Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons.

ABSTRACT: Many bacteria use operons to coregulate genes, but it remains unclear how operons benefit bacteria. We integrated E. coli's 788 polycistronic operons and 1,231 transcription units into an existing whole-cell model and found inconsistencies between the proposed operon structures and the RNA-seq read counts that the model was parameterized from. We resolved these inconsistencies through iterative, model-guided corrections to both datasets, including the correction of RNA-seq counts of short genes that were misreported as zero by existing alignment algorithms. The resulting model suggested two main modes by which operons benefit bacteria. For 86% of low-expression operons, adding operons increased the co-expression probabilities of their constituent proteins, whereas for 92% of high-expressio

SUBMITTER: Sun G 

PROVIDER: S-EPMC10957310 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature