Rho-dependent Transcription Termination: More Questions than Answers

  • Banerjee Sharmistha (Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road) ;
  • Chalissery Jisha (Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road) ;
  • Bandey Irfan (Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road) ;
  • Sen Ranjan (Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road)
  • Published : 2006.02.01

Abstract

Escherichia coli protein Rho is required for the factor-dependent transcription termination by an RNA polymerase and is essential for the viability of the cell. It is a homohexameric protein that recognizes and binds preferably to C-rich sites in the transcribed RNA. Once bound to RNA, it utilizes RNA-dependent ATPase activity and subsequently ATPase-dependent helicase activity to unwind RNA-DNA hybrids and release RNA from a transcribing elongation complex. Studies over the past few decades have highlighted Rho as a molecule and have revealed much of its mechanistic properties. The recently solved crystal structure could explain many of its physiological functions in terms of its structure. Despite all these efforts, many of the fundamental questions pertaining to Rho recognition sites, differential ATPase activity in response to different RNAs, translocation of Rho along the nascent transcript, interactions with elongation complex and finally unwinding and release of RNA remain obscure. In the present review we have attempted to summarize 'the knowns' and 'the unknowns' of the Rho protein revealed by the recent developments in this field. An attempt has also been made to understand the physiology of Rho in the light of its phylogeny.

Keywords

References

  1. Adhya, S. and M. Gottesman. 1978. Control of transcription termination. Annu. Rev. Biochem. 47, 967-96 https://doi.org/10.1146/annurev.bi.47.070178.004535
  2. Alifano, P., F. Rivellini, D. Limauro, C.B. Bruni, and M.S. Carlomagno. 1991. A consensus motif common to all Rho-dependent prokaryotic transcription terminators. Cell 64, 553-563 https://doi.org/10.1016/0092-8674(91)90239-U
  3. Bear, D.G., C.L. Andrews, J.D. Singer, W.D. Morgan, R.A. Grant, P.H. von Hippel, and T. Platt. 1985. Escherichia coli transcription termination factor Rho has a two-domain structure in its activated form. Proc. Natl. Acad. Sci. USA 82, 1911-1915
  4. Bear, D.G., P.S. Hicks, K.W. Escudero, C.L. Andrews, J.A. McSwiggen, and P.H. von Hippel. 1988. Interactions of Escherichia coli transcription termination factor Rho with RNA. II. Electron microscopy and nuclease protection experiments. J. Mol. Biol. 199, 623-635 https://doi.org/10.1016/0022-2836(88)90306-3
  5. Bogden, C.E., D. Fass, N. Bergman, M.D. Nichols, and J.M. Berger. 1999. The structural basis for terminator recognition by the Rho transcription termination factor. Mol. Cell 3, 487-493 https://doi.org/10.1016/S1097-2765(00)80476-1
  6. Brennan, C.A., A.J. Dombroski, and T. Platt. 1987. Transcription termination factor Rho is an RNA-DNA helicase. Cell 48, 945-952 https://doi.org/10.1016/0092-8674(87)90703-3
  7. Burgess, B.R. and J.P. Richardson. 2001a. RNA passes through the hole of the protein hexamer in the complex with the Escherichia coli Rho factor. J. Biol. Chem. 276, 4182- 4189 https://doi.org/10.1074/jbc.M007066200
  8. Burgess, B.R. and J.P. Richardson. 2001b. Transcription factor Rho does not require a free end to act as an RNA-DNA helicase on an RNA. J. Biol. Chem. 276, 17106-17110 https://doi.org/10.1074/jbc.M101856200
  9. Burns, C.M., W.L. Nowatzke, and J.P. Richardson. 1999. Activation of Rho-dependent transcription termination by NusG. Dependence on terminator location and acceleration of RNA release. J. Biol. Chem. 274, 5245-5251 https://doi.org/10.1074/jbc.274.8.5245
  10. Burns, C.M., L.V. Richardson, and J.P. Richardson. 1998. Combinatorial effects of NusA and NusG on transcription elongation and Rho-dependent termination in Escherichia coli. J. Mol. Biol. 278, 307-316 https://doi.org/10.1006/jmbi.1998.1691
  11. Chen, C.Y. and J.P. Richardson. 1987. Sequence elements essential for Rho-dependent transcription termination at lambda tR1. J. Biol. Chem. 262, 11292-11299
  12. Das, A., D. Court, and S. Adhya. 1976. Isolation and characterization of conditional lethal mutants of Escherichia coli defective in transcription termination factor Rho. Proc. Natl. Acad. Sci. USA 73, 1959-1963
  13. Dolan, J.W., N.F. Marshall, and J.P. Richardson. 1990. Transcription termination factor Rho has three distinct structural domains. J. Biol. Chem. 265, 5747-5754
  14. Galluppi, G.R. and J.P. Richardson. 1980. ATP-induced changes in the binding of RNA synthesis termination protein Rho to RNA. J. Mol. Biol. 138, 513-539 https://doi.org/10.1016/S0022-2836(80)80016-7
  15. Gan, E. and J.P. Richardson. 1999. ATP and other nucleotides stabilize the Rho-mRNA complex. Biochemistry 38, 16882- 6888 https://doi.org/10.1021/bi991559i
  16. Geiselmann, J. and P.H. von Hippel. 1992. Functional interactions of ligand cofactors with Escherichia coli transcription termination factor Rho. I. Binding of ATP. Protein Sci. 1, 850-860 https://doi.org/10.1002/pro.5560010703
  17. Geiselmann, J., T.D. Yager, S.C. Gill, P. Calmettes, and P.H. von Hippel. 1992a. Physical properties of the Escherichia coli transcription termination factor Rho. 1. Association states and geometry of the Rho hexamer. Biochemistry 31, 111-121 https://doi.org/10.1021/bi00116a017
  18. Geiselmann, J., S.E. Seifried, T.D. Yager, C. Liang, and P.H. von Hippel. 1992b. Physical properties of the Escherichia coli transcription termination factor Rho. 2. Quaternary structure of the Rho hexamer. Biochemistry 31, 121-132 https://doi.org/10.1021/bi00116a018
  19. Gogol, E.P., S.E. Seifried, and P.H. von Hippel. 1991. Structure and assembly of the Escherichia coli transcription termination factor Rho and its interaction with RNA. I. Cryoelectron microscopic studies. J. Mol. Biol. 221, 1127-1138 https://doi.org/10.1016/0022-2836(91)90923-T
  20. Graham, J.E. 2004. Sequence-specific Rho-RNA interactions in transcription termination. Nucleic Acids Res. 32, 3093-3100 https://doi.org/10.1093/nar/gkh630
  21. Guarente, L.P. and J. Beckwith. 1978. Mutant RNA polymerase of Escherichia coli terminates transcription in strains making defective Rho factor. Proc. Natl. Acad. Sci. USA 75, 294-297
  22. Guerin, M., N. Robichon, J. Geiselmann, and A.R. Rahmouni. 1998. A simple polypyrimidine repeat acts as an artificial rho-dependent terminator in vivo and in vitro. Nucleic Acids Res. 26, 4895-4900 https://doi.org/10.1093/nar/26.21.4895
  23. Harinarayanan, R. and J. Gowrishankar. 2003. 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. 332, 31-46 https://doi.org/10.1016/S0022-2836(03)00753-8
  24. Jin, D.J., R.R. Burgess, J.P. Richardson, and C.A. Gross. 1992. Termination efficiency at Rho-dependent terminators depends on kinetic coupling between RNA polymerase and Rho. Proc. Natl. Acad. Sci. USA 89, 1453-1457
  25. Jin, D.J., W.A. Walter, and C.A. Gross. 1988. Characterization of the termination phenotypes of rifampicin-resistant mutants. J. Mol. Biol. 202, 245-253 https://doi.org/10.1016/0022-2836(88)90455-X
  26. Kassavetis, G.A. and M.J. Chamberlin. 1981. Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro. J. Biol. Chem. 256, 2777-2786
  27. Kim, D.E. and S.S. Patel. 1999. The mechanism of ATP hydrolysis at the noncatalytic sites of the transcription termination factor Rho. J. Biol. Chem. 274, 32667-32671 https://doi.org/10.1074/jbc.274.46.32667
  28. Kim, D.E. and S.S. Patel. 2001. The kinetic pathway of RNA binding to the Escherichia coli transcription termination factor Rho. J. Biol. Chem. 276, 13902-13910 https://doi.org/10.1074/jbc.M011043200
  29. Kim, D.E., K. Shigesada, and S.S. Patel. 1999. Transcription termination factor Rho contains three noncatalytic nucleotide binding sites. J. Biol. Chem. 274, 11623-11628 https://doi.org/10.1074/jbc.274.17.11623
  30. Lang, W.H., T. Platt, and R.H. Reeder. 1998. Escherichia coli Rho factor induces release of yeast RNA polymerase II but not polymerase I or III. Proc. Natl. Acad. Sci. USA 95, 4900-4905
  31. Li, J., R. Horwitz, S. McCracken, and J. Greenblatt. 1992. NusG, a new Escherichia coli elongation factor involved in transcriptional antitermination by the N protein of phage lambda. J. Biol. Chem. 267, 6012-6019
  32. Li, J., S.W. Mason, and J. Greenblatt. 1993. Elongation factor NusG interacts with termination factor Rho to regulate termination and antitermination of transcription. Genes Dev. 7, 161-172 https://doi.org/10.1101/gad.7.1.161
  33. Linder, P., P.F. Lasko, M. Ashburner, P. Leroy, P.J. Nielsen, K. Nishi, J. Schnier, and P.P. Slonimski. 1989. Birth of the D-E-A-D box. Nature 337, 121-122 https://doi.org/10.1038/337121a0
  34. Linderoth, N.A. and R.L. Calendar. 1991. The Psu protein of bacteriophage P4 is an antitermination factor for rho-dependent transcription termination. J. Bacteriol. 173, 6722-6731 https://doi.org/10.1128/jb.173.21.6722-6731.1991
  35. Miwa, Y.,T. Horiguchi, and K. Shigesada. 1995. Structural and functional dissections of transcription termination factor Rho by random mutagenesis. J. Mol. Biol. 254, 815-837 https://doi.org/10.1006/jmbi.1995.0658
  36. Modrak, D. and J.P. Richardson. 1994. The RNA-binding domain of transcription termination factor Rho: isolation, characterization, and determination of sequence limits. Biochemistry 33, 8292-8299 https://doi.org/10.1021/bi00193a016
  37. Mooney, R.A., I. Artsimovitch, and R. Landick. 1998. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180, 3265-3275
  38. Morgan, W.D., D.G. Bear, and P.H. von Hippel. 1983. Rho-dependent termination of transcription. I. Identification and characterization of termination sites for transcription from the bacteriophage lambda PR promoter. J. Biol. Chem. 258, 9553-9564
  39. Morgan, W.D., D.G. Bear, B.L. Litchman, and P.H. von Hippel. 1985. RNA sequence and secondary structure requirements for Rho-dependent transcription termination. Nucleic Acids Res. 13, 3739-3754 https://doi.org/10.1093/nar/13.10.3739
  40. Nehrke, K.W. and T. Platt. 1994. A quaternary transcription termination complex. Reciprocal stabilization by Rho factor and NusG protein. J. Mol. Biol. 243, 830-839 https://doi.org/10.1006/jmbi.1994.1685
  41. Nehrke, K.W., F. Zalatan, and T. Platt. 1993. NusG alters Rho-dependent termination of transcription in vitro independent of kinetic coupling. Gene Expr. 3, 119-133
  42. Nowatzke, W.L. and J.P. Richardson. 1996. Characterization of an unusual Rho factor from the high G + C gram-positive bacterium Micrococcus luteus. J. Biol. Chem. 271, 742-747 https://doi.org/10.1074/jbc.271.2.742
  43. Nudler, E. and M.E. Gottesman. 2002. Transcription termination and anti-termination in E. coli. Genes Cells 7, 755-768 https://doi.org/10.1046/j.1365-2443.2002.00563.x
  44. Opperman, T. and J.P. Richardson. 1994. Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene. J. Bacteriol. 176, 5033-5043 https://doi.org/10.1128/jb.176.16.5033-5043.1994
  45. Pereira, S. and T. Platt. 1995a. A mutation in the ATP binding domain of Rho alters its RNA binding properties and uncouples ATP hydrolysis from helicase activity. J. Biol. Chem. 270, 30401-30407 https://doi.org/10.1074/jbc.270.51.30401
  46. Pereira, S. and T. Platt. 1995b. Analysis of E. coli Rho factor: mutations affecting secondary-site interactions. J. Mol. Biol. 251, 30-40 https://doi.org/10.1006/jmbi.1995.0413
  47. Platt, T. 1981. Termination of transcription and its regulation in the tryptophan operon of E. coli. Cell 24, 10-23 https://doi.org/10.1016/0092-8674(81)90496-7
  48. Quirk, P.G., E.A. Dunkley, Jr., P. Lee, and T.A. Krulwich. 1993. Identification of a putative Bacillus subtilis rho gene. J. Bacteriol. 175, 647-654 https://doi.org/10.1128/jb.175.3.647-654.1993
  49. Richardson, J.P. 1991. Preventing the synthesis of unused transcripts by Rho factor. Cell 64, 1047-1049 https://doi.org/10.1016/0092-8674(91)90257-Y
  50. Richardson, J.P. 1993. Transcription termination. Crit. Rev. Biochim. Mol. Biol. 28, 1-30 https://doi.org/10.3109/10409239309082571
  51. Richardson, J.P. 2002. Rho-dependent termination and ATPases in transcript termination. Biochim. Biophys. Acta. 1577, 251-260 https://doi.org/10.1016/S0167-4781(02)00456-6
  52. Richardson, J.P. 2003. Loading Rho to terminate transcription. Cell 114, 157-159 https://doi.org/10.1016/S0092-8674(03)00554-3
  53. Richardson, J.P. and J.L. Greenblatt. 1996. Control of RNA chain elongation and termination, p. 822-848. In F.C. Neidhardt, (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. ASM Press, Washington, DC
  54. Richardson, L.V. and J.P. Richardson. 1992. Cytosine nucleoside inhibition of the ATPase of Escherichia coli termination factor Rho: evidence for a base specific interaction between Rho and RNA. Nucleic Acids Res. 20, 5383-5387 https://doi.org/10.1093/nar/20.20.5383
  55. Richardson, L.V. and J.P. Richardson. 1996. Rho-dependent termination of transcription is governed primarily by the upstream Rho utilization (rut) sequences of a terminator. J. Biol. Chem. 271, 21597-21603 https://doi.org/10.1074/jbc.271.35.21597
  56. Roberts, J.W. 1969. Termination factor for RNA synthesis. Nature 224, 1168-1174 https://doi.org/10.1038/2241168a0
  57. Schneider, D., L. Gold, and T. Platt. 1993. Selective enrichment of RNA species for tight binding to Escherichia coli Rho factor. FASEB J. 7, 201-207 https://doi.org/10.1096/fasebj.7.1.7678562
  58. Seifried, S.E., J.B. Easton, and P.H. von Hippel. 1992. ATPase activity of transcription-termination factor Rho: functional dimer model. Proc. Natl. Acad. Sci. USA 89, 10454-10458
  59. Shigesada, K. and M. Imai. 1978. Studies on the altered Rho factor in nitA mutants of Escherichia coli defective in transcription termination. II. Purification and molecular properties of the mutant Rho. J. Mol. Biol. 120, 467-486 https://doi.org/10.1016/0022-2836(78)90349-2
  60. Skordalakes, E. and J.M. Berger. 2003. Structure of the rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell 114, 135-146 https://doi.org/10.1016/S0092-8674(03)00512-9
  61. Skordalakes, E., A.P. Brogan, B.S. Park, H. Kohn, and J.M. Berger. 2005. Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin. Structure (Camb) 13, 99-109 https://doi.org/10.1016/j.str.2004.10.013
  62. Sparkowski, J. and A. Das. 1992. Simultaneous gain and loss of functions caused by a single amino acid substitution in the beta subunit of Escherichia coli RNA polymerase: suppression of NusA and Rho mutations and conditional lethality. Genetics 130, 411-428
  63. Steinmetz, E.J. and T. Platt. 1994. Evidence supporting a tethered tracking model for helicase activity of Escherichia coli Rho factor. Proc. Natl. Acad. Sci. USA 91, 1401-1405
  64. Steinmetz, E.J., C.A. Brennan, and T. Platt. 1990. A short intervening structure can block Rho factor helicase action at a distance. J. Biol. Chem. 265, 18408-18413
  65. Stitt, B.L. 1988. Escherichia coli transcription termination protein Rho has three hydrolytic sites for ATP. J. Biol. Chem. 263, 11130-11137
  66. Sullivan, S.L. and M.E. Gottesman. 1992. Requirement for E. coli NusG protein in factor-dependent transcription termination. Cell 68, 989-994 https://doi.org/10.1016/0092-8674(92)90041-A
  67. Sullivan, S.L., D.F. Ward, and M.E. Gottesman. 1992. Effect of Escherichia coli nusG function on lambda N-mediated transcription antitermination. J. Bacteriol. 174, 1339-1344 https://doi.org/10.1128/jb.174.4.1339-1344.1992
  68. Tsurushita, N., K. Shigesada, and M. Imai. 1989. Mutant Rho factors with increased transcription termination activities. I. Functional correlations of the primary and secondary polynucleotide binding sites with the efficiency and site-selectivity of Rho-dependent termination. J. Mol. Biol. 210, 23-37 https://doi.org/10.1016/0022-2836(89)90288-X
  69. Uptain, S.M., C.M. Kane, and M.J. Chamberlin, 1997. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66, 117-172 https://doi.org/10.1146/annurev.biochem.66.1.117
  70. Walstrom, K.M., J.M. Dozono, S. Robic, and P.H. von Hippel. 1997a. Kinetics of the RNA-DNA helicase activity of Escherichia coli transcription termination factor Rho. 1. Characterization and analysis of the reaction. Biochemistry 36, 7980-7992 https://doi.org/10.1021/bi963179s
  71. Walstrom, K.M., J.M. Dozono, and P.H. von Hippel. 1997b. Kinetics of the RNA-DNA helicase activity of Escherichia coli transcription termination factor Rho. 2. Processivity, ATP consumption, and RNA binding. Biochemistry 36, 7993-8004 https://doi.org/10.1021/bi963180r
  72. Wang, Y. and P.H. von Hippel, 1993. Escherichia coli transcription termination factorRho. II. Binding of oligonucleotide cofactors. J. Biol. Chem. 268, 13947-13955
  73. Washburn, R.S., A. Marra, A.P. Bryant, M. Rosenberg, and D.R. Gentry. 2001. Rho is not essential for viability or virulence in Staphylococcus aureus. Antimicrob. Agents Chemother. 45, 1099-1103 https://doi.org/10.1128/AAC.45.4.1099-1103.2001
  74. Wei, R.R. and J.P. Richardson. 2001a. Identification of an RNA-binding Site in the ATP binding domain of Escherichia coli Rho by $H_2O_2$/Fe-EDTA cleavage protection studies. J. Biol. Chem. 276, 28380-28387 https://doi.org/10.1074/jbc.M102444200
  75. Wei, R.R. and J.P. Richardson. 2001b. Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding. J. Mol. Biol. 314, 1007-1015 https://doi.org/10.1006/jmbi.2000.5207
  76. Wilson, K.S. and P.H. von Hippel. 1994. Stability of Escherichia coli transcription complexes near an intrinsic terminator. J. Mol. Biol. 244, 36-51 https://doi.org/10.1006/jmbi.1994.1702
  77. Xu, Y., H. Kohn, and W.R. Widger. 2002. Mutations in the Rho transcription termination factor that affect RNA tracking. J. Biol. Chem. 277, 30023-30030 https://doi.org/10.1074/jbc.M111009200
  78. Yu, X., T. Horiguchi, K. Shigesada, and E.H. Egelman. 2000. Three-dimensional reconstruction of transcription termination factor Rho: orientation of the N-terminal domain and visualization of an RNA-binding site. J. Mol. Biol. 299, 1279-1287 https://doi.org/10.1006/jmbi.2000.3810
  79. Zalatan, F., J. Galloway-Salvo, and T. Platt. 1993. Deletion analysis of the Escherichia coli rho-dependent transcription terminator trp t'. J. Biol. Chem. 268, 17051-17056