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PMID: 26495981 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function.

PLoS genetics ·Vol. 11 ·No. 10 ·2015-10-00 ·Pages e1005613

Del Campo C, Bartholomäus A, Fedyunin I, Ignatova Z

Abstract

Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.

MeSH Terms
Binding Sites Escherichia coli/genetics Nucleic Acid Conformation Nucleotide Motifs/genetics Protein Biosynthesis/genetics Protein Structure, Secondary RNA Stability/genetics RNA, Messenger/chemistry,genetics Ribonucleases/genetics Ribosomes/genetics Sequence Analysis, RNA Transcriptome/genetics
Chemicals
RNA, Messenger Ribonucleases
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Del Campo Cristian
Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Biochemistry and Molecular Biology, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany.
Bartholomäus Alexander
Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Biochemistry and Molecular Biology, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany.
Fedyunin Ivan
Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
Ignatova Zoya
Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Biochemistry and Molecular Biology, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany.
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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1005613
Published
2015-10-00
Epub
2015-00-23
Pages
e1005613
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC4619774
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pgen.1005613 PMC Full Text View journal details
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