Regulation of Transcription Termination of Small RNAs and by Small RNAs: Molecular Mechanisms and Biological Functions

Abstract

Accurate and efficient transcription termination is an important step for cells to generate functional RNA transcripts. In bacteria, two mechanisms are responsible for terminating transcription: intrinsic (Rho-independent) termination and Rho-dependent termination. Growing examples suggest that neither type of transcription termination is static, but instead are highly dynamic and regulated. Regulatory small RNAs (sRNAs) are key players in bacterial stress responses, are frequently expressed under specific growth conditions, and are predominantly terminated through the intrinsic termination mechanism. Once made, sRNAs can base-pair with mRNA targets and regulate mRNA translation and stability. Recent findings suggest that alterations in the efficiency of intrinsic termination for sRNAs under various growth conditions may affect the availability of a given sRNA and the ability of the sRNA to function properly. Moreover, alterations of mRNA structure, translation, and accessibility by sRNAs have the potential to impact the access of Rho factor to mRNAs and thus termination of the mRNA. Indeed, recent studies have revealed that some sRNAs can modulate target gene expression by stimulating or inhibiting Rho-dependent termination, thus expanding the regulatory power of bacterial sRNAs. Here we review the current knowledge on intrinsic termination of sRNAs and sRNA-mediated Rho-dependent termination of protein coding genes in bacteria.

Keywords: ChiX; CsrA; Hfq; Rho; SgrS; SraL.

Figure 1

Production of the polyU tail of sRNAs by Rho-independent termination and the role of a polyU tail in Hfq binding and sRNA function. (A) Functional structure of an Hfq-dependent sRNA. The polyU tail of seven or longer is responsible for binding to the Hfq proximal face. The seed region is defined as the region which pairs with target mRNAs and is generally located 5′ to the terminator. (B) (i): Termination at the seventh or longer position within the T stretch is necessary for functional sRNAs. (ii): Transcripts with 3′ extensions resulting from termination site read-through bind poorly to Hfq, resulting in non-functional sRNAs. (iii): The transcripts with the U tail shortened by premature termination are no longer able to bind Hfq, resulting in non-functional sRNAs. (C) Low temperature increases both the level of transcription initiation and the termination efficiency for the gene encoding the DsrA sRNA. (D) Termination efficiency at the sgrS terminator is improved by glucose-phosphate stress, which also induces transcription initiation of sgrS by SgrR, a transcriptional regulator. Increased transcription termination will result in more production of SgrS and less expression of the downstream setA mRNA.

Figure 2

sRNA-based negative or positive regulation of Rho-dependent transcription attenuation in bacteria. (A) Translation inhibition by sRNA assists Rho-dependent termination. When the accumulation of Salmonella ChiX or E. coli Spot 42 sRNA is low, the mRNAs chiPQ and galETKM are translated well. When ChiX or Spot42 sRNA is produced at high levels, under specific environmental conditions, sRNA annealing blocks the ribosome binding site of the corresponding mRNA target (chiP or galK, respectively); reduced translation allows Rho loading onto a cryptic rut site to terminate transcription inside the genes (dotted pale portion of box represents untranscribed portion of the mRNA). (B) Antagonization of Rho-dependent attenuation by sRNAs. In genes with long 5′ UTRs, rut sites can allow Rho termination, blocking expression of the downstream gene (dotted box represents untranscribed coding region). sRNAs binding within the 5′ UTR can block Rho access to the rut sites, thus acting as anti-terminators for the downstream CDS.