The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells

Area of Science:

• Bacterial gene expression
• RNA metabolism
• Molecular biology

Background:

• Polyadenylation by poly(A) polymerase I (PAP I) is vital for mRNA decay and RNA quality control in Escherichia coli.
• The full extent of polyadenylation in E. coli and its regulatory mechanisms remain largely uncharacterized.

Purpose of the Study:

• To investigate the prevalence and mechanisms of polyadenylation in E. coli.
• To identify the roles of PAP I and polynucleotide phosphorylase (PNPase) in RNA modification.

Main Methods:

• Comparative transcriptome analysis using macroarrays to compare wild-type and pcnB deletion strains.
• Detailed transcript analysis of over 240 specific RNA molecules.
• Real-time PCR to quantify polyadenylation levels of specific transcripts like lpp and ompA.

Main Results:

• Over 90% of E. coli open reading frames (ORFs) undergo polyadenylation by PAP I during exponential growth, as full-length transcripts or decay intermediates.
• Rho-independent transcription terminators appear to function as polyadenylation signals for PAP I.
• Rho-dependent terminated mRNAs are likely modified by polynucleotide phosphorylase (PNPase) with long polynucleotide tails, not PAP I.
• Significant variations in polyadenylation extent for individual transcripts (e.g., lpp, ompA) were observed in wild-type cells.

Conclusions:

• Bacterial polyadenylation by PAP I is far more prevalent than previously assumed.
• Distinct mechanisms govern polyadenylation and polynucleotide tail addition based on transcription termination signals.
• Understanding these RNA modification pathways is critical for bacterial RNA homeostasis.