Learning from the Leaders: Gene Regulation by the Transcription Termination Factor Rho

Overview

Journal Trends Biochem Sci

Specialty Biochemistry

Date 2016 Jun 22

PMID 27325240

Citations 36

Authors

Michelle A Kriner

Anastasia Sevostyanova

Eduardo A Groisman

Affiliations

Soon will be listed here.

Abstract

The RNA helicase Rho triggers 20-30% of transcription termination events in bacteria. While Rho is associated with most transcription elongation complexes, it only promotes termination of a subset. Recent studies of individual Rho-dependent terminators located within the 5' leader regions of bacterial mRNAs have identified novel mechanisms that govern Rho target specificity and have revealed unanticipated physiological functions for Rho. In particular, the multistep nature of Rho-dependent termination enables regulatory input from determinants beyond the sequence of the Rho loading site, and allows a given Rho-dependent terminator to respond to multiple signals. Further, the unique position of Rho as a sensor of cellular translation has been exploited to regulate the transcription of genes required for protein synthesis, including those specifying Mg(2+) transporters.

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References

Hollands K, Proshkin S, Sklyarova S, Epshtein V, Mironov A, Nudler E . Riboswitch control of Rho-dependent transcription termination. Proc Natl Acad Sci U S A. 2012; 109(14):5376-81. PMC: 3325659. DOI: 10.1073/pnas.1112211109. View

Banerjee S, Chalissery J, Bandey I, Sen R . Rho-dependent transcription termination: more questions than answers. J Microbiol. 2006; 44(1):11-22. PMC: 1838574. View

Boudvillain M, Figueroa-Bossi N, Bossi L . Terminator still moving forward: expanding roles for Rho factor. Curr Opin Microbiol. 2013; 16(2):118-24. DOI: 10.1016/j.mib.2012.12.003. View

Ward D, GOTTESMAN M . Suppression of transcription termination by phage lambda. Science. 1982; 216(4549):946-51. DOI: 10.1126/science.6281888. View

Dutta D, Chalissery J, Sen R . Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA. J Biol Chem. 2008; 283(29):20243-51. DOI: 10.1074/jbc.M801926200. View

Romani A . Regulation of magnesium homeostasis and transport in mammalian cells. Arch Biochem Biophys. 2006; 458(1):90-102. DOI: 10.1016/j.abb.2006.07.012. View

Jacob F, MONOD J . Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961; 3:318-56. DOI: 10.1016/s0022-2836(61)80072-7. View

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(4):609-22. DOI: 10.1016/0022-2836(88)90305-1. View

Roberts J . Termination factor for RNA synthesis. Nature. 1969; 224(5225):1168-74. DOI: 10.1038/2241168a0. View

10.

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(12):1309-16. DOI: 10.1038/nsmb.1711. View

11.

Rossi J, Egan J, Hudson L, Landy A . The tyrT locus: termination and processing of a complex transcript. Cell. 1981; 26(3 Pt 1):305-14. DOI: 10.1016/0092-8674(81)90199-9. View

12.

Washburn R, Gottesman M . Transcription termination maintains chromosome integrity. Proc Natl Acad Sci U S A. 2010; 108(2):792-7. PMC: 3021005. DOI: 10.1073/pnas.1009564108. View

13.

Wei R, Richardson J . Identification of an RNA-binding Site in the ATP binding domain of Escherichia coli Rho by H2O2/Fe-EDTA cleavage protection studies. J Biol Chem. 2001; 276(30):28380-7. DOI: 10.1074/jbc.M102444200. View

14.

Maguire M, Cowan J . Magnesium chemistry and biochemistry. Biometals. 2002; 15(3):203-10. DOI: 10.1023/a:1016058229972. View

15.

Brennan C, Dombroski A, Platt T . Transcription termination factor rho is an RNA-DNA helicase. Cell. 1987; 48(6):945-52. DOI: 10.1016/0092-8674(87)90703-3. View

16.

Wu A, Christie G, Platt T . Tandem termination sites in the tryptophan operon of Escherichia coli. Proc Natl Acad Sci U S A. 1981; 78(5):2913-7. PMC: 319469. DOI: 10.1073/pnas.78.5.2913. View

17.

Sudha 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(3):548-60. DOI: 10.1016/j.jmb.2011.08.053. View

18.

Bischoff L, Berninghausen O, Beckmann R . Molecular basis for the ribosome functioning as an L-tryptophan sensor. Cell Rep. 2014; 9(2):469-75. DOI: 10.1016/j.celrep.2014.09.011. View

19.

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(4):623-35. DOI: 10.1016/0022-2836(88)90306-3. View

20.

Chattopadhyay S, Garcia-Mena J, DeVito J, Wolska K, Das A . Bipartite function of a small RNA hairpin in transcription antitermination in bacteriophage lambda. Proc Natl Acad Sci U S A. 1995; 92(9):4061-5. PMC: 42102. DOI: 10.1073/pnas.92.9.4061. View