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Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data
- Source :
- Scientific Reports, Scientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
- Publication Year :
- 2017
-
Abstract
- Bacterial translation initiation is influenced by base pairing between the Shine-Dalgarno (SD) sequence in the 5′ UTR of mRNA and the anti-SD (aSD) sequence at the free 3′ end of the 16S rRNA (3′ TAIL) due to: 1) the SD/aSD sequence binding location and 2) SD/aSD binding affinity. In order to understand what makes an SD/aSD interaction optimal, we must define: 1) terminus of the 3′ TAIL and 2) extent of the core aSD sequence within the 3′ TAIL. Our approach to characterize these components in Escherichia coli and Bacillus subtilis involves 1) mapping the 3′ boundary of the mature 16S rRNA using high-throughput RNA sequencing (RNA-Seq), and 2) identifying the segment within the 3′ TAIL that is strongly preferred in SD/aSD pairing. Using RNA-Seq data, we resolve previous discrepancies in the reported 3′ TAIL in B. subtilis and recovered the established 3′ TAIL in E. coli. Furthermore, we extend previous studies to suggest that both highly and lowly expressed genes favor SD sequences with intermediate binding affinity, but this trend is exclusive to SD sequences that complement the core aSD sequences defined herein.
- Subjects :
- 0301 basic medicine
Untranslated region
Base pair
Sequence analysis
lcsh:Medicine
Bacillus subtilis
Article
03 medical and health sciences
RNA, Ribosomal, 16S
mental disorders
Escherichia coli
3' Flanking Region
lcsh:Science
Peptide Chain Initiation, Translational
Gene
Genetics
Messenger RNA
Multidisciplinary
Binding Sites
biology
Base Sequence
Sequence Analysis, RNA
lcsh:R
RNA
High-Throughput Nucleotide Sequencing
Ribosomal RNA
biology.organism_classification
RNA, Bacterial
030104 developmental biology
lcsh:Q
Ribosomes
Subjects
Details
- ISSN :
- 20452322
- Volume :
- 7
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Scientific reports
- Accession number :
- edsair.doi.dedup.....e1dcbac913230e770228f371e01b44fa