Solution Structure of YaeO, a Rho-specific Inhibitor of Transcription Termination

Gutiérrez, Pablo; Kozlov, Guennadi; Gabrielli, Lisa; Elias, Demetra; Osborne, Michael J.; Gallouzi, Imed Eddine; Gehring, Kalle

doi:10.1074/jbc.m702010200

Cited by 30 publications

(45 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This is consistent with in vitro binding results that show that the YaeO-Rho interaction is salt dependent and can be disrupted at high ionic strengths (Pichoff et al, 1998). Importantly, the structural model was used to design the D14K, E19K, and E52K YaeO mutants that prevent inhibition of Rho activity using an in vivo b-galactosidase assay (Gutierrez et al, 2007).…”

Section: Yaeo-rho: Inhibition Of Rho-dependent Transcription Termisupporting

confidence: 76%

“…Overexpression of YaeO can cause the pleiotropic suppression of conditional lethal mutations in cell division and heat shock genes, such as ftsQ, ftsA, grpE, groEL, and groES (Pichoff et al, 1998). We first determined the NMR solution structure of YaeO that revealed a topologically similar fold to that of the RNA-binding domain of small ribonucleoproteins (Sm-fold) (Gutierrez et al, 2007). In order to understand the mechanism of transcription termination inhibition by YaeO, NMR experiments were used to characterize the interaction of YaeO with Rho in vitro.…”

Section: Yaeo-rho: Inhibition Of Rho-dependent Transcription Termimentioning

confidence: 99%

See 1 more Smart Citation

Preparation and Characterization of Bacterial Protein Complexes for Structural Analysis

Matte

Kozlov

Trempe

et al. 2009

Advances in Protein Chemistry and Structural Biology

Self Cite

View full text Add to dashboard Cite

Section: Yaeo-rho: Inhibition Of Rho-dependent Transcription Termisupporting

confidence: 76%

Section: Yaeo-rho: Inhibition Of Rho-dependent Transcription Termimentioning

confidence: 99%

Preparation and Characterization of Bacterial Protein Complexes for Structural Analysis

Matte

Kozlov

Trempe

et al. 2009

Advances in Protein Chemistry and Structural Biology

Self Cite

View full text Add to dashboard Cite

“…Bacteriophage P4 protein Psu (44,45), E. coli Hfq (46), and YaeO (47,48) proteins and the most recently discovered specific RNA sequence, RARE, in Salmonella (28) are the other inhibitors of the Rho function. They bind directly to Rho and inhibit its function.…”

Section: Discussionmentioning

confidence: 99%

Transcription Elongation Factor NusA Is a General Antagonist of Rho-dependent Termination in Escherichia coli

Qayyum

Dey

Sen

2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

NusA is an essential protein that binds to RNA polymerase and also to the nascent RNA and influences transcription by inducing pausing and facilitating the process of transcription termination/antitermination. Its participation in Rho-dependent transcription termination has been perceived, but the molecular nature of this involvement is not known. We hypothesized that, because both Rho and NusA are RNA-binding proteins and have the potential to target the same RNA, the latter is likely to influence the global pattern of the Rho-dependent termination. Analyses of the nascent RNA binding properties and consequent effects on the Rho-dependent termination functions of specific NusA-RNA binding domain mutants revealed an existence of Rho-NusA direct competition for the overlapping nut (NusA-binding site) and rut (Rho-binding site) sites on the RNA. This leads to delayed entry of Rho at the rut site that inhibits the latter's RNA release process. High density tiling microarray profiles of these NusA mutants revealed that a significant number of genes, together with transcripts from intergenic regions, are up-regulated. Interestingly, the majority of these genes were also up-regulated when the Rho function was compromised. These results provide strong evidence for the existence of NusA-binding sites in different operons that are also the targets of Rho-dependent terminations. Our data strongly argue in favor of a direct competition between NusA and Rho for the access of specific sites on the nascent transcripts in different parts of the genome. We propose that this competition enables NusA to function as a global antagonist of the Rho function, which is unlike its role as a facilitator of hairpin-dependent termination.The bacterial transcription terminator, Rho, functions as a hexameric RNA-dependent ATPase that is capable of translocating along the RNA. It dislodges the elongating RNA polymerase (RNAP) 4 once it is loaded onto the nascent RNA (1, 2). Its termination function is facilitated upon interaction with the transcription elongation factor, NusG (3-5). Recent genomics studies have revealed that Rho-dependent termination occurs at more than one-third of the operons of a dividing Escherichia coli (6, 7). This mode of transcription termination is involved in many physiological processes, like control of translation (2), riboswitch formation (8), inhibition of unwanted antisense transcription, etc. (7). Rho is capable of loading onto unstructured stretches of RNA (the rut ([R]ho [ut]ilization) sites), and once it is bound to the RNA, it translocates in a processive manner along the 5Јto 3Ј direction, which may induce unwanted termination of transcription. Interestingly, in vivo negative regulation by cellular factors or any control switch of the Rho function has not been documented. In principle, any RNA-binding protein that has overlapping binding sites with the rut sites on the nascent RNA could influence the Rho activity by a direct competition for occupancy of the same sites.NusA, a ubiquitous transcription elo...

show abstract

“…Hence, a biological study to elucidate the physiological relevance of the putative molecular function of SF173 is currently in progress. In addition, our structural inspection, which indicated a partial structural homology of SF173 to colicin D and RPP21, implies a possible long-distance correlation in terms of genomic evolution among the bacteriocin/colicin-immunity, Rho-dependent transcription termination, and RNase P systems, all of which are associated with tRNA utilization [27,29,30].…”

Section: Discussionmentioning

confidence: 99%

“…Thus, YaeP (98.5% sequence identity to SF173) and YaeQ (100% sequence identity to SF174) could also be identified as SF173 and SF174 orthologues, respectively. Although the structure and function of YaeP and YaeQ proteins are uncharacterized, YaeO has been identified as a Rho-specific inhibitor of transcription termination [27]. Bacteria have two major mechanisms for transcription termination, one of which is dependent on the transcription terminator protein Rho.…”

Section: Structural Correlation With Rof/rnase P-like Domain Proteinsmentioning

confidence: 99%

Crystal Structure of Shigella flexneri SF173 Reveals a Dimeric Helical Bundle Conformation

et al. 2018

View full text Add to dashboard Cite

Abstract:We report the crystal structure and bioinformatic analysis of SF173, a functionally uncharacterized protein from the human enteropathogenic bacteria Shigella flexneri. The structure shows a tightly interlinked dimer formed by adimeric core comprising α2 and α3 helices from both subunits and swapping the N-terminal α1 helix of each monomer. Structural inspection and genomic analysis results suggest that the SF173 might play its putative function by binding to SF172, the partially overlapped upstream product in the operon. As YaeO (an SF172 orthologue) has been identified to be an inhibitor of the bacterial transcription terminator Rho protein, SF173 is suggested to be involved in the regulation of Rho-dependent transcription termination, by inhibiting the Rho protein binding to SF172/YaeO.

show abstract

Solution Structure of YaeO, a Rho-specific Inhibitor of Transcription Termination

Cited by 30 publications

References 37 publications

Preparation and Characterization of Bacterial Protein Complexes for Structural Analysis

Preparation and Characterization of Bacterial Protein Complexes for Structural Analysis

Transcription Elongation Factor NusA Is a General Antagonist of Rho-dependent Termination in Escherichia coli

Crystal Structure of Shigella flexneri SF173 Reveals a Dimeric Helical Bundle Conformation

Contact Info

Product

Resources

About