σ28-dependent small RNA regulation of flagella biosynthesis

Abstract

Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor σ28 (fliA) in Escherichia coli. Interestingly, the four sRNAs have varied effects on flagellin protein levels, flagella number and cell motility. UhpU, corresponding to the 3’ UTR of a metabolic gene, likely has hundreds of targets including a transcriptional regulator at the top flagella regulatory cascade connecting metabolism and flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs and uniquely act on ribosomal protein mRNAs connecting ribosome production and flagella synthesis. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.

Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni

“…Reminiscent of FlmE and FlmR, four UTR-derived, σ 28 -dependent E. coli sRNAs (UhpU, MotR, FliX, and FlgO) have recently been described to have varied effects on flagellin protein levels, flagellar number, and motility 60 . These effects are mediated by regulation of diverse targets by the four sRNAs, including middle and late flagellar genes, a transcriptional regulator, and a ribosomal protein mRNA 60 . While there is no sequence homology between the E. coli and C .…”

“…While 3’UTR-derived sRNAs control multiple physiological processes in diverse bacterial species 40 , 41 , also with implications for larger regulatory networks such as the bacterial envelope stress response 78 , 79 , processing of flagellar mRNAs to produce sRNAs that function in the same pathway is a relatively new concept. To the best of our knowledge, only two sRNAs that potentially repress flagellar biogenesis and that are also processed from flagellar mRNAs have been reported in E. coli : FlgO and FliX, which are processed from the 3’UTRs of FliA-dependent flgL and fliC mRNAs, respectively 60 , 80 . While FlgO has a minor impact on flagellar number and motility, FliX seems to repress these two traits via regulation of several middle and late flagellar genes and an mRNA encoding ribosomal proteins 60 .…”

“…To the best of our knowledge, only two sRNAs that potentially repress flagellar biogenesis and that are also processed from flagellar mRNAs have been reported in E. coli : FlgO and FliX, which are processed from the 3’UTRs of FliA-dependent flgL and fliC mRNAs, respectively 60 , 80 . While FlgO has a minor impact on flagellar number and motility, FliX seems to repress these two traits via regulation of several middle and late flagellar genes and an mRNA encoding ribosomal proteins 60 .…”

Extraribosomal Functions of Bacterial Ribosomal Proteins—An Update, 2023

“…The regulatory activity of the Nus factors has been recently proposed to be involved in the complex regulatory cascade of flagella biosynthesis [ 149 ]. One of the flagella-specific sRNAs implicated in the regulation of flagellar operons, MotR, appears to base pair internal to the rpsJ (uS10) coding sequence and promote Hfq binding to the rpsJ leader sequence, which in turn results in increased rpsJ translation.…”

“…One of the flagella-specific sRNAs implicated in the regulation of flagellar operons, MotR, appears to base pair internal to the rpsJ (uS10) coding sequence and promote Hfq binding to the rpsJ leader sequence, which in turn results in increased rpsJ translation. Due to its elevated concentration in the cell, uS10, in conjunction with NusB, may increase transcription antitermination of long flagellar operons, contributing to flagellin protein levels, flagella numbers, and cell motility [ 149 ].…”