Operon mRNAs are organized into ORF-centric structures that predict translation efficiency.

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Bacterial messenger RNAs (mRNAs) are often organized into operons, containing multiple open reading frames (ORFs) on a single polycistronic mRNA molecule.
• Individual ORFs within an operon are translated at significantly different rates, varying up to 100-fold.
• The regulatory mechanisms governing this differential translation remain largely unelucidated.

Purpose of the Study:

• To investigate the role of mRNA secondary structure in regulating differential translation of ORFs within bacterial operons.
• To determine if intrinsic mRNA structure influences translation efficiency in vivo and in vitro.

Main Methods:

• Genome-wide analysis of mRNA secondary structures across operons.
• Correlation analysis between ORF structure and translation rates in vivo.
• Assessment of mRNA structure stability under inhibited translation and in vitro refolding conditions.

Main Results:

• Operonic mRNAs exhibit distinct secondary structures within each ORF, with structural variations occurring at ORF boundaries.
• A strong correlation was observed between ORF mRNA structure and its translation rate in vivo.
• This correlation between structure and translation efficiency persisted, though reduced, even when translation was inhibited or the mRNA was refolded in vitro.

Conclusions:

• Intrinsic mRNA secondary structure acts as a blueprint for translation efficiency in bacterial operons.
• Translation itself reinforces and refines this structural blueprint, ultimately dictating the translation rate of each ORF.
• This self-reinforcing mechanism provides a novel layer of gene expression regulation at the post-transcriptional level.