Genomes and Genes
Summary: A protein which effects termination of RNA synthesis during the genetic transcription process by dissociating the ternary transcription complex RNA;-RNA POLYMERASE DNA at the termination of a gene.
- Gong F, Yanofsky C. Analysis of tryptophanase operon expression in vitro: accumulation of TnaC-peptidyl-tRNA in a release factor 2-depleted S-30 extract prevents Rho factor action, simulating induction. J Biol Chem. 2002;277:17095-100 pubmed..This ribosome remains stalled at the tna stop codon and blocks the access of Rho factor to the tna transcript, thereby preventing transcription termination...
- Italiani V, Zuleta L, Marques M. The transcription termination factor Rho is required for oxidative stress survival in Caulobacter crescentus. Mol Microbiol. 2002;44:181-94 pubmed..These results indicate that the Rho factor is essential for an efficient response to certain stresses in Caulobacter.
- Schwartz A, Margeat E, Rahmouni A, Boudvillain M. Transcription termination factor rho can displace streptavidin from biotinylated RNA. J Biol Chem. 2007;282:31469-76 pubmed..Although the ring-shaped Rho factor exhibits in vitro RNA-dependent ATPase and directional RNA-DNA helicase activities, the actual molecular ..
- Shankar S, Hatoum A, Roberts J. A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript. Mol Cell. 2007;27:914-27 pubmed..Furthermore, as NusA is not required for the antipausing activity of Q(82) in vitro, we distinguish two distinct activities of antiterminators, namely antipausing and RNA occlusion, and discuss their roles in Q(82) function. ..
- Skordalakes E, Berger J. Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell. 2006;127:553-64 pubmed..The structure explains the molecular effects of numerous mutations and provides new insights into the links between substrate recognition, ATP turnover, and coordinated strand movement. ..
- Zheng C, Friedman D. Reduced Rho-dependent transcription termination permits NusA-independent growth of Escherichia coli. Proc Natl Acad Sci U S A. 1994;91:7543-7 pubmed..Thus, NusA-dependent coupling should be less important in a mutant with low Rho activity. The fact that E. coli grows without NusA argues that NusA should be considered an accessory factor rather than a subunit of RNA polymerase. ..
- Kaplan D, O Donnell M. Rho factor: transcription termination in four steps. Curr Biol. 2003;13:R714-6 pubmedb>Rho factor is a hexameric ring-shaped helicase which terminates transcription in Escherichia coli. Two recent crystal structures of Rho in complex with nucleic acid reveal how this helicase ring loads onto mRNA and encircles it.
- Shashni R, Mishra S, Kalayani B, Sen R. Suppression of in vivo Rho-dependent transcription termination defects: evidence for kinetically controlled steps. Microbiology. 2012;158:1468-81 pubmed publisher..Finally, these results indicated that one of the major roles of NusG in in vivo Rho-dependent termination is to enhance the speed of RNA release from the EC...
- Jin D, Burgess R, Richardson J, Gross C. Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho. Proc Natl Acad Sci U S A. 1992;89:1453-7 pubmed
- Chen X, Stitt B. The binding of C10 oligomers to Escherichia coli transcription termination factor Rho. J Biol Chem. 2004;279:16301-10 pubmed
- Opperman T, Richardson J. Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene. J Bacteriol. 1994;176:5033-43 pubmed..Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution...
- Schwartz A, Rabhi M, Jacquinot F, Margeat E, Rahmouni A, Boudvillain M. A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase. Nat Struct Mol Biol. 2009;16:1309-16 pubmed publisherThe bacterial Rho factor is a ring-shaped ATP-dependent helicase that tracks along RNA transcripts and disrupts RNA-DNA duplexes and transcription complexes in its path...
- Modrak D, Richardson J. The RNA-binding domain of transcription termination factor rho: isolation, characterization, and determination of sequence limits. Biochemistry. 1994;33:8292-9 pubmed..Thus, the results show that this fragment, which contains an RNP1 sequence motif, will be a good model for future physical-chemical studies of the protein-RNA interactions of rho. ..
- Bear D, Hicks P, Escudero K, Andrews C, McSwiggen J, von Hippel P. Interactions of Escherichia coli transcription termination factor rho with RNA. II. Electron microscopy and nuclease protection experiments. J Mol Biol. 1988;199:623-35 pubmed..These findings and those of the companion paper are discussed in terms of various models for the structure of the rho-RNA complex in transcription termination. ..
- Cardinale C, Washburn R, Tadigotla V, Brown L, Gottesman M, Nudler E. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science. 2008;320:935-8 pubmed publisher..Transcription can be terminated by Rho factor, an essential protein in enterobacteria...
- Chalissery J, Banerjee S, Bandey I, Sen R. Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex. J Mol Biol. 2007;371:855-72 pubmed..The rate of ATP hydrolysis regulates the processivity of translocation along the RNA and is directly correlated with the efficiency of RNA release. NusG improves the speed of RNA release and is not involved in any other step. ..
- Ingham C, Dennis J, Furneaux P. Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis. Mol Microbiol. 1999;31:651-63 pubmed..This contrasts with E. coli in which NusG is essential but NusA becomes dispensable if Rho terminates transcription less efficiently. ..
- Pani B, Banerjee S, Chalissery J, Muralimohan A, Abishek M, Loganathan R, et al. Mechanism of inhibition of Rho-dependent transcription termination by bacteriophage P4 protein Psu. J Biol Chem. 2006;281:26491-500 pubmed..We propose that Psu inhibits Rho-dependent termination by slowing down the translocation of Rho along the RNA because of its slow ATPase activity. ..
- Vieu E, Rahmouni A. Dual role of boxB RNA motif in the mechanisms of termination/antitermination at the lambda tR1 terminator revealed in vivo. J Mol Biol. 2004;339:1077-87 pubmed
- Martinez A, Opperman T, Richardson J. Mutational analysis and secondary structure model of the RNP1-like sequence motif of transcription termination factor Rho. J Mol Biol. 1996;257:895-908 pubmed
- Wei R, Richardson J. Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding. J Mol Biol. 2001;314:1007-15 pubmed
- Li J, Mason S, Greenblatt J. Elongation factor NusG interacts with termination factor rho to regulate termination and antitermination of transcription. Genes Dev. 1993;7:161-72 pubmed..Therefore, the interaction of NusG with rho is important both for rho-dependent termination and for antitermination by N at rho-dependent terminators...
- Miwa Y, Horiguchi T, Shigesada K. Structural and functional dissections of transcription termination factor rho by random mutagenesis. J Mol Biol. 1995;254:815-37 pubmed
- Kalyani B, Muteeb G, Qayyum M, Sen R. Interaction with the nascent RNA is a prerequisite for the recruitment of Rho to the transcription elongation complex in vitro. J Mol Biol. 2011;413:548-60 pubmed publisher..We concluded that the nascent RNA loading of Rho and its interaction with the rut site are mandatory and prerequisites for its recruitment to the EC under in vitro experimental conditions. ..
- Alifano P, Rivellini F, Limauro D, Bruni C, Carlomagno M. A consensus motif common to all Rho-dependent prokaryotic transcription terminators. Cell. 1991;64:553-63 pubmed
- d Aubenton Carafa Y, Brody E, Thermes C. Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J Mol Biol. 1990;216:835-58 pubmed..It also predicts with reasonable accuracy the in vitro termination efficiency of known rho-independent terminators, as well as predicting the existence of 35 as yet uncharacterized terminators. ..
- Geiselmann J, Seifried S, Yager T, Liang C, von Hippel P. Physical properties of the Escherichia coli transcription termination factor rho. 2. Quaternary structure of the rho hexamer. Biochemistry. 1992;31:121-32 pubmed..Fluorescence energy transfer data are presented and integrated with data from the literature to arrive at a self-consistent model for the quaternary structure of the rho hexamer. ..
- Boudvillain M, Figueroa Bossi N, Bossi L. Terminator still moving forward: expanding roles for Rho factor. Curr Opin Microbiol. 2013;16:118-24 pubmed publisherb>Rho factor is a molecular motor that translocates along nascent RNA and acts on the transcription elongation complex to promote termination...
- Pani B, Ranjan A, Sen R. Interaction surface of bacteriophage P4 protein Psu required for complex formation with the transcription terminator Rho. J Mol Biol. 2009;389:647-60 pubmed publisher..We propose that the globular N-terminal domain of Psu confers structural integrity to the functionally important C-terminal tail, which interacts directly with the hexameric Rho...
- Peters J, Vangeloff A, Landick R. Bacterial transcription terminators: the RNA 3'-end chronicles. J Mol Biol. 2011;412:793-813 pubmed publisher..In this review, we consider the current state of knowledge about bacterial termination mechanisms and the relationship between terminator sequence and steps in the termination mechanism. ..
- Brennan C, Dombroski A, Platt T. Transcription termination factor rho is an RNA-DNA helicase. Cell. 1987;48:945-52 pubmedE. coli rho factor can unwind a short RNA-DNA duplex in vitro...
- Lesnik E, Sampath R, Levene H, Henderson T, McNeil J, Ecker D. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res. 2001;29:3583-94 pubmed
- Burgess B, Richardson J. RNA passes through the hole of the protein hexamer in the complex with the Escherichia coli Rho factor. J Biol Chem. 2001;276:4182-9 pubmed..These data are consistent with binding of the rut region of RNA around the crown, with its 3'-segment passing through the center of the Rho hexamer. ..
- Dolan J, Marshall N, Richardson J. Transcription termination factor rho has three distinct structural domains. J Biol Chem. 1990;265:5747-54 pubmed..This result plus the finding that ADP and ATP inhibit the cleavage in the linker between the two domains indicate that those domains interact intimately in spite of their functional distinctions. ..
- Gomelsky M, Kaplan S. The Rhodobacter sphaeroides 2.4.1 rho gene: expression and genetic analysis of structure and function. J Bacteriol. 1996;178:1946-54 pubmed..The gene downstream of rho is homologous to thdF, whose product is involved in thiophene and furan oxidation...
- Banerjee S, Chalissery J, Bandey I, Sen R. Rho-dependent transcription termination: more questions than answers. J Microbiol. 2006;44:11-22 pubmed..An attempt has also been made to understand the physiology of Rho in the light of its phylogeny. ..
- Dombroski A, Platt T. Structure of rho factor: an RNA-binding domain and a separate region with strong similarity to proven ATP-binding domains. Proc Natl Acad Sci U S A. 1988;85:2538-42 pubmed..The implications of discrete domains for RNA and nucleotide binding are discussed in the context of requirements for specific interactions between RNA-binding and ATP-hydrolysis sites during transcription termination. ..
- Steinmetz E, Platt T. Evidence supporting a tethered tracking model for helicase activity of Escherichia coli Rho factor. Proc Natl Acad Sci U S A. 1994;91:1401-5 pubmed..DNA helix. This "tethered tracking" model is consistent with other properties of Rho factor, including the presence of two classes of RNA binding sites on the Rho hexamer and the 1:1 stoichiometry in the ..
- Pereira S, Platt T. Analysis of E. coli rho factor: mutations affecting secondary-site interactions. J Mol Biol. 1995;251:30-40 pubmed
- Thomsen N, Berger J. Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell. 2009;139:523-34 pubmed publisher..For a video summary of this article, see the PaperFlick file with the Supplemental Data available online. ..
- Magyar A, Zhang X, Kohn H, Widger W. The antibiotic bicyclomycin affects the secondary RNA binding site of Escherichia coli transcription termination factor Rho. J Biol Chem. 1996;271:25369-74 pubmed..The data suggested that the antibiotic binds to Rho, influencing the secondary RNA binding (tracking) site on Rho and slows the tracking of Rho toward the bound RNA polymerase. ..
- Harinarayanan R, Gowrishankar J. Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. J Mol Biol. 2003;332:31-46 pubmed
- Pereira S, Platt T. A mutation in the ATP binding domain of rho alters its RNA binding properties and uncouples ATP hydrolysis from helicase activity. J Biol Chem. 1995;270:30401-7 pubmed..The single F232C mutation thus appears to uncouple the protein's ATPase activity from its helicase function, so rho can no longer harness available energy for use in subsequent reactions. ..
- Xu Y, Kohn H, Widger W. Mutations in the rho transcription termination factor that affect RNA tracking. J Biol Chem. 2002;277:30023-30 pubmed
- Richardson J. Rho-dependent termination and ATPases in transcript termination. Biochim Biophys Acta. 2002;1577:251-260 pubmed..Actions of the Rho structure in the channel on the 3' segment that are coupled to ATP hydrolysis pull the RNA from its contacts with the template and RNA polymerase, thus causing termination of its synthesis. ..
- Tenaillon O, Rodríguez Verdugo A, Gaut R, McDonald P, Bennett A, Long A, et al. The molecular diversity of adaptive convergence. Science. 2012;335:457-61 pubmed publisher..We inferred the pervasive presence of epistasis among beneficial mutations, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho. ..
- McSwiggen J, Bear D, von Hippel P. Interactions of Escherichia coli transcription termination factor rho with RNA. I. Binding stoichiometries and free energies. J Mol Biol. 1988;199:609-22 pubmed..The possible significance of these results for models of rho-dependent transcription termination is discussed in the companion paper. ..
- Brennan C, Steinmetz E, Spear P, Platt T. Specificity and efficiency of rho-factor helicase activity depends on magnesium concentration and energy coupling to NTP hydrolysis. J Biol Chem. 1990;265:5440-7 pubmed..The implications of our findings for substrate specificity and energy coupling in the helicase reaction are discussed. ..
- Honorine R, Mosrin Huaman C, Hervouet Coste N, Libri D, Rahmouni A. Nuclear mRNA quality control in yeast is mediated by Nrd1 co-transcriptional recruitment, as revealed by the targeting of Rho-induced aberrant transcripts. Nucleic Acids Res. 2011;39:2809-20 pubmed publisher..Previously, we have shown that the heterologous expression of bacterial Rho factor in yeast interferes in normal mRNP biogenesis leading to the production of full-length yet aberrant transcripts ..
- Clayton L, Hall A, Johnson M. A role for Rho-like GTPases in the polarisation of mouse eight-cell blastomeres. Dev Biol. 1999;205:322-31 pubmed..These results suggest that Rho family GTPases are involved in the polarisation of early mouse blastomeres. ..
- Johansson R, Persson K. Phenotypic modulation of cultured bladder smooth muscle cells and the expression of inducible nitric oxide synthase. Am J Physiol Regul Integr Comp Physiol. 2004;286:R642-8 pubmed..Phenotypic changes and impairment in actin cytoskeleton formation may potentiate cytokine activation and in turn increase nitric oxide production in the bladder during disease. ..