Bacterial transcription as a target for antibacterial drug development

Microbiology and Molecular Biology Reviews

Volumn 80, Issue 1, 2016, Pages 139-160

  Ma, Cong ^a   Yang, Xiao ^a   Lewis, Peter J ^a  

^a UNIVERSITY OF NEWCASTLE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; BICOZAMYCIN; DSHS 00507; FIDAXOMICIN; GE 23077; HELICASE; MICROCIN J25; RIFAMYCIN; RNA POLYMERASE; SALINAMIDE; SORANGICIN; STREPTOLYDIGIN; TAGETITOXIN; TRANSCRIPTION TERMINATION FACTOR RHO; UNCLASSIFIED DRUG; AMINOGLYCOSIDE; ANTIINFECTIVE AGENT; BACTERIAL PROTEIN; CYCLOPEPTIDE; DNA DIRECTED RNA POLYMERASE; TRANSCRIPTION FACTOR;

AMYCOLATOPSIS MEDITERRANEI; BACTERIAL TRANSCRIPTION; DNA TEMPLATE; EUKARYOTIC CELL; GENETIC TRANSCRIPTION; HUMAN; IC50; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PROMOTER REGION; REVIEW; RNA STRUCTURE; RNA SYNTHESIS; STAPHYLOCOCCUS AUREUS; STRUCTURE ACTIVITY RELATION; THERMUS AQUATICUS; THERMUS THERMOPHILUS; TRANSCRIPTION ELONGATION; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; ANTAGONISTS AND INHIBITORS; BACTERIUM; BIOSYNTHESIS; DRUG DESIGN; DRUG EFFECTS; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR MODEL; SPECIES DIFFERENCE;

AMINOGLYCOSIDES; ANTI-BACTERIAL AGENTS; BACTERIA; BACTERIAL PROTEINS; DNA-DIRECTED RNA POLYMERASES; DRUG DESIGN; GENE EXPRESSION REGULATION, BACTERIAL; HUMANS; MODELS, MOLECULAR; PEPTIDES, CYCLIC; RIFAMYCINS; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84964089322     PISSN: 10922172     EISSN: 10985557     Source Type: Journal    
DOI: 10.1128/MMBR.00055-15     Document Type: Review

References (231)

1. Brown SP, Cornforth DM, Mideo N. 2012. Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control. Trends Microbiol 20:336-342. http://dx.doi.org/10.1016/j.tim.2012.04.005.
2. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638. http://dx.doi.org/10.1126/science.1110591.
3. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578-6583. http://dx.doi.org/10.1073/pnas.95.12.6578.
4. CDC. 2013. Antibiotic resistance threats in the United States, 2013. CDC, Atlanta, GA.
5. WHO. 2014. Antimicrobial resistance: global report on surveilance 2014. WHO, Geneva, Switzerland.
6. O'Neill J. 2014. Antimicrobial resistance: tackling a crisis for the health and wealth of nations. Wellcome Trust and HM Government, London, United Kingdom.
7. Cooper MA, Shlaes D. 2011. Fix the antibiotics pipeline. Nature 472:32. http://dx.doi.org/10.1038/472032a.
8. Davies J, Davies D. 2010. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417-433. http://dx.doi.org/10.1128/MMBR.00016-10.
9. Barker KF. 1999. Antibiotic resistance: a current perspective. Br J Clin Pharmacol 48:109-124.
10. Nikaido H. 1994. Prevention of drug access to bacterial targets: permeability barriers and active efflux. Science 264:382-388. http://dx.doi.org/10.1126/science.8153625.
11. Davies J. 1994. Inactivation of antibiotics and the dissemination of resistance genes. Science 264:375-382. http://dx.doi.org/10.1126/science.8153624.
12. Li XZ, Nikaido H. 2009. Efflux-mediated drug resistance in bacteria: an update. Drugs 69:1555-1623. http://dx.doi.org/10.2165/11317030-000000000-00000.
13. Spratt BG. 1994. Resistance to antibiotics mediated by target alterations. Science 264:388-393. http://dx.doi.org/10.1126/science.8153626.
14. Brzoska AJ, Hassan KA, de Leon EJ, Paulsen IT, Lewis PJ. 2013. Single-step selection of drug resistant Acinetobacter baylyi ADP1 mutants reveals a functional redundancy in the recruitment of multidrug efflux systems. PLoS One 8:e56090. http://dx.doi.org/10.1371/journal.pone.0056090.
15. Cramer P. 2002. Multisubunit RNA polymerases. Curr Opin Struct Biol 12:89-97. http://dx.doi.org/10.1016/S0959-440X (02) 00294-4.
16. Calvori C, Frontali L, Leoni L, Tecce G. 1965. Effect of rifamycin on protein synthesis. Nature 207:417-418. http://dx.doi.org/10.1038/207417a0.
17. Scott LJ. 2013. Fidaxomicin: a review of its use in patients with Clostridium difficile infection. Drugs 73:1733-1747. http://dx.doi.org/10.1007/s40265-013-0134-z.
18. Kohn H, Widger W. 2005. The molecular basis for the mode of action of bicyclomycin. Curr Drug Targets Infect Disord 5:273-295. http://dx.doi.org/10.2174/1568005054880136.
19. Perez JC, Groisman EA. 2009. Evolution of transcriptional regulatory circuits in bacteria. Cell 138:233-244. http://dx.doi.org/10.1016/j.cell.2009.07.002.
20. Chopra I. 2007. Bacterial RNA polymerase: a promising target for the discovery of new antimicrobial agents. Curr Opin Investig Drugs 8:600-607.
21. Murakami KS, Darst SA. 2003. Bacterial RNA polymerases: the wholo story. Curr Opin Struct Biol 13:31-39. http://dx.doi.org/10.1016/S0959-440X (02) 00005-2.
22. Seshasayee AS, Sivaraman K, Luscombe NM. 2011. An overview of prokaryotic transcription factors: a summary of function and occurrence in bacterial genomes. Subcell Biochem 52:7-23. http://dx.doi.org/10.1007/978-90-481-9069-0-2.
23. Burgess RR, Anthony L. 2001. How sigma docks to RNA polymerase and what sigma does. Curr Opin Microbiol 4:126-131. http://dx.doi.org/10.1016/S1369-5274 (00) 00177-6.
24. Cook VM, Dehaseth PL. 2007. Strand opening-deficient Escherichia coli RNA polymerase facilitates investigation of closed complexes with promoter DNA: effects of DNA sequence and temperature. J Biol Chem 282:21319-21326. http://dx.doi.org/10.1074/jbc. M702232200.
25. Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH. 2006. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314:1144-1147. http://dx.doi.org/10.1126/science.1131399.
26. Chakraborty A, Wang D, Ebright YW, Korlann Y, Kortkhonjia E, Kim T, Chowdhury S, Wigneshweraraj S, Irschik H, Jansen R, Nixon BT, Knight J, Weiss S, Ebright RH. 2012. Opening and closing of the bacterial RNA polymerase clamp. Science 337:591-595. http://dx.doi.org/10.1126/science.1218716.
27. Mooney RA, Artsimovitch I, Landick R. 1998. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J Bacteriol 180:3265-3275.
28. Yarnell WS, Roberts JW. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284:611-615. http://dx.doi.org/10.1126/science.284.5414.611.
29. Skordalakes E, Berger JM. 2003. Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell 114:135-146. http://dx.doi.org/10.1016/S0092-8674 (03) 00512-9.
30. Werner F, Grohmann D. 2011. Evolution of multisubunit RNA polymerases in the three domains of life. Nat Rev Microbiol 9:85-98. http://dx.doi.org/10.1038/nrmicro2507.
31. Burgess RR. 1969. Separation and characterization of the subunits of ribonucleic acid polymerase. J Biol Chem 244:6168-6176.
32. Yang X, Lewis PJ. 2008. Overproduction and purification of recombinant Bacillus subtilis RNA polymerase. Protein Expr Purif 59:86-93. http://dx.doi.org/10.1016/j.pep. 2008.01.006.
33. Keller A, Yang X, Wiedermannova J, Delumeau O, Krasny L, Lewis PJ. 2014: A new subunit of RNA polymerase found in Gram-positive bacteria. J Bacteriol 196:3622-3632. http://dx.doi.org/10.1128/JB.02020-14.
34. Darst SA. 2001. Bacterial RNA polymerase. Curr Opin Struct Biol 11:155-162. http://dx.doi.org/10.1016/S0959-440X (00) 00185-8.
35. Murakami KS. 2015. Structural biology of bacterial RNA polymerase. Biomolecules 5:848-864. http://dx.doi.org/10.3390/biom5020848.
36. Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA. 1999. Crystal structure of Thermus aquaticus core RNA polymerase at 3. 3 A resolution. Cell 98:811-824. http://dx.doi.org/10.1016/S0092-8674 (00) 81515-9.
37. Murakami KS. 2013. X-ray crystal structure of Escherichia coli RNA polymerase sigma70 holoenzyme. J Biol Chem 288:9126-9134. http://dx.doi.org/10.1074/jbc. M112.430900.
38. Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, Yokoyama S. 2002. Crystal structure of a bacterial RNA polymerase holoenzyme at 2. 6 A resolution. Nature 417:712-719. http://dx.doi.org/10.1038/nature752.
39. Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH. 2012. Structural basis of transcription initiation. Science 338:1076-1080. http://dx.doi.org/10.1126/science.1227786.
40. Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. 2015. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 4. http://dx.doi.org/10.7554/eLife.08504.
41. Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I. 2007. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448:157-162. http://dx.doi.org/10.1038/nature05932.
42. Korzheva N, Mustaev A, Kozlov M, Malhotra A, Nikiforov V, Goldfarb A, Darst SA. 2000. A structural model of transcription elongation. Science 289:619-625. http://dx.doi.org/10.1126/science.289.5479.619.
43. Borukhov S, Nudler E. 2008. RNA polymerase: the vehicle of transcription. Trends Microbiol 16:126-134. http://dx.doi.org/10.1016/j.tim.2007.12.006.
44. Yang X, Molimau S, Doherty GP, Johnston EB, Marles-Wright J, Rothnagel R, Hankamer B, Lewis RJ, Lewis PJ. 2009. The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA. EMBO Rep 10:997-1002. http://dx.doi.org/10.1038/embor.2009.155.
45. Archambault J, Friesen JD. 1993. Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev 57:703-724.
46. Ebright RH. 2000. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 304:687-698. http://dx.doi.org/10.1006/jmbi.2000.4309.
47. Vannini A, Cramer P. 2012. Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol Cell 45:439-446. http://dx.doi.org/10.1016/j.molcel.2012.01.023.
48. Rudd MD, Luse DS. 1996. Amanitin greatly reduces the rate of transcription by RNA polymerase II ternary complexes but fails to inhibit some transcript cleavage modes. J Biol Chem 271:21549-21558. http://dx.doi.org/10.1074/jbc.271.35.21549.
49. Brueckner F, Cramer P. 2008. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol 15:811-818. http://dx.doi.org/10.1038/nsmb.1458.
50. Mariani R, Maffioli SI. 2009. Bacterial RNA polymerase inhibitors: an organized overview of their structure, derivatives, biological activity and current clinical development status. Curr Med Chem 16:430-454. http://dx.doi.org/10.2174/092986709787315559.
51. Buurman ET, Foulk MA, Gao N, Laganas VA, McKinney DC, Moustakas DT, Rose JA, Shapiro AB, Fleming PR. 2012. Novel rapidly diversifiable antimicrobial RNA polymerase switch region inhibitors with confirmed mode of action in Haemophilus influenzae. J Bacteriol 194:5504-5512. http://dx.doi.org/10.1128/JB.01103-12.
52. Mariner KR, Trowbridge R, Agarwal AK, Miller K, O'Neill AJ, Fishwick CW, Chopra I. 2010. Furanyl-rhodanines are unattractive drug candidates for development as inhibitors of bacterial RNA polymerase. Antimicrob Agents Chemother 54:4506-4509. http://dx.doi.org/10.1128/AAC.00753-10.
53. Zhu W, Haupenthal J, Groh M, Fountain M, Hartmann RW. 2014. New insights into the bacterial RNA polymerase inhibitor CBR703 as a starting point for optimization as an anti-infective agent. Antimicrob Agents Chemother 58:4242-4245. http://dx.doi.org/10.1128/AAC.02600-14.
54. Moy TI, Daniel A, Hardy C, Jackson A, Rehrauer O, Hwang YS, Zou D, Nguyen K, Silverman JA, Li Q, Murphy C. 2011. Evaluating the activity of the RNA polymerase inhibitor myxopyronin B against Staphylococcus aureus. FEMS Microbiol Lett 319:176-179. http://dx.doi.org/10.1111/j.1574-6968.2011.02282.x.
55. Nudler E. 2009. RNA polymerase active center: the molecular engine of transcription. Annu Rev Biochem 78:335-361. http://dx.doi.org/10.1146/annurev. biochem.76.052705.164655.
56. Suh WC, Ross W, Record MT, Jr. 1993. Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site. Science 259:358-361. http://dx.doi.org/10.1126/science.8420002.
57. Roberts JW, Shankar S, Filter JJ. 2008. RNA polymerase elongation factors. Annu Rev Microbiol 62:211-233. http://dx.doi.org/10.1146/annurev. micro.61.080706.093422.
58. Brueckner F, Ortiz J, Cramer P. 2009. A movie of the RNA polymerase nucleotide addition cycle. Curr Opin Struct Biol 19:294-299. http://dx.doi.org/10.1016/j.sbi.2009.04.005.
59. Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R. 2007. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448:163-168. http://dx.doi.org/10.1038/nature05931.
60. Sensi P, Greco AM, Ballotta R. 1959. Rifomycin. I. Isolation and properties of rifomycin B and rifomycin complex. Antibiot Annu 7:262-270.
61. Sensi P. 1983. History of the development of rifampin. Rev Infect Dis 5(Suppl 3):S402-S406. http://dx.doi.org/10.1093/clinids/5.Supplement-3.S402.
62. Onyebujoh P, Zumla A, Ribeiro I, Rustomjee R, Mwaba P, Gomes M, Grange JM. 2005. Treatment of tuberculosis: present status and future prospects. Bull World Health Organ 83:857-865.
63. Lienhardt C, Vernon A, Raviglione MC. 2010. New drugs and new regimens for the treatment of tuberculosis: review of the drug development pipeline and implications for national programmes. Curr Opin Pulm Med 16:186-193. http://dx.doi.org/10.1097/MCP.0b013e328337580c.
64. Aristoff PA, Garcia GA, Kirchhoff PD, Showalter HD. 2010. Rifamycins-obstacles and opportunities. Tuberculosis (Edinb) 90:94-118. http://dx.doi.org/10.1016/j.tube.2010.02.001.
65. Jiang ZD, DuPont HL. 2005. Rifaximin: in vitro and in vivo antibacterial activity-a review. Chemotherapy 51(Suppl 1):S67-S72.
66. Campbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, Darst SA. 2001. Structural mechanism for rifampicin inhibition of bacterial rna polymerase. Cell 104:901-912. http://dx.doi.org/10.1016/S0092-8674 (01) 00286-0.
67. Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG. 2005. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell 122:351-363. http://dx.doi.org/10.1016/j.cell.2005.07.014.
68. McClure WR, Cech CL. 1978. On the mechanism of rifampicin inhibition of RNA synthesis. J Biol Chem 253:8949-8956.
69. Molodtsov V, Nawarathne IN, Scharf NT, Kirchhoff PD, Showalter HD, Garcia GA, Murakami KS. 2013. X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins. J Med Chem 56:4758-4763. http://dx.doi.org/10.1021/jm4004889.
70. Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S. 2012. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet 44:106-110. http://dx.doi.org/10.1038/ng.1038.
71. Srivastava A, Degen D, Ebright YW, Ebright RH. 2012. Frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in Staphylococcus aureus. Antimicrob Agents Chemother 56:6250-6255. http://dx.doi.org/10.1128/AAC.01060-12.
72. Sung JC, Padilla DJ, Garcia-Contreras L, Verberkmoes JL, Durbin D, Peloquin CA, Elbert KJ, Hickey AJ, Edwards DA. 2009. Formulation and pharmacokinetics of self-assembled rifampicin nanoparticle systems for pulmonary delivery. Pharm Res 26:1847-1855. http://dx.doi.org/10.1007/s11095-009-9894-2.
73. Kozlov M, Nudler E, Nikiforov V, Mustaev A. 2013. Reactive rifampicin derivative able to damage transcription complex. Bioconjug Chem 24:443-447. http://dx.doi.org/10.1021/bc3005667.
74. Darst SA, Opalka N, Chacon P, Polyakov A, Richter C, Zhang G, Wriggers W. 2002. Conformational flexibility of bacterial RNA polymerase. Proc Natl Acad Sci U S A 99:4296-4301. http://dx.doi.org/10.1073/pnas.052054099.
75. Gill SK, Xu H, Kirchhoff PD, Cierpicki T, Turbiak AJ, Wan B, Zhang N, Peng KW, Franzblau SG, Garcia GA, Showalter HD. 2012. Structurebased design of novel benzoxazinorifamycins with potent binding affinity to wild-type and rifampin-resistant mutant Mycobacterium tuberculosis RNA polymerases. J Med Chem 55:3814-3826. http://dx.doi.org/10.1021/jm201716n.
76. Cramer P, Bushnell DA, Kornberg RD. 2001. Structural basis of transcription: RNA polymerase II at 2. 8 angstrom resolution. Science 292:1863-1876. http://dx.doi.org/10.1126/science.1059493.
77. Rothstein DM, Shalish C, Murphy CK, Sternlicht A, Campbell LA. 2006. Development potential of rifalazil and other benzoxazinorifamycins. Expert Opin Invest Drugs 15:603-623. http://dx.doi.org/10.1517/13543784.15.6.603.
78. Geisler WM, Pascual ML, Mathew J, Koltun WD, Morgan F, Batteiger BE, Mayes A, Tao S, Hurwitz SJ, Sayada C, Schinazi RF. 2014. Randomized, double-blind, multicenter safety and efficacy study of rifalazil compared with azithromycin for treatment of uncomplicated genital Chlamydia trachomatis infection in women. Antimicrob Agents Chemother 58:4014-4019. http://dx.doi.org/10.1128/AAC.02521-14.
79. Jansen R, Wray V, Irschik H, Reichenbach H, Höfle G. 1985. Antibiotics from gliding bacteria. XXX. Isolation and spectroscopic structure elucidation of sorangicin A, a new type of macrolide-polyether antibiotic from gliding bacteria. Tetrahedron Lett 26:6031-6034.
80. Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA. 2005. Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J 24:674-682. http://dx.doi.org/10.1038/sj.emboj.7600499.
81. Ramaswamy S, Musser JM. 1998. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tuber Lung Dis 79:3-29. http://dx.doi.org/10.1054/tuld.1998.0002.
82. Rommele G, Wirz G, Solf R, Vosbeck K, Gruner J, Wehrli W. 1990. Resistance of Escherichia coli to rifampicin and sorangicin A-a comparison. J Antibiot (Tokyo) 43:88-91. http://dx.doi.org/10.7164/antibiotics.43.88.
83. Agarwal AK, Johnson AP, Fishwick CWG. 2008. Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase. Tetrahedron 64:10049-10054. http://dx.doi.org/10.1016/j.tet.2008.08.037.
84. Agarwal AK, Peter Johnson A, Fishwick CWG. 2009. Addendum to "Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase" [Tetrahedron 64 (43) (2008) 10049-10054]. Tetrahedron 65:1077. http://dx.doi.org/10.1016/j.tet.2008.11.039.
85. Ciciliato I, Corti E, Sarubbi E, Stefanelli S, Gastaldo L, Montanini N, Kurz M, Losi D, Marinelli F, Selva E. 2004. Antibiotics GE23077, novel inhibitors of bacterial RNA polymerase. I. Taxonomy, isolation and characterization. J Antibiot (Tokyo) 57:210-217.
86. Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH. 2014. GE23077 binds to the RNA polymerase 'i' and 'i+1= sites and prevents the binding of initiating nucleotides. eLife 3:e02450.
87. Sarubbi E, Monti F, Corti E, Miele A, Selva E. 2004. Mode of action of the microbial metabolite GE23077, a novel potent and selective inhibitor of bacterial RNA polymerase. Eur J Biochem 271:3146-3154. http://dx.doi.org/10.1111/j.1432-1033.2004.04244.x.
88. Mariani R, Granata G, Maffioli SI, Serina S, Brunati C, Sosio M, Marazzi A, Vannini A, Patel D, White R, Ciabatti R. 2005. Antibiotics GE23077, novel inhibitors of bacterial RNA polymerase. 3. Chemical derivatization. Bioorg Med Chem Lett 15:3748-3752. http://dx.doi.org/10.1016/j.bmcl.2005.05.060.
89. Malinen AM, Turtola M, Parthiban M, Vainonen L, Johnson MS, Belogurov GA. 2012. Active site opening and closure control translocation of multisubunit RNA polymerase. Nucleic Acids Res 40:7442-7451. http://dx.doi.org/10.1093/nar/gks383.
90. Jovanovic M, Burrows PC, Bose D, Camara B, Wiesler S, Zhang X, Wigneshweraraj S, Weinzierl RO, Buck M. 2011. Activity map of the Escherichia coli RNA polymerase bridge helix. J Biol Chem 286:14469-14479. http://dx.doi.org/10.1074/jbc. M110.212902.
91. Cheung AC, Cramer P. 2012. A movie of RNA polymerase II transcription. Cell 149:1431-1437. http://dx.doi.org/10.1016/j.cell.2012.06.006.
92. Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. 2006. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127:941-954. http://dx.doi.org/10.1016/j.cell.2006.11.023.
93. Miropolskaya N, Artsimovitch I, Klimasauskas S, Nikiforov V, Kulbachinskiy A. 2009. Allosteric control of catalysis by the F loop of RNA polymerase. Proc Natl Acad Sci U S A 106:18942-18947. http://dx.doi.org/10.1073/pnas.0905402106.
94. Deboer C, Dietz A, Savage GM, Silver WS. 1955. Streptolydigin, a new antimicrobial antibiotic. I. Biologic studies of streptolydigin. Antibiot Annu 3:886-892.
95. Crum GF, Devries WH, Eble TE, Large CM, Shell JW. 1955. Streptolydigin, a new antimicrobial antibiotic. II. Isolation and characterization. Antibiot Annu 3:893-896.
96. Lewis C, Nikitas CT, Schwartz DF, Wilkins JR. 1955. Streptolydigin, a new antimicrobial antibiotic. III. In vitro and in vivo laboratory studies. Antibiot Annu 3:897-902.
97. McClure WR. 1980. On the mechanism of streptolydigin inhibition of Escherichia coli RNA polymerase. J Biol Chem 255:1610-1616.
98. Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. 2005. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 19:655-666. http://dx.doi.org/10.1016/j.molcel.2005.07.020.
99. Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD, Jr, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, Ebright RH, Arnold E. 2005. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 122:541-552. http://dx.doi.org/10.1016/j.cell.2005.07.017.
100. Halling SM, Burtis KC, Doi RH. 1978. Beta= subunit of bacterial RNA polymerase is responsible for streptolydigin resistance in Bacillus subtilis. Nature 272:837-839. http://dx.doi.org/10.1038/272837a0.
101. Yang X, Price CW. 1995. Streptolydigin resistance can be conferred by alterations to either the beta or beta= subunits of Bacillus subtilis RNA polymerase. J Biol Chem 270:23930-23933. http://dx.doi.org/10.1074/jbc.270.41.23930.
102. Trischman JA, Tapiolas DM, Jensen PR, Dwight R, Fenical W, McKee TC, Ireland CM, Stout TJ, Clardy J. 1994. Salinamides A and B: antiinflammatory depsipeptides from a marine streptomycete. J Am Chem Soc 116:757-758. http://dx.doi.org/10.1021/ja00081a042.
103. Moore BS, Trischman JA, Seng D, Kho D, Jensen PR, Fenical W. 1999. Salinamides, antiinflammatory depsipeptides from a marine streptomycete. J Org Chem 64:1145-1150. http://dx.doi.org/10.1021/jo9814391.
104. Miao S, Anstee MR, LaMarco K, Matthew J, Huang LHT, Brasseur MM. 1997. Inhibition of bacterial RNA polymerases. Peptide metabolites from the cultures of Streptomyces sp. J Nat Prod 60:858-861.
105. Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH. 2014. Transcription inhibition by the depsipeptide antibiotic salinamide A. eLife 3:e02451.
106. Artsimovitch I, Chu C, Lynch AS, Landick R. 2003. A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science 302:650-654. http://dx.doi.org/10.1126/science.1087526.
107. Malinen AM, Nandymazumdar M, Turtola M, Malmi H, Grocholski T, Artsimovitch I, Belogurov GA. 2014. CBR antimicrobials alter coupling between the bridge helix and the beta subunit in RNA polymerase. Nat Commun 5:3408. http://dx.doi.org/10.1038/ncomms4408.
108. Bae B, Nayak D, Ray A, Mustaev A, Landick R, Darst SA. 2015. CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix capmediated effects on nucleotide addition. Proc Natl Acad Sci U S A 112:E4178-E4187. http://dx.doi.org/10.1073/pnas.1502368112.
109. Villain-Guillot P, Gualtieri M, Bastide L, Leonetti JP. 2007. In vitro activities of different inhibitors of bacterial transcription against Staphylococcus epidermidis biofilm. Antimicrob Agents Chemother 51:3117-3121. http://dx.doi.org/10.1128/AAC.00343-07.
110. Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH. 2015. Structural basis of transcription inhibition by CBR hydroxamidines and CBR pyrazoles. Structure 23:1470-1481. http://dx.doi.org/10.1016/j.str.2015.06.009.
111. Nickels BE, Hochschild A. 2004. Regulation of RNA polymerase through the secondary channel. Cell 118:281-284. http://dx.doi.org/10.1016/j.cell.2004.07.021.
112. Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL. 2004. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118:311-322. http://dx.doi.org/10.1016/j.cell.2004.07.009.
113. Lamour V, Rutherford ST, Kuznedelov K, Ramagopal UA, Gourse RL, Severinov K, Darst SA. 2008. Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein. J Mol Biol 383:367-379. http://dx.doi.org/10.1016/j.jmb.2008.08.011.
114. Blankschien MD, Lee JH, Grace ED, Lennon CW, Halliday JA, Ross W, Gourse RL, Herman C. 2009. Super DksAs: substitutions in DksA enhancing its effects on transcription initiation. EMBO J 28:1720-1731. http://dx.doi.org/10.1038/emboj.2009.126.
115. Rutherford ST, Lemke JJ, Vrentas CE, Gaal T, Ross W, Gourse RL. 2007. Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase. J Mol Biol 366:1243-1257. http://dx.doi.org/10.1016/j.jmb.2006.12.013.
116. Vassylyeva MN, Svetlov V, Dearborn AD, Klyuyev S, Artsimovitch I, Vassylyev DG. 2007. The carboxy-terminal coiled-coil of the RNA polymerase beta=-subunit is the main binding site for Gre factors. EMBO Rep 8:1038-1043. http://dx.doi.org/10.1038/sj.embor.7401079.
117. Mitchell RE, Durbin RD. 1981. Tagetitoxin, a toxin produced by Pseudomonas syringae pv. tagetis: purification and partial characterization. Physiol Plant Pathol 18:157-168. http://dx.doi.org/10.1016/S0048-4059 (81) 80037-9.
118. Steinberg TH, Mathews DE, Durbin RD, Burgess RR. 1990. Tagetitoxin: a new inhibitor of eukaryotic transcription by RNApolymerase III. J Biol Chem 265:499-505.
119. Mathews DE, Durbin RD. 1994. Mechanistic aspects of tagetitoxin inhibition of RNA polymerase from Escherichia coli. Biochemistry 33:11987-11992. http://dx.doi.org/10.1021/bi00205a038.
120. Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I. 2005. Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol 12:1086-1093. http://dx.doi.org/10.1038/nsmb1015.
121. Artsimovitch I, Svetlov V, Nemetski SM, Epshtein V, Cardozo T, Nudler E. 2011. Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop. J Biol Chem 286:40395-40400. http://dx.doi.org/10.1074/jbc. M111.300889.
122. Svetlov V, Artsimovitch I, Nudler E. 2012. Response to Klyuyev and Vassylyev: on the mechanism of tagetitoxin inhibition of transcription. Transcription 3:51-55. http://dx.doi.org/10.4161/trns.19749.
123. Klyuyev S, Vassylyev DG. 2012. The binding site and mechanism of the RNA polymerase inhibitor tagetitoxin: an issue open to debate. Transcription 3:46-50. http://dx.doi.org/10.4161/trns.19468.
124. Aliev AE, Karu K, Mitchell RE, Porter MJ. 2015. The structure of tagetitoxin. Org Biomol Chem. http://dx.doi.org/10.1039/c5ob02076j.
125. Salomon RA, Farias RN. 1992. Microcin 25, a novel antimicrobial peptide produced by Escherichia coli. J Bacteriol 174:7428-7435.
126. Blond A, Peduzzi J, Goulard C, Chiuchiolo MJ, Barthelemy M, Prigent Y, Salomon RA, Farias RN, Moreno F, Rebuffat S. 1999. The cyclic structure of microcin J25, a 21-residue peptide antibiotic from Escherichia coli. Eur J Biochem 259:747-755.
127. Bayro MJ, Mukhopadhyay J, Swapna GV, Huang JY, Ma LC, Sineva E, Dawson PE, Montelione GT, Ebright RH. 2003. Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot. JAmChemSoc 125:12382-12383. http://dx.doi.org/10.1021/ja036677e.
128. Rosengren KJ, Clark RJ, Daly NL, Goransson U, Jones A, Craik DJ. 2003. Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone. J Am Chem Soc 125:12464-12474. http://dx.doi.org/10.1021/ja0367703.
129. Wilson KA, Kalkum M, Ottesen J, Yuzenkova J, Chait BT, Landick R, Muir T, Severinov K, Darst SA. 2003. Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail. J Am Chem Soc 125:12475-12483. http://dx.doi.org/10.1021/ja036756q.
130. Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH. 2004. Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNApolymerase secondary channel. Mol Cell 14:739-751. http://dx.doi.org/10.1016/j.molcel.2004.06.010.
131. Adelman K, Yuzenkova J, La Porta A, Zenkin N, Lee J, Lis JT, Borukhov S, Wang MD, Severinov K. 2004. Molecular mechanism of transcription inhibition by peptide antibiotic Microcin J25. Mol Cell 14:753-762. http://dx.doi.org/10.1016/j.molcel.2004.05.017.
132. Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH. 2008. The RNA polymerase "switch region" is a target for inhibitors. Cell 135:295-307. http://dx.doi.org/10.1016/j.cell.2008.09.033.
133. Irschik H, Gerth K, Hofle G, Kohl W, Reichenbach H. 1983. The myxopyronins, new inhibitors of bacterial RNA synthesis from Myxococcus fulvus (Myxobacterales). J Antibiot (Tokyo) 36:1651-1658. http://dx.doi.org/10.7164/antibiotics.36.1651.
134. Kohl W, Irschik H, Reichenbach H, Höfle G. 1983. Antibiotika aus Gleitenden Bakterien, XVII. Myxopyronin A und B-zwei neue Antibiotika aus Myxococcus fulvus Stamm Mx f50. Liebigs Annalen der Chemie 1983:1656-1667.
135. Belogurov GA, Vassylyeva MN, Sevostyanova A, Appleman JR, Xiang AX, Lira R, Webber SE, Klyuyev S, Nudler E, Artsimovitch I, Vassylyev DG. 2009. Transcription inactivation through local refolding of the RNA polymerase structure. Nature 457:332-335. http://dx.doi.org/10.1038/nature07510.
136. Srivastava A, Talaue M, Liu S, Degen D, Ebright RY, Sineva E, Chakraborty A, Druzhinin SY, Chatterjee S, Mukhopadhyay J, Ebright YW, Zozula A, Shen J, Sengupta S, Niedfeldt RR, Xin C, Kaneko T, Irschik H, Jansen R, Donadio S, Connell N, Ebright RH. 2011. New target for inhibition of bacterial RNA polymerase: 'switch region'. Curr Opin Microbiol 14:532-543. http://dx.doi.org/10.1016/j.mib.2011.07.030.
137. Irschik H, Jansen R, Hofle G, Gerth K, Reichenbach H. 1985. The corallopyronins, new inhibitors of bacterial RNA synthesis from Myxobacteria. J Antibiot (Tokyo) 38:145-152. http://dx.doi.org/10.7164/antibiotics.38.145.
138. Irschik H, Augustiniak H, Gerth K, Hofle G, Reichenbach H. 1995. The ripostatins, novel inhibitors of eubacterial RNA polymerase isolated from myxobacteria. J Antibiot (Tokyo) 48:787-792. http://dx.doi.org/10.7164/antibiotics.48.787.
139. Rice LB. 2010. Progress and challenges in implementing the research on ESKAPE pathogens. Infect Control Hosp Epidemiol 31(Suppl 1):S7-S10. http://dx.doi.org/10.1086/655995.
140. Molodtsov V, Fleming PR, Eyermann CJ, Ferguson AD, Foulk MA, McKinney DC, Masse CE, Buurman ET, Murakami KS. 2015. X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein. J Med Chem 58:3156-3171. http://dx.doi.org/10.1021/acs.jmedchem.5b00050.
141. Anonymous. 2010. Fidaxomicin: difimicin; lipiarmycin; OPT 80; OPT-80; PAR 101; PAR-101. Drugs R D 10:37-45. http://dx.doi.org/10.2165/11537730-000000000-00000.
142. Coronelli C, White RJ, Lancini GC, Parenti F. 1975. Lipiarmycin, a new antibiotic from Actinoplanes. II. Isolation, chemical, biological and biochemical characterization. J Antibiot (Tokyo) 28:253-259.
143. Erb W, Grassot JM, Linder D, Neuville L, Zhu J. 2015. Enantioselective synthesis of putative lipiarmycin aglycon related to fidaxomicin/tiacumicin B. Angew Chem Int Ed Engl 54:1929-1932. http://dx.doi.org/10.1002/anie.201409475.
144. FDA. 2011. FDA approves treatment for Clostridium difficile infection. http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/2011/ucm257024.htm.
145. Tupin A, Gualtieri M, Leonetti JP, Brodolin K. 2010. The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site. EMBOJ 29:2527-2537. http://dx.doi.org/10.1038/emboj.2010.135.
146. Artsimovitch I, Seddon J, Sears P. 2012. Fidaxomicin is an inhibitor of the initiation of bacterial RNA synthesis. Clin Infect Dis 55(Suppl 2):S127-S131. http://dx.doi.org/10.1093/cid/cis358.
147. Arhin F, Belanger O, Ciblat S, Dehbi M, Delorme D, Dietrich E, Dixit D, Lafontaine Y, Lehoux D, Liu J, McKay GA, Moeck G, Reddy R, Rose Y, Srikumar R, Tanaka KS, Williams DM, Gros P, Pelletier J, Parr TR, Jr, Far AR. 2006. A new class of small molecule RNA polymerase inhibitors with activity against rifampicin-resistant Staphylococcus aureus. Bioorg Med Chem 14:5812-5832. http://dx.doi.org/10.1016/j.bmc.2006.05.035.
148. Seneca A, Kane JH, Rockenbach J. 1952. Bactericidal, protozoicidal and fungicidal properties of thiolutin. Antibiot Chemother (Northfield) 2:357-360.
149. Oliva B, O'Neill A, Wilson JM, O'Hanlon PJ, Chopra I. 2001. Antimicrobial properties and mode of action of the pyrrothine holomycin. Antimicrob Agents Chemother 45:532-539. http://dx.doi.org/10.1128/AAC.45.2.532-539.2001.
150. Khachatourians GG, Tipper DJ. 1974. Inhibition of messenger ribonucleic acid synthesis in Escherichia coli by thiolutin. J Bacteriol 119:795-804.
151. Tipper DJ. 1973. Inhibition of yeast ribonucleic acid polymerases by thiolutin. J Bacteriol 116:245-256.
152. Irschik H, Schummer D, Hofle G, Reichenbach H, Steinmetz H, Jansen R. 2007. Etnangien, a macrolide-polyene antibiotic from Sorangium cellulosum that inhibits nucleic acid polymerases. J Nat Prod 70:1060-1063. http://dx.doi.org/10.1021/np070115h.
153. Paget MS, Helmann JD. 2003. The sigma70 family of sigma factors. Genome Biol 4:203. http://dx.doi.org/10.1186/gb-2003-4-1-203.
154. Feklistov A, Sharon BD, Darst SA, Gross CA. 2014. Bacterial sigma factors: a historical, structural, and genomic perspective. Annu Rev Microbiol 68:357-376. http://dx.doi.org/10.1146/annurev-micro-092412-155737.
155. Yang X, Lewis PJ. 2010. The interaction between bacterial transcription factors and RNA polymerase during the transition from initiation to elongation. Transcription 1:66-69. http://dx.doi.org/10.4161/trns.1.2.12791.
156. Washburn RS, Gottesman ME. 2015. Regulation of transcription elongation and termination. Biomolecules 5:1063-1078. http://dx.doi.org/10.3390/biom5021063.
157. Davies KM, Dedman AJ, van Horck S, Lewis PJ. 2005. The NusA: RNA polymerase ratio is increased at sites of rRNA synthesis in Bacillus subtilis. Mol Microbiol 57:366-379. http://dx.doi.org/10.1111/j.1365-2958.2005.04669.x.
158. Doherty GP, Meredith DH, Lewis PJ. 2006. Subcellular partitioning of transcription factors in Bacillus subtilis. J Bacteriol 188:4101-4110. http://dx.doi.org/10.1128/JB.01934-05.
159. Lewis PJ, Doherty GP, Clarke J. 2008. Transcription factor dynamics. Microbiology 154:1837-1844. http://dx.doi.org/10.1099/mic.0.2008/018549-0.
160. Klumpp S, Hwa T. 2008. Stochasticity and traffic jams in the transcription of ribosomal RNA: intriguing role of termination and antitermination. Proc Natl Acad Sci U S A 105:18159-18164. http://dx.doi.org/10.1073/pnas.0806084105.
161. Skordalakes E, Berger JM. 2006. Structural insights into RNAdependent ring closure and ATPase activation by the Rho termination factor. Cell 127:553-564. http://dx.doi.org/10.1016/j.cell.2006.08.051.
162. Epshtein V, Dutta D, Wade J, Nudler E. 2010. An allosteric mechanism of Rho-dependent transcription termination. Nature 463:245-249. http://dx.doi.org/10.1038/nature08669.
163. Miyoshi T, Miyairi N, Aoki H, Kosaka M, Sakai H. 1972. Bicyclomycin, a new antibiotic. I. Taxonomy, isolation and characterization. J Antibiot (Tokyo) 25:569-575.
164. Malik M, Li L, Zhao X, Kerns RJ, Berger JM, Drlica K. 2014. Lethal synergy involving bicyclomycin: an approach for reviving old antibiotics. J Antimicrob Chemother 69:3227-3235. http://dx.doi.org/10.1093/jac/dku285.
165. Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Hartig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rugheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stulke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Volker U, Bessieres P, et al. 2012. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335:1103-1106. http://dx.doi.org/10.1126/science.1206848.
166. Nowatzke WL, Keller E, Koch G, Richardson JP. 1997. Transcription termination factor Rho is essential for Micrococcus luteus. J Bacteriol 179:5238-5240.
167. Magyar A, Zhang X, Kohn H, Widger WR. 1996. The antibiotic bicyclomycin affects the secondary RNA binding site of Escherichia coli transcription termination factor Rho. J Biol Chem 271:25369-25374. http://dx.doi.org/10.1074/jbc.271.41.25369.
168. Carrano L, Bucci C, De Pascalis R, Lavitola A, Manna F, Corti E, Bruni CB, Alifano P. 1998. Effects of bicyclomycin on RNA- and ATP-binding activities of transcription termination factor Rho. Antimicrob Agents Chemother 42:571-578.
169. Zwiefka A, Kohn H, Widger WR. 1993. Transcription termination factor rho: the site of bicyclomycin inhibition in Escherichia coli. Biochemistry 32:3564-3570. http://dx.doi.org/10.1021/bi00065a007.
170. Magyar A, Zhang X, Abdi F, Kohn H, Widger WR. 1999. Identifying the bicyclomycin binding domain through biochemical analysis of antibioticresistant rho proteins. J Biol Chem 274:7316-7324. http://dx.doi.org/10.1074/jbc.274.11.7316.
171. Moyse KA, Knight JS, Richardson JP. 2000. The bicyclomycin sensitivities of 38 bicyclomycin-resistant mutants of transcription termination protein rho and the location of their mutations support a structural model of rho based on the F (1) ATPase. J Mol Biol 302:565-579. http://dx.doi.org/10.1006/jmbi.2000.4090.
172. Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM. 2005. Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin. Structure 13:99-109. http://dx.doi.org/10.1016/j.str.2004.10.013.
173. Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL. 2003. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185:5673-5684. http://dx.doi.org/10.1128/JB.185.19.5673-5684.2003.
174. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Debarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauel C, et al. 2003. Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100:4678-4683. http://dx.doi.org/10.1073/pnas.0730515100.
175. Arthur TM, Anthony LC, Burgess RR. 2000. Mutational analysis of beta =260-309, a sigma 70 binding site located on Escherichia coli core RNA polymerase. J Biol Chem 275:23113-23119. http://dx.doi.org/10.1074/jbc. M002040200.
176. Johnston EB, Lewis PJ, Griffith R. 2009. The interaction of Bacillus subtilis sigmaA with RNA polymerase. Protein Sci 18:2287-2297. http://dx.doi.org/10.1002/pro.239.
177. Ma C, Yang X, Kandemir H, Mielczarek M, Johnston EB, Griffith R, Kumar N, Lewis PJ. 2013. Inhibitors of bacterial transcription initiation complex formation. ACS Chem Biol 8:1972-1980. http://dx.doi.org/10.1021/cb400231p.
178. Bai H, Sang G, You Y, Xue X, Zhou Y, Hou Z, Meng J, Luo X. 2012. Targeting RNA polymerase primary sigma70 as a therapeutic strategy against methicillin-resistant Staphylococcus aureus by antisense peptide Nucleic acid. PLoS One 7:e29886. http://dx.doi.org/10.1371/journal.pone.0029886.
179. Husecken K, Negri M, Fruth M, Boettcher S, Hartmann RW, Haupenthal J. 2013. Peptide-based investigation of the Escherichia coli RNA polymerase sigma (70) :core interface as target site. ACS Chem Biol http://dx.doi.org/10.1021/cb3005758.
180. Yang X, Ma C, Lewis PJ. 2015. Identification of inhibitors of bacterial RNA polymerase. Methods http://dx.doi.org/10.1016/j.ymeth.2015.05.005.
181. Kandemir H, Ma C, Kutty SK, Black DS, Griffith R, Lewis PJ, Kumar N. 2014. Synthesis and biological evaluation of 2, 5-di (7-indolyl)-1, 3, 4-oxadiazoles, and 2- and 7-indolyl 2-(1, 3, 4-thiadiazolyl) ketones as antimicrobials. Bioorg Med Chem 22:1672-1679. http://dx.doi.org/10.1016/j.bmc.2014.01.025.
182. Mielczarek M, Devakaram RV, Ma C, Kandemir H, Yang X, Bhadbhade D, St. Black CR, Griffith R, Lewis PJ, Kumar N. 2015. Synthesis and biological activity of novel mono-indole and mono-benzofuran inhibitors of bacterial transcription initiation complex formation. BMC Bioorg Med Chem 23:1763-1775. http://dx.doi.org/10.1016/j.bmc.2015.02.037.
183. Mielczarek M, Devakaram RV, Ma C, Yang X, Kandemir H, Purwono B, Black DS, Griffith R, Lewis PJ, Kumar N. 2014. Synthesis and biological activity of novel bis-indole inhibitors of bacterial transcription initiation complex formation. Org Biomol Chem 12:2882-2894. http://dx.doi.org/10.1039/c4ob00460d.
184. Ma C, Yang X, Lewis PJ. 2015. Bacterial transcription inhibitor of RNA polymerase holoenzyme formation by structure-based drug design: from in silico screening to validation. ACS Infect Dis http://dx.doi.org/10.1021/acsinfecdis.5b00058.
185. Andre E, Bastide L, Villain-Guillot P, Latouche J, Rouby J, Leonetti JP. 2004. A multiwell assay to isolate compounds inhibiting the assembly of the prokaryotic RNA polymerase. Assay Drug Dev Technol 2:629-635. http://dx.doi.org/10.1089/adt.2004.2.629.
186. Andre E, Bastide L, Michaux-Charachon S, Gouby A, Villain-Guillot P, Latouche J, Bouchet A, Gualtieri M, Leonetti JP. 2006. Novel synthetic molecules targeting the bacterial RNA polymerase assembly. J Antimicrob Chemother 57:245-251. http://dx.doi.org/10.1093/jac/dki426.
187. Mooney RA, Davis SE, Peters JM, Rowland JL, Ansari AZ, Landick R. 2009. Regulator trafficking on bacterial transcription units in vivo. Mol Cell 33:97-108. http://dx.doi.org/10.1016/j.molcel.2008.12.021.
188. Richardson JP, Greenblatt J. 1996. Control of RNA chain elongation and termination, p 822-848. In Neidhardt FC, Curtiss R, III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (ed), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, DC.
189. Cardinale CJ, Washburn RS, Tadigotla VR, Brown LM, Gottesman ME, Nudler E. 2008. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. Coli. Science 320:935-938. http://dx.doi.org/10.1126/science.1152763.
190. Cohen SE, Walker GC. 2011. New discoveries linking transcription to DNA repair and damage tolerance pathways. Transcription 2:37-40. http://dx.doi.org/10.4161/trns.2.1.14228.
191. Epshtein V, Kamarthapu V, McGary K, Svetlov V, Ueberheide B, Proshkin S, Mironov A, Nudler E. 2014. UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature 505:372-377. http://dx.doi.org/10.1038/nature12928.
192. Ma C, Mobli M, Yang X, Keller AN, King GF, Lewis PJ. 2015. RNA polymerase-induced remodelling of NusA produces a pause enhancement complex. Nucleic Acids Res 43:2829-2840. http://dx.doi.org/10.1093/nar/gkv108.
193. Ha KS, Toulokhonov I, Vassylyev DG, Landick R. 2010. The NusA N-terminal domain is necessary and sufficient for enhancement of transcriptional pausing via interaction with the RNA exit channel of RNA polymerase. J Mol Biol 401:708-725. http://dx.doi.org/10.1016/j.jmb.2010.06.036.
194. Chaudhuri RR, Allen AG, Owen PJ, Shalom G, Stone K, Harrison M, Burgis TA, Lockyer M, Garcia-Lara J, Foster SJ, Pleasance SJ, Peters SE, Maskell DJ, Charles IG. 2009. Comprehensive identification of essential Staphylococcus aureus genes using transposon-mediated differential hybridisation (TMDH). BMC Genomics 10:291. http://dx.doi.org/10.1186/1471-2164-10-291.
195. de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A, Cruaud C, Samair S, Lechaplais C, Gyapay G, Richez C, Durot M, Kreimeyer A, Le Fevre F, Schachter V, Pezo V, Doring V, Scarpelli C, Medigue C, Cohen GN, Marliere P, Salanoubat M, Weissenbach J. 2008. A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol 4:174. http://dx.doi.org/10.1038/msb.2008.10.
196. Torres M, Balada JM, Zellars M, Squires C, Squires CL. 2004. In vivo effect of NusB and NusG on rRNA transcription antitermination. J Bacteriol 186:1304-1310. http://dx.doi.org/10.1128/JB.186.5.1304-1310.2004.
197. Burmann BM, Luo X, Rosch P, Wahl MC, Gottesman ME. 2010. Fine tuning of the E. Coli NusB: NusE complex affinity to BoxA RNA is required for processive antitermination. Nucleic Acids Res 38:314-326. http://dx.doi.org/10.1093/nar/gkp736.
198. Greive SJ, Lins AF, von Hippel PH. 2005. Assembly of an RNA-protein complex. Binding of NusB and NusE (S10) proteins to boxA RNA nucleates the formation of the antitermination complex involved in controlling rRNA transcription in Escherichia coli. J Biol Chem 280:36397-36408.
199. Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, Byrd RA, Ji X. 2011. Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination. Nucleic Acids Res 39:7803-7815. http://dx.doi.org/10.1093/nar/gkr418.
200. Berg KL, Squires C, Squires CL. 1989. Ribosomal RNA operon antitermination. Function of leader and spacer region box B-box A sequences and their conservation in diverse micro-organisms. J Mol Biol 209:345-358.
201. Luo X, Hsiao HH, Bubunenko M, Weber G, Court DL, Gottesman ME, Urlaub H, Wahl MC. 2008. Structural and functional analysis of the E. Coli NusB-S10 transcription antitermination complex. Mol Cell 32:791-802. http://dx.doi.org/10.1016/j.molcel.2008.10.028.
202. Drogemuller J, Strauss M, Schweimer K, Wohrl BM, Knauer SH, Rosch P. 2015. Exploring RNA polymerase regulation by NMRspectroscopy. Sci Rep 5:10825. http://dx.doi.org/10.1038/srep10825.
203. Burmann BM, Schweimer K, Luo X, Wahl MC, Stitt BL, Gottesman ME, Rosch P. 2010. A NusE: NusG complex links transcription and translation. Science 328:501-504. http://dx.doi.org/10.1126/science.1184953.
204. Werner F. 2012. A nexus for gene expression-molecular mechanisms of Spt5 and NusG in the three domains of life. J Mol Biol 417:13-27. http://dx.doi.org/10.1016/j.jmb.2012.01.031.
205. Hung SC, Gottesman ME. 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 247:428-442. http://dx.doi.org/10.1006/jmbi.1994.0151.
206. Sullivan SL, Gottesman ME. 1992. Requirement for E. Coli NusG protein in factor-dependent transcription termination. Cell 68:989-994. http://dx.doi.org/10.1016/0092-8674 (92) 90041-A.
207. Burova E, Hung SC, Sagitov V, Stitt BL, Gottesman ME. 1995. Escherichia coli NusG protein stimulates transcription elongation rates in vivo and in vitro. J Bacteriol 177:1388-1392.
208. Zellars M, Squires CL. 1999. Antiterminator-dependent modulation of transcription elongation rates by NusB and NusG. Mol Microbiol 32:1296-1304. http://dx.doi.org/10.1046/j.1365-2958.1999.01442.x.
209. Artsimovitch I, Landick R. 2000. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc Natl Acad Sci U S A 97:7090-7095. http://dx.doi.org/10.1073/pnas.97.13.7090.
210. Mooney RA, Schweimer K, Rosch P, Gottesman M, Landick R. 2009. Two structurally independent domains of E. Coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators. J Mol Biol 391:341-358. http://dx.doi.org/10.1016/j.jmb.2009.05.078.
211. Sevostyanova A, Artsimovitch I. 2010. Functional analysis of Thermus thermophilus transcription factor NusG. Nucleic Acids Res 38:7432-7445. http://dx.doi.org/10.1093/nar/gkq623.
212. Martinez-Rucobo FW, Sainsbury S, Cheung AC, Cramer P. 2011. Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J 30:1302-1310. http://dx.doi.org/10.1038/emboj.2011.64.
213. Chalissery J, Muteeb G, Kalarickal NC, Mohan S, Jisha V, Sen R. 2011. Interaction surface of the transcription terminator Rho required to form a complex with the C-terminal domain of the antiterminator NusG. J Mol Biol 405:49-64. http://dx.doi.org/10.1016/j.jmb.2010.10.044.
214. Burmann BM, Knauer SH, Sevostyanova A, Schweimer K, Mooney RA, Landick R, Artsimovitch I, Rosch P. 2012. An alpha helix to beta barrel domain switch transforms the transcription factor RfaH into a translation factor. Cell 150:291-303. http://dx.doi.org/10.1016/j.cell.2012.05.042.
215. NandyMazumdar M, Artsimovitch I. 2015. Ubiquitous transcription factors display structural plasticity and diverse functions: NusG proteins-shifting shapes and paradigms. Bioessays 37:324-334. http://dx.doi.org/10.1002/bies.201400177.
216. Tomar SK, Artsimovitch I. 2013. NusG-Spt5 proteins-universal tools for transcription modification and communication. Chem Rev 113:8604-8619. http://dx.doi.org/10.1021/cr400064k.
217. Belogurov GA, Mooney RA, Svetlov V, Landick R, Artsimovitch I. 2009. Functional specialization of transcription elongation factors. EMBO J 28:112-122. http://dx.doi.org/10.1038/emboj.2008.268.
218. Fairman-Williams ME, Guenther UP, Jankowsky E. 2010. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 20:313-324. http://dx.doi.org/10.1016/j.sbi.2010.03.011.
219. Eisen A, Lucchesi JC. 1998. Unraveling the role of helicases in transcription. Bioessays 20:634-641.
220. Gilhooly NS, Gwynn EJ, Dillingham MS. 2013. Superfamily 1 helicases. Front Biosci 5:206-216.
221. Truglio JJ, Croteau DL, Van Houten B, Kisker C. 2006. Prokaryotic nucleotide excision repair: the UvrABC system. Chem Rev 106:233-252. http://dx.doi.org/10.1021/cr040471u.
222. Delumeau O, Lecointe F, Muntel J, Guillot A, Guedon E, Monnet V, Hecker M, Becher D, Polard P, Noirot P. 2011. The dynamic protein partnership of RNA polymerase in Bacillus subtilis. Proteomics 11:2992-3001. http://dx.doi.org/10.1002/pmic.201000790.
223. Noirot-Gros MF, Dervyn E, Wu LJ, Mervelet P, Errington J, Ehrlich SD, Noirot P. 2002. An expanded view of bacterial DNA replication. Proc Natl Acad Sci U S A 99:8342-8347. http://dx.doi.org/10.1073/pnas.122040799.
224. Gwynn EJ, Smith AJ, Guy CP, Savery NJ, McGlynn P, Dillingham MS. 2013. The conserved C-terminus of the PcrA/UvrD helicase interacts directly with RNA polymerase. PLoS One 8:e78141. http://dx.doi.org/10.1371/journal.pone.0078141.
225. Sukhodolets MV, Jin DJ. 1998. RapA, a novel RNA polymeraseassociated protein, is a bacterial homolog of SWI2/SNF2. J Biol Chem 273:7018-7023. http://dx.doi.org/10.1074/jbc.273.12.7018.
226. Sukhodolets MV, Cabrera JE, Zhi H, Jin DJ. 2001. RapA, a bacterial homolog of SWI2/SNF2, stimulatesRNApolymerase recycling in transcription. Genes Dev 15:3330-3341. http://dx.doi.org/10.1101/gad.936701.
227. Liu B, Zuo Y, Steitz TA. 2015. Structural basis for transcription reactivation by RapA. Proc Natl Acad Sci U S A 112:2006-2010. http://dx.doi.org/10.1073/pnas.1417152112.
228. Wiedermannova J, Sudzinova P, Koval T, Rabatinova A, Sanderova H, Ramaniuk O, Rittich S, Dohnalek J, Fu Z, Halada P, Lewis P, Krasny L. 2014. Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis. Nucleic Acids Res 42:5151-5163. http://dx.doi.org/10.1093/nar/gku113.
229. Darst SA. 2004. New inhibitors targeting bacterial RNA polymerase. Trends Biochem Sci 29:159-160. http://dx.doi.org/10.1016/j.tibs.2004.02.005.
230. Villain-Guillot P, Bastide L, Gualtieri M, Leonetti JP. 2007. Progress in targeting bacterial transcription. Drug Discov Today 12:200-208. http://dx.doi.org/10.1016/j.drudis.2007.01.005.
231. Ho MX, Hudson BP, Das K, Arnold E, Ebright RH. 2009. Structures of RNA polymerase-antibiotic complexes. Curr Opin Struct Biol 19:715-723. http://dx.doi.org/10.1016/j.sbi.2009.10.010.