Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

Area of Science:

• Microbiology
• Molecular Biology
• Genomics

Background:

• Bacterial messenger RNAs (mRNAs) have very short lifespans, undergoing rapid transcription, translation, and degradation.
• The functional implications of diverse mRNA molecular states within bacterial cells remain largely uncharacterized.

Purpose of the Study:

• To quantitatively map the 3' status of cellular RNAs in Escherichia coli during steady-state growth.
• To investigate the prevalence and impact of mRNA fragments on gene expression analysis.

Main Methods:

• Quantitative analysis of cellular RNA 3' ends in Escherichia coli.
• Characterization of RNA fragments, distinguishing between decay intermediates and nascent transcripts.
• Assessment of ribosome association for different RNA species.

Main Results:

• A significant fraction (median >60%) of cellular RNA molecules in E. coli are fragments of canonical full-length mRNAs.
• The majority of these RNA fragments are identified as decay intermediates.
• mRNA decay intermediates are underrepresented in ribosome-associated transcripts, suggesting they are not actively translated.

Conclusions:

• Bacterial cells contain substantial heterogeneity in mRNA molecules, with a large proportion being degradation products.
• The prevalence of non-functional mRNA fragments can significantly distort transcriptomic analyses, particularly differential gene expression studies.
• Distinguishing functional, full-length mRNAs from decay intermediates is crucial for accurate understanding of bacterial gene regulation and mRNA dynamics.