Activity-Cloud Organization of Shine-Dalgarno Sequences to Guide Translation Engineering in <i>Escherichia coli</i>.

ABSTRACT: Modifying the six-nucleotide Shine-Dalgarno (SD) core motif inside the ribosome binding site (RBS) constitutes a straightforward approach for tuning bacterial translation. However, existing methods for adjusting the effective translation rate (ETR) lack predictability. Even single-nucleotide substitutions can induce substantial alterations in translation efficiency. Moreover, this unpredictability is exacerbated by variations in the leader sequence, spacer region, or coding context. By focusing on the SD core as a key, experimentally tunable determinant of translation initiation in Escherichia coli, we introduce a coarse-grained framework that organizes SD core variants into activity clouds with consistent expression levels. This representation converts a dense sequence-to-phenotype

SUBMITTER: Zach P 

PROVIDER: S-EPMC12917692 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature