Bacterial sRNAs can bind to mRNAs through complementary binding to regulate gene expression. What determines whether the sRNA/mRNA binding will promote or repress mRNA translation?

sRNAs are small non-coding RNA molecules that play a role in gene regulation in bacteria. They usually range from 50 to 200 nucleotides in length. sRNAs can bind to target mRNAs through base-pairing, which allows them to influence the translation process. mRNAs, on the other hand, are molecules created during transcription that carry the genetic information required for assembling proteins via the process of translation.

The binding of sRNA to mRNA can either promote or repress translation. Promotion of translation occurs when the sRNA binding removes secondary mRNA structures that inhibit the binding of the ribosome to mRNA, thereby increasing translational efficiency. In contrast, repression of translation is usually a result of the sRNA binding competing with ribosome binding, blocking access to the translation initiation site, or sequestering translational regulatory proteins.

Several factors can determine whether sRNA/mRNA binding will promote or repress translation: 1. Binding site location: If the sRNA binding site is in the vicinity of a ribosome-binding site or the translational start codon of an mRNA, sRNA binding can block ribosome binding and repress translation. If the sRNA binding site is located elsewhere and leads to structural changes that facilitate ribosome binding, the binding can promote translation. 2. Sequence complementarity: The degree of sequence complementarity between the sRNA and mRNA can influence the stability of the complex and thus determine whether translation is promoted or repressed. High complementarity could lead to a more stable sRNA/mRNA complex and may favor transcript degradation or translation repression, while partial complementarity could lead to altered mRNA secondary structures, promoting translation. 3. Cofactors: Some sRNAs require proteins called cofactors to be functional. Cofactors can directly influence the function of sRNAs and determine the outcome of sRNA/mRNA interactions. For example, the Hfq protein can bind both the sRNA and its target mRNA, altering RNA stability, and influencing translation regulation. 4. Environmental conditions: The regulatory outcome of sRNA/mRNA binding can also depend on the specific environmental conditions, such as temperature or nutrient availability. Under certain conditions, sRNA binding to mRNA may favor translation promotion, while under other conditions, it may favor repression. In summary, the promotion or repression of mRNA translation by sRNA/mRNA binding is determined by factors such as binding site location, sequence complementarity, the presence of cofactors, and environmental conditions.