1887

Chapter 17 : Control of Transcription Termination and Antitermination

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Control of Transcription Termination and Antitermination, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap17-1.gif /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap17-2.gif

Abstract:

This chapter provides a review of the current structural and kinetic models for transcription elongation and termination. It describes the regulatory molecules that are known to influence the elongation/termination decision by RNA polymerase (RNAP), with the emphasis on the most recent findings and on the mechanism of ‘‘active’’ regulators whose actions are not limited to changes in RNA folding. Interactions between RNAP and the nucleic acid chains, as well as the RNA:DNA pairing in the hybrid, all contribute to the extraordinary stability of the elongating transcription elongation complexes (TECs). RNA release is triggered at sites where the nascent RNA folds into a stable, GC-rich hairpin followed by a stretch of the U-rich RNA. Rho is the main termination protein in , where it is thought to control ~ 50% of all termination events. Feedback control of the operons that encode ribosomal protein synthesis is commonly accomplished by autogenous regulation by one of the products. Alc protein terminates transcription at several sites on a nonmodified host DNA, but not on the phage DNA that contains hydroxymethyl cytosine residue. The operon in is regulated in response to the availability of a substrate β-glucoside by BglG induced antitermination. The RNA binding by BglG is regulated by BglF-mediated phosphorylation: in the absence of inducer, BglF phosphorylates BglG and inhibits its RNA binding activity; when β-glucosides are available, BglF dephosphorylates BglG, which now binds to its target and prevents transcription termination.

Citation: Artsimovitch I. 2005. Control of Transcription Termination and Antitermination, p 311-326. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch17

Key Concept Ranking

RNA Polymerase II
0.5621118
Transcription Termination
0.4117995
0.5621118
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1.
Figure 1.

Schematic model of the TEC. RNAP (gray oval) is bound to the DNA duplex (black circles; T, template strand; NT, nontemplate strand) from ~-20 to ~+15 relative to the position of the 50 end of the encoded RNA (as judged from the protection against cleavage by various probes that it confers to the DNA). The 12 to 13 bp of the DNA duplex are melted in the transcription bubble. The nontemplate DNA strand is exposed on the surface of RNAP ( ), where it becomes available for interactions with the regulatory proteins ( ).The nascent RNA (white circles) is annealed to the template strand to form 8 to 9 bp of the RNA● DNA hybrid (bound in the HBS) and is extruded from the TECs at ~14 nt from the 30 end. In the active TECs, the 3′ end of the RNA is located in the active site. In the backtracked TECs, the 3′ portion of the RNA (dashed circles) is threaded through the active site into the secondary channel, thus preventing the substrate NTP entry. Three principal interactions are distinguished ( ): the DNA-binding site (DBS), the front zip-lock (FZ), and the rear zip-lock (RZ). Cross-linking analysis of the RNAP core (αββ′ complex) bound to the RNA and DNA to form the TEC (see reference and references therein) identifies the β′ jaw/β lobe module as the DBS, the active site as the FZ, and a combination of β flap, β region D, and β′ rudder as the RZ. Although originally the rudder was postulated to play a key role in RNA displacement, recent evidence indicates that the rudder stabilizes the TEC through direct contacts with RNA, but is not required for either RNA displacement or the maintenance of the transcription bubble ( ).

Citation: Artsimovitch I. 2005. Control of Transcription Termination and Antitermination, p 311-326. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Branched regulatory pathways in transcript elongation. At least two TEC states that are competent for elongation can be distinguished ( ). The activated pathway (asterisk) may require binding of the NTP in an "allosteric" site ( ) or a conformational change induced by a substitution in RNAP. The unactivated pathway is characterized by a lower rate of NMP addition and represents a collection of intermediate states from which all the off-pathway states (pause, arrest, termination, and editing) are formed. This mechanism incorporates a previously proposed pathway (on a gray background) where certain nucleic acid signals trigger isomerization of TEC into a slow intermediate state ( ). From the slow intermediate (n), the TEC can either slowly escape to the elongation pathway (upon nucleotide addition), or further isomerize into different types of pause, arrest, and termination complexes. Formation of an RNA hairpin would result in class I pausing, whereas backtracking would lead to a class II pause or arrest; termination could occur via either of these pathways. The principal difference between the slow intermediate and the parallel-path mechanisms is that the slow state is assumed to be short-lived in the former, and returns to the activated pathway upon NMP addition (escape) or NTP binding (reverse isomerization), but could persist for many rounds of catalysis in the latter. Isomerization into the termination and arrested states is irreversible and may proceed via formation of a significant kinetic intermediate ( ).

Citation: Artsimovitch I. 2005. Control of Transcription Termination and Antitermination, p 311-326. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

Antitermination mechanisms. Isomerization of a rapidly elongating TEC into a terminating complex proceeds through several steps at both Rho-dependent (top) and intrinsic (bottom) sites. Regulatory mechanisms that target one or more steps are known. As pausing precedes termination, RNA release can be inhibited by factors that also inhibit pausing (λ N, λ Q, and ). In contrast, other factors may preferentially inhibit hairpin formation at intrinsic terminators (alternative RNA structures, ssRNA-binding proteins, and possibly p7) or Rho access to the nascent RNA (the stalled ribosome, maybe Psu). Antitermination factors may also actively stabilize the TEC against dissociation (λ N and λ Q). Two alternative models for the mechanism of the nascent RNA release have been proposed. In a forward translocation model, RNAP slides forward (without necessarily changing its conformation), leaving the transcript behind ( ). In an allosteric model, a regulatory signal (e.g., formation of a terminator hairpin) triggers a series of cooperative conformational changes in the TEC that lead to opening of a crab-claw-shaped TEC and the concomitant release of the nucleic acids ( ).

Citation: Artsimovitch I. 2005. Control of Transcription Termination and Antitermination, p 311-326. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch17
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817640.chap17
1. Allison, T. J.,, T. C. Wood,, D. M. Briercheck,, F. Rastinejad,, J. P. Richardson,, and G. S. Rule. 1998. Crystal structure of the RNA-binding domain from transcription termination factor rho. Nat. Struct. Biol. 5:352356.
2. Amster-Choder, O.,, and A. Wright. 1997. BglG, the response regulator of the Escherichia coli bgl operon, is phosphorylated on a histidine residue. J. Bacteriol. 179:56215624.
3. Artsimovitch, I.,, and R. Landick. 1998. Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release. Genes Dev. 12:31103122.
4. Artsimovitch, I.,, and R. Landick. 2000. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA 97:70907095.
5. Artsimovitch, I.,, and R. Landick. 2002. RfaH stimulates chain elongation by bacterial transcription complexes after recruitment by the exposed nontemplate DNA strand. Cell 109:193203.
6. Bae, W.,, B. Xia,, M. Inouye,, and K. Severinov. 2000. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc. Natl. Acad. Sci. USA 97:77847789.
7. Bailey, M. J.,, C. Hughes,, and V. Koronakis. 2000. In vitro recruitment of the RfaH regulatory protein into a specialised transcription complex, directed by the nucleic acid ops element. Mol. Gen. Genet. 262:10521059.
8. Bailey, M. J.,, C. Hughes,, and V. Koronakis. 1997. RfaH and the ops element, components of a novel system controlling bacterial transcription elongation. Mol. Microbiol. 26:845851.
9. Banik-Maiti, S.,, R. King,, and R. Weisberg. 1997. The antiterminator RNA of phage HK022. J. Mol. Biol. 272:677687.
10. Briercheck, D. M.,, T. C. Wood,, T. J. Allison,, J. P. Richardson,, and G. S. Rule. 1998. The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions. Nat. Struct. Biol. 5:393399.
11. Burgess, B. R.,, and J. P. Richardson. 2001. RNA passes through the hole of the protein hexamer in the complex with the Escherichia coli Rho factor. J. Biol. Chem. 276:41824189.
12. Callaci, S.,, E. Heyduk,, and T. Heyduk. 1998. Conformational changes of Escherichia coli RNA polymerase sigma70 factor induced by binding to the core enzyme. J. Biol. Chem. 273:3299532001.
13. Chattopadhyay, S.,, S. C. Hung,, A. C. Stuart,, A. G. Palmer III,, J. Garcia-Mena,, A. Das,, and M. E. Gottesman. 1995. Interaction between the phage HK022 Nun protein and the nut RNA of phage lambda. Proc. Natl. Acad. Sci. USA 92:1213112135.
14. Condon, C.,, C. Squires,, and C. L. Squires. 1995. Control of rRNA transcription in Escherichia coli. Microbiol. Rev. 59: 623645.
15. Cramer, P. 2002. Multisubunit RNA polymerases. Curr. Opin. Struct. Biol. 12:8997.
16. Das, A.,, M. Pal,, J. Mena,, W. Whalen,, K. Wolska,, R. Crossley,, W. Rees,, P. von Hippel,, N. Costantino,, D. Court,, M. Mazzulla,, A. Altieri,, R. Byrd,, S. Chattopadhyay,, J. DeVito,, and B. Ghosh. 1996. Components of multiprotein-RNA complex that controls transcription elongation in Escherichia coli phage lambda. Methods Enzymol. 274:374402.
17. d’Aubenton Carafa, Y.,, E. Brody,, and C. Thermes. 1990. Prediction of Rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol. 216:835858.
18. Davenport, R. J.,, G. J. Wuite,, R. Landick,, and C. Bustamante. 2000. Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science 287:24972500.
19. Epshtein, V.,, A. S. Mironov,, and E. Nudler. 2003. The riboswitch- mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. USA 100:50525056.
20. Erie, D. 2002. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochim. Biophys. Acta 1577:224239.
21. Erie, D. A.,, O. Hajiseyedjavadi,, M. C. Young,, and P. H. von Hippel. 1993. Multiple RNA polymerase conformations and GreA: control of fidelity of transcription. Science 262:867873.
22. Erijman, L.,, and R. M. Clegg. 1998. Reversible stalling of transcription elongation complexes by high pressure. Biophys. J. 75:453462.
23. Faber, C.,, M. Scharpf,, T. Becker,, H. Sticht,, and P. Rosch. 2001. The structure of the coliphage HK022 Nun proteinlambda- phage boxB RNA complex. Implications for the mechanism of transcription termination. J. Biol. Chem. 276:3206432070.
24. Forde, N. R.,, D. Izhaky,, G. R. Woodcock,, G. J. Wuite,, and C. Bustamante. 2002. Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. USA 99:1168211687.
25. Foster, J. E.,, S. F. Holmes,, and D. A. Erie. 2001. Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell 106:243252.
26. Gollnick, P.,, and P. Babitzke. 2002. Transcription attenuation. Biochim. Biophys. Acta 1577:240250.
27. Gong, F.,, and C. Yanofsky. 2002. Instruction of translating ribosome by nascent peptide. Science 297:18641867.
28. Grayhack, E. J.,, X. Yang,, L. F. Lau,, and J. W. Roberts. 1985. Phage lambda gene Q antiterminator recognizes RNA polymerase near the promoter and accelerates it through a pause site. Cell 42:259269.
29. Grundy, F. J.,, and T. M. Henkin. 1993. tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell 74:475482.
30. Grundy, F. J.,, S. C. Lehman,, and T. M. Henkin. 2003. The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc. Natl. Acad. Sci. USA 100:1205712062.
31. Grundy, F. J.,, W. C. Winkler,, and T. M. Henkin. 2002. tRNA-mediated transcription antitermination in vitro: codonanticodon pairing independent of the ribosome. Proc. Natl. Acad. Sci. USA 99:1112111126.
32. Guajardo, R.,, and R. Sousa. 1997. A model for the mechanism of polymerase translocation. J. Mol. Biol. 265:819.
33. Gusarov, I.,, and E. Nudler. 2001. Control of intrinsic transcription termination by N and NusA: the basic mechanisms. Cell 107:437449.
34. Gusarov, I.,, and E. Nudler. 1999. The mechanism of intrinsic transcription termination. Mol. Cell 3:495504.
35. Harrington, K. J.,, R. B. Laughlin,, and S. Liang. 2001. Balanced branching in transcription termination. Proc. Natl. Acad. Sci. USA 98:50195024.
36. Henkin, T. M. 2000. Transcription termination control in bacteria. Curr. Opin. Microbiol. 3:149153.
37. Henkin, T. M.,, and C. Yanofsky. 2002. Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. Bioessays 24:700707.
38. Henthorn, K. S.,, and D. I. Friedman. 1996. Identification of functional regions of the Nun transcription termination protein of phage HK022 and the N antitermination protein of phage gamma using hybrid nun-N genes. J. Mol. Biol. 257:920.
39. Houman, F.,, M. R. Diaz-Torres,, and A. Wright. 1990. Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding protein. Cell 62:11531163.
40. Hung, S.,, and M. Gottesman. 1995. Phage HK022 Nun protein arrests transcription on phage lambda DNA in vitro and competes with the phage lambda N antitermination protein. J. Mol. Biol. 247:428442.
41. Hung, S. C.,, and M. E. Gottesman. 1997. The Nun protein of bacteriophage HK022 inhibits translocation of Escherichia coli RNA polymerase without abolishing its catalytic activities. Genes Dev. 11:26702678.
42. Kashlev, M.,, and N. Komissarova. 2002. Transcription termination: primary intermediates and secondary adducts. J. Biol. Chem. 277:1450114508.
43. Kashlev, M.,, E. Nudler,, A. Goldfarb,, T. White,, and E. Kutter. 1993. Bacteriophage T4 Alc protein: a transcription termination factor sensing local modification of DNA. Cell 75:147154.
44. King, R.,, S. Banik-Maiti,, D. Jin,, and R. Weisberg. 1996. Transcripts that increase the processivity and elongation rate of RNA polymerase. Cell 87:893903.
45. Komissarova, N.,, J. Becker,, S. Solter,, M. Kireeva,, and M. Kashlev. 2002. Shortening of RNA:DNA hybrid in transcription elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell 10:11511162.
46. Komissarova, N.,, and M. Kashlev. 1997. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272:1532915338.
47. Korzheva, N.,, and A. Mustaev. 2001. Transcription elongation complex: structure and function. Curr. Opin. Microbiol. 4:119125.
48. Korzheva, N.,, A. Mustaev,, M. Kozlov,, A. Malhotra,, V. Nikiforov,, A. Goldfarb,, and S. A. Darst. 2000. A structural model of transcription elongation. Science 289:619625.
49. Korzheva, N.,, A. Mustaev,, E. Nudler,, V. Nikiforov,, and A. Goldfarb. 1998. Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. Cold Spring Harbor Symp. Quant. Biol. 63:337345.
50. Kuznedelov, K.,, N. Korzheva,, A. Mustaev,, and K. Severinov. 2002. Structure-based analysis of RNA polymerase function: the largest subunit’s rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA-DNA hybrid length. EMBO J. 21:13691378.
51. Landick, R. 2001. RNA polymerase clamps down. Cell 105:567570.
52. Landick, R.,, C. L. Turnbough, Jr.,, and C. Yanofsky,. 1996. Transcription attenuation, p. 12631286. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella:Cellular and Molecular Biology, 2nd ed., vol. 1. ASM Press, Washington, D.C.
53. 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 95:49004905.
54. Lee, D. N.,, L. Phung,, J. Stewart,, and R. Landick. 1990. Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. J. Biol. Chem. 265:1514515153.
55. Li, X.,, L. Lindahl,, and J. M. Zengel. 1996. Ribosomal protein L4 from Escherichia coli utilizes nonidentical determinants for its structural and regulatory functions. RNA 2: 2437.
56. Linderoth, N. A.,, G. Tang,, and R. Calendar. 1997. In vivo and in vitro evidence for an anti-Rho activity induced by the phage P4 polarity suppressor protein Psu. Virology 227:131141.
57. Mandal, M.,, B. Boese,, J. E. Barrick,, W. C. Winkler,, and R. R. Breaker. 2003. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113:577586.
58. Marr, M. T.,, and J. W. Roberts. 2000. Function of transcription cleavage factors GreA and GreB at a regulatory pause site. Mol. Cell 6:12751285.
59. McDaniel, B. A.,, F. J. Grundy,, I. Artsimovitch,, and T. M. Henkin. 2003. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl. Acad. Sci. USA 100:30833088.
60. McDowell, J. C.,, J. W. Roberts,, D. J. Jin,, and C. Gross. 1994. Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science 266:822825.
61. Mironov, A. S.,, I. Gusarov,, R. Rafikov,, L. E. Lopez,, K. Shatalin,, R. A. Kreneva,, D. A. Perumov,, and E. Nudler. 2002. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111:747756.
62. Mogridge, J.,, T. Mah,, and J. Greenblatt. 1995. A protein- RNA interaction network facilitates the templateindependent cooperative assembly on RNA polymerase of a stable antitermination complex containing the lambda N protein. Genes Dev. 9:28312845.
63. Mooney, R. A.,, I. Artsimovitch,, and R. Landick. 1998. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180:32653275.
64. Morgan, W. D.,, D. G. Bear,, and P. H. von Hippel. 1984. Specificity of release by Escherichia coli transcription termination factor rho of nascent mRNA transcripts initiated at the lambda PR. J. Biol. Chem. 259:86648671.
65. Naryshkin, N.,, A. Revyakin,, Y. Kim,, V. Mekler,, and R. H. Ebright. 2000. Structural organization of the RNA polymerase-promoter open complex. Cell 101:601611.
66. Nechaev, S.,, Y. Yuzenkova,, A. Niedziela-Majka,, T. Heyduk,, and K. Severinov. 2002. A novel bacteriophage-encoded RNA polymerase binding protein inhibits transcription initiation and abolishes transcription termination by host RNA polymerase. J. Mol. Biol. 320:1122.
67. Nickels, B. E.,, C. W. Roberts,, H. I. Sun,, J. W. Roberts,, and A. Hochschild. 2002. The s70 subunit of RNA polymerase is contacted by the lQ antiterminator during early elongation. Mol. Cell 10:611622.
68. Noller, H.,, and M. Nomura,. 1996. Ribosomes, p. 167186. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 1. ASM Press, Washington, D.C.
69. Nudler, E.,, and M. E. Gottesman. 2002. Transcription termination and anti-termination in E. coli. Genes Cells 7:755768.
70. Palangat, M.,, and R. Landick. 2001. Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II. J. Mol. Biol. 311:265282.
71. Park, J. S.,, M. T. Marr,, and J. W. Roberts. 2002. E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell 109:757767.
72. Pasman, Z.,, and P. von Hippel. 2002. Active Escherichia coli transcription elongation complexes are functionally homogeneous. J. Mol. Biol. 322:505.
73. Pasman, Z.,, and P. H. von Hippel. 2000. Regulation of rhodependent transcription termination by NusG is specific to the Escherichia coli elongation complex. Biochemistry 39: 55735585.
74. Rees, W. A.,, S. E. Weitzel,, A. Das,, and P. H. von Hippel. 1997. Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage lambda. J. Mol. Biol. 273:797813.
75. Reynolds, R.,, R. M. Bermu´ dez-Cruz,, and M. J. Chamberlin. 1992. Parameters affecting transcription termination by Escherichia coli RNA polymerase. Analysis of 13 rhoindependent terminators. J. Mol. Biol. 224:3151.
76. Richardson, J. 2002. Rho-dependent termination and ATPases in transcript termination. Biochim. Biophys. Acta 1577:251260.
77. Ring, B.,, W. Yarnell,, and J. Roberts. 1996. Function of E. coli RNA polymerase s factor s70 in promoter-proximal pausing. Cell 86:485493.
78. Robert, J.,, S. B. Sloan,, R. A. Weisberg,, M. E. Gottesman,, R. Robledo,, and D. Harbrecht. 1987. The remarkable specificity of a new transcription termination factor suggests that the mechanisms of termination and antitermination are similar. Cell 51:483492.
79. Roberts, J. W.,, W. Yarnell,, E. Bartlett,, J. Guo,, M. Marr,, D. C. Ko,, H. Sun,, and C. W. Roberts. 1998. Antitermination by bacteriophage lambda Q protein. Cold Spring Harbor Symp. Quant. Biol. 63:319325.
80. Selby, C. P.,, and A. Sancar. 1994. Mechanisms of transcription- repair coupling and mutation frequency decline. Microbiol. Rev. 58:317329.
81. Selby, C. P.,, and A. Sancar. 1995. Structure and function of transcription-repair coupling factor. II. Catalytic properties. J. Biol. Chem. 270:48904895.
82. Sen, R.,, R. A. King,, and R. A. Weisberg. 2001. Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA. Mol. Cell 7:9931001.
83. Severinov, K. 2000. RNA polymerase structure-function: insights into points of transcriptional regulation. Curr. Opin. Microbiol. 3:118125.
84. Severinov, K.,, and S. A. Darst. 1997. A mutant RNA polymerase that forms unusual open promoter complexes. Proc. Natl. Acad. Sci. USA 94:1348113486.
85. Severinov, K.,, M. Kashlev,, E. Severinova,, I. Bass,, K. McWilliams,, E. Kutter,, V. Nikiforov,, L. Snyder,, and A. Goldfarb. 1994. A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc. J. Biol. Chem. 269:1425414259.
86. Sha, Y.,, L. Lindahl,, and J. M. Zengel. 1995. RNA determinants required for L4-mediated attenuation control of the S10 r-protein operon of Escherichia coli. J. Mol. Biol. 245:486498.
87. Sha, Y.,, L. Lindahl,, and J. M. Zengel. 1995. Role of NusA in L4-mediated attenuation control of the S10 r-protein operon of Escherichia coli. J. Mol. Biol. 245:474485.
88. Sidorenkov, I.,, N. Komissarova,, and M. Kashlev. 1998. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell 2:5564.
89. Sullivan, S.,, and M. Gottesman. 1992. Requirement for E. coli NusG protein in factor-dependent transcription termination. Cell 68:989994.
90. Telesnitsky, A.,, and M. Chamberlin. 1989. Terminatordistal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7. Biochemistry 28:52105218.
91. Torres, M.,, C. Condon,, J. M. Balada,, C. Squires,, and C. L. Squires. 2001. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 20:38113820.
92. Toulokhonov, I.,, I. Artsimovitch,, and R. Landick. 2001. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292:730733.
93. Uptain, S.,, C. Kane,, and M. Chamberlin. 1997. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66:117172.
94. Uptain, S. M.,, and M. J. Chamberlin. 1997. Escherichia coli RNA polymerase terminates transcription efficiently at rhoindependent terminators on single-stranded DNA templates. Proc. Natl. Acad. Sci. USA 94:1354813553.
95. Valbuzzi, A.,, and C. Yanofsky. 2001. Inhibition of the B. subtilis regulatory protein TRAP by the TRAP-inhibitory protein, AT. Science 293:20572059.
96. von Hippel, P. H. 1998. An integrated model of the transcription complex in elongation, termination, and editing. Science 281:660665.
97. von Hippel, P. H.,, and T. D. Yager. 1991. Transcript elongation and termination are competitive kinetic processes. Proc. Natl. Acad. Sci. USA 88:23072311.
98. Watnick, R. S.,, and M. E. Gottesman. 1998. Escherichia coli NusA is required for efficient RNA binding by phage HK022 nun protein. Proc. Natl. Acad. Sci. USA 95:15461551.
99. Watnick, R. S.,, S. C. Herring,, A. G. Palmer III,, and M. E. Gottesman. 2000. The carboxyl terminus of phage HK022 Nun includes a novel zinc-binding motif and a tryptophan required for transcription termination. Genes Dev. 14:731739.
100. Weisberg, R. A.,, and M. E. Gottesman. 1999. Processive antitermination. J. Bacteriol. 181:359367.
101. Wilson, K. S.,, C. R. Conant,, and P. H. von Hippel. 1999. Determinants of the stability of transcription elongation complexes: interactions of the nascent RNA with theDNA template and the RNA polymerase. J. Mol. Biol. 289:11791194.
102. Winkler, W.,, A. Nahvi,, and R. R. Breaker. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952956.
103. Winkler, W. C.,, S. Cohen-Chalamish,, and R. R. Breaker. 2002. An mRNA Structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. USA 99:1590815913.
104. Winkler, W. C.,, A. Nahvi,, N. Sudarsan,, J. E. Barrick,, and R. R. Breaker. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 10:701707.
105. Worbs, M.,, R. Huber,, and M. C. Wahl. 2000. Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon. EMBO J. 19:807818.
106. Yager, T. D.,, and P. H. von Hippel. 1991. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30:10971118.
107. Yarnell, W. S.,, and J. W. Roberts. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284:611615.
108. Yin, H.,, I. Artsimovitch,, R. Landick,, and J. Gelles. 1999. Nonequilibrium mechanism of transcription termination from observations of single RNA polymerase molecules. Proc. Natl. Acad. Sci. USA 96:1312413129.
109. Zalieckas, J. M.,, L. V. Wray, Jr.,, A. E. Ferson,, and S. H. Fisher. 1998. Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons. Mol. Microbiol. 27:10311038.
110. Zengel, J. M.,, and L. Lindahl. 1993. Domain I of 23S rRNA competes with a paused transcription complex for ribosomal protein L4 of Escherichia coli. Nucleic Acids Res. 21:24292435.
111. Zengel, J. M.,, Y. Sha,, and L. Lindahl. 2002. Surprising flexibility of leader RNA determinants for r-protein L4- mediated transcription termination in the Escherichia coil S10 operon. RNA 8:572578.
112. Zhang, G.,, E. A. Campbell,, L. Minakhin,, C. Richter,, K. Severinov,, and S. A. Darst. 1999. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell 98:811824.
113. Zheng, C.,, and D. Friedman. 1994. Reduced Rho-dependent transcription termination permits NusA-independent growth of Escherichia coli. Proc. Natl. Acad. Sci. USA 91:75437547.
114. Zhu, A. Q.,, and P. H. von Hippel. 1998. Rho-dependent termination within the trp t0 terminator. II. Effects of kinetic competition and rho processivity. Biochemistry 37:1121511222.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error