detection of putative transcription start sites from RNA-seq data of enriched 5′-ends of primary transcripts
- Determination and length distribution of 5′-untranslated regions in B. methanolicus MGA3
- Identification of ribosome binding sites in B. methanolicus MGA3
- Identification of promoter motifs in B. methanolicus MGA3
- Determination of operon structures based on the whole transcriptome data set
- Identification of novel transcripts in B. methanolicus MGA3
- Uncovering of cis-regulatory RNA elements by the analysis of 5′-UTRs
- Transcript abundances of B. methanolicus MGA3
- Discussion
- Analysis of 5′-UTRs in B. methanolicus MGA3
- Characteristics of translation start sites, ribosome binding sites, promoters and operons in B. methanolicus MGA3
- Description of novel transcripts in B. methanolicus MGA3
- Discovery of cis-regulatory RNA elements in the B. methanolicus MGA3 genome
- The mRNA abundances in B. methanolicus MGA3 reflect its metabolic organization
- Conclusion
- Availability of supporting data
- Additional files
- Competing interests
- Authors’ contributions
- Acknowledgements
- Author details
- References