Specific Binding of Escherichia coli Ribosomal Protein S1 to boxA Transcriptional Antiterminator RNA

Abstract

We show that ribosomal protein S1 specifically binds theboxA transcriptional antiterminator RNAs of bacteriophage λ and the Escherichia coli ribosomal RNA operons. Although S1 competes with the NusB-S10 antitermination complex for binding to boxA, it does not affect antitermination by the λ N protein in vitro, and its role, if any, in rRNA synthesis is still unknown.

Functional importance of regions in Escherichia coli elongation factor NusA that interact with RNA polymerase, the bacteriophage λ N protein and RNA

“…We have shown previously that there are nucleotides in both boxA and boxB that are important for NusA association with the N– nut site complex (Mogridge et al ., 1995). We have also shown previously that ribosomal protein S1 specifically binds boxA RNA (Mogridge and Greenblatt, 1998), suggesting that the S1 homology region of NusA may interact with boxA . If the S1 homology region interacts with one portion of the nut site, it is possible that at least one of the KH homology regions interacts with the other.…”

“…Because this type of domain is found in other RNA‐interacting proteins involved in the initiation of translation and turnover of mRNA (Bycroft et al ., 1997), it must have some non‐specific RNA‐binding capacity. However, the S1 protein was also able to select specific RNA ligands from a random pool of RNAs and bind boxA ‐containing RNA with some selectivity, suggesting that S1 domains are capable of sequence‐specific binding (Ringquist et al ., 1995; Mogridge and Greenblatt, 1998). The KH domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K protein (Siomi et al ., 1993).…”

Translation initiation region sequence preferences in Escherichia coli

“…The SD variants were constructed by mutating the sequence, forming an 8 base pair duplex with the complementary aSD, and reducing its length from 8 nucleotides to 1. Each set contained a unique sequence upstream of the SD: one containing no translational enhancer ("no enhancer"), one containing a previously-described strong A/U rich enhancer, and one with a weak enhancer [ 19 , 33 ]. Transcription of the reporter genes was controlled by the IPTG inducible tac promoter [ 34 ].…”

The Sm-like RNA chaperone Hfq mediates transcription antitermination at Rho-dependent terminators

“…The antitermination activity of the tandem complex may therefore be multi‐factorial (Figure 8B), as certainly is the case for the composite rrn and λN antitermination complexes (Roberts et al , 2008; Sen et al , 2008). The recurrence of boxA ‐like sequences in Rho‐dependent terminators (Ciampi, 2006) and binding of Hfq‐RNAP mediator S1 protein (Sukhodolets and Garges, 2003) to boxA RNA (Mogridge and Greenblatt, 1998) further suggests a commonality of mechanisms. Interestingly, disruption of the tandem translation/transcription complex at the end of ORFs (or upon conditional perturbation; Roberts et al , 2008; Rabhi et al , 2010) may both activate transcription termination and recruitment of RNA degradation factors that frequently associate with Hfq (Butland et al , 2005; Brennan and Link, 2007; Hu et al , 2009), thereby linking the three major steps of RNA metabolism in the same regulatory mechanism (Figure 8C).…”