Rifampicin-resistance, rpoB polymorphism and RNA polymerase genetic engineering

Journal of Biotechnology

Volumn 202, Issue , 2015, Pages 60-77

  Alifano, Pietro ^a   Palumbo, Carla ^a   Pasanisi, Daniela ^a   Talà, Adelfia ^a  

^a UNIVERSITY OF SALENTO   (Italy)

Author keywords

Bacterial secondary metabolism; Bacterial virulence; Drug discovery; Rifampicin resistance; Strain improvement

Indexed keywords

CYTOLOGY; DISEASE CONTROL; DISEASES; ESCHERICHIA COLI; GENE ENCODING; GENETIC ENGINEERING; METABOLISM; MOLECULAR BIOLOGY; PHYSIOLOGY; POLYMERS; TRANSCRIPTION;

ANTI-BACTERIAL ACTIVITY; BACTERIAL VIRULENCE; CHROMOSOMAL MUTATION; DRUG DISCOVERY; REGULATORY MECHANISM; SECONDARY METABOLISM; STRAIN IMPROVEMENT; STRUCTURE-FUNCTION RELATIONSHIP;

RNA;

BACTERIAL PROTEIN; DNA DIRECTED RNA POLYMERASE; RIFAMPICIN; RNA POLYMERASE BETA SUBUNIT;

ANTIBIOTIC RESISTANCE; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DEVELOPMENT; DRUG EFFECTS; GENETIC ENGINEERING; GENETICS; REPRODUCTIVE FITNESS;

BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BACTERIAL PROTEINS; DNA-DIRECTED RNA POLYMERASES; DRUG DISCOVERY; DRUG RESISTANCE, BACTERIAL; GENETIC ENGINEERING; GENETIC FITNESS; MODELS, MOLECULAR; RIFAMPIN;

EID: 84940007632     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2014.11.024     Document Type: Article

References (206)

1. Alduina R., Lo Piccolo L., D'Alia D., Ferraro C., Gunnarsson N., Donadio S., Puglia A.M. Phosphate-controlled regulator for the biosynthesis of the dalbavancin precursor A40926. J. Bacteriol. 2007, 189:8120-8129.
2. Alduina R., Gierdina A., Gallo G., Renzone G., Ferraro C., Contino A., Scaloni A., Donadio S., Puglia A.M. Expression in Streptomyces lividans of Nonomuraea genes cloned in an artificial chromosome. Appl. Microbiol. Biotechnol. 2005, 68:656-662.
3. Alifano P. Fitness costs of antibiotic resistance. Antibiotics: Targets, Mechanisms and Resistance 2014, 109-132. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. C.O. Gualerzi, L. Brandi, A. Fabbretti, C.L. Pon (Eds.).
4. Alifano P., Ciampi M.S., Nappo A.G., Bruni C.B., Carlomagno M.S. In vivo analysis of the mechanisms responsible for strong transcriptional polarity in a "sense" mutant within an intercistronic region. Cell 1988, 55:351-360.
5. Alifano P., Rivellini F., Limauro D., Bruni C.B., Carlomagno M.S. A consensus motif common to all Rho-dependent prokaryotic transcription terminators. Cell 1991, 64:553-563.
6. Alifano P., Rivellini F., Nappo A.G., Bruni C.B., Carlomagno M.S. Alternative patterns of his operon transcription and mRNA processing generated by metabolic perturbation. Gene 1994, 146:15-21.
7. Aronson J. When I use a word . That's show business. Br. Med. J. 1999, 319:972.
8. Artsimovitch I., Patlan V., Sekine S., Vassylyeva M.N., Hosaka T., Ochi K., Yokoyama S., Vassylyev D.G. Structural basis for transcription regulation by alarmone ppGpp. Cell 2004, 117:299-310.
9. Azad A.K., Sirakova T.D., Fernandes N.D., Kolattukudy P.E. Gene knockout reveals a novel gene cluster for the synthesis of a class of cell wall lipids unique to pathogenic mycobacteria. J. Biol. Chem. 1997, 272:16741-16745.
10. Bailey M.J., Hughes C., Koronakis V. In vitro recruitment of the RfaH regulatory protein into a specialised transcription complex, directed by the nucleic acid ops element. Mol. Gen. Genet. 2000, 262:1052-1059.
11. Barker M.M., Gaal T., Gourse R.L. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J. Mol. Biol. 2001, 305:689-702.
12. Barker M.M., Gaal T., Josaitis C.A., Gourse R.L. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol. 2001, 305:673-688.
13. Bartlett M.S., Gaal T., Ross W., Gourse R.L. RNA polymerase mutants that destabilize RNA polymerase-promoter complexes alter NTP-sensing by rrn P1 promoters. J. Mol. Biol. 1998, 279:331-345.
14. Bear D.G., Hicks P.S., Escudero K.W., Andrews C.L., McSwiggen J.A., von Hippel P.H. Interactions of Escherichia coli transcription termination factor Rho with RNA. II. Electron microscopy and nuclease protection experiments. J. Mol. Biol. 1988, 199:623-635.
15. Billington O.J., McHugh T.D., Gillespie S.H. Physiological cost of rifampin resistance induced in vitro in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 1999, 43:1866-1869.
16. Bibb M.J. Regulation of secondary metabolism in Streptomycetes. Curr. Opin. Microbiol. 2005, 8:208-215.
17. Bisson G.P., Mehaffy C., Broeckling C., Prenni J., Rifat D., Lun D.S., Burgos M., Weissman D., Karakousis P.C., Dobos K. Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampin-resistant, rpoB mutant Mycobacterium tuberculosis. J. Bacteriol. 2012, 194:6441-6452.
18. Blatter E.E., Ross W., Tang H., Gourse R.L., Ebright R.H. Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 1994, 78:889-896.
19. Bordes P., Wigneshweraraj S., Chaney M., Dago A., Morett E., Buck M. Communication between Esigma(54), promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF sigma-dependent activator during transcription activation. Mol. Microbiol. 2004, 54:489-506.
20. Borukhov S., Lee J., Laptenko O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol. Microbiol. 2005, 55:1315-1324.
21. Bose D., Joly N., Pape T., Rappas M., Schumacher J., Buck M., Zhang X. Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins. Biochem. Soc. Trans. 2008, 36:83-88.
22. Bose D., Pape T., Burrows P.C., Rappas M., Wigneshweraraj S.R., Buck M., Zhang X. Organization of an activator-bound RNA polymerase holoenzyme. Mol. Cell 2008, 32:337-346.
23. Boudvillain M., Figueroa-Bossi N., Bossi L. Terminator still moving forward: expanding roles for Rho factor. Curr. Opin. Microbiol. 2013, 16:118-124.
24. Bougdour A., Gottesman S. ppGpp regulation of RpoS degradation via anti-adaptor protein IraP. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:12896-12901.
25. Browning D.F., Busby S.J. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2004, 2:57-65.
26. Buck M., Gallegos M., Studholme D., Guo Y., Gralla J. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J. Bacteriol. 2000, 182:4129-4136.
27. Burmann B.M., Schweimer K., Luo X., Wahl M.C., Stitt B.L., Gottesman M.E., Rosch P. A NusE:NusG complex links transcription and translation. Science 2010, 328:501-504.
28. Busby S., Ebright R.H. Transcription activation at class II CAP-dependent promoters. Mol. Microbiol. 1997, 23:853-859.
29. Camacho L.R., Constant P., Raynaud C., Laneelle M.A., Triccas J.A., Gicquel B., Daffe M., Guilhot C. Analysis of the phthiocerol dimycocerosate locus of Mycobacterium tuberculosis. Evidence that this lipid is involved in the cell wall permeability barrier. J. Biol. Chem. 2001, 276:19845-19854.
30. Campbell E.A., Korzheva N., Mustaev A., Murakami K., Nair S., Goldfarb A., Darst S.A. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 2001, 104:901-912.
31. Campbell E.A., Pavlova O., Zenkin N., Leon F., Irschik H., Jansen R., Severinov K., Darst S.A. Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J. 2005, 24:674-682.
32. Carata E., Peano C., Tredici S.M., Ferrari F., Talà A., Corti G., Bicciato S., De Bellis G., Alifano P. Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production. Microb. Cell Fact. 2009, 8:18-32.
33. Carlomagno M.S., Nappo A. The antiterminator NusB enhances termination at a sub-optimal Rho site. J. Mol. Biol. 2001, 309:19-28.
34. Cashel M., Gentry D.R., Hernandez V.H., Vinella D. The stringent response. Escherichia coli and Salmonella: Cellular and Molecular Biology 1996, 1458-1496. ASM Press, Washington, DC. F.C. Neidhardt (Ed.).
35. Chakraborty A., Wang D., Ebright Y.W., Korlann Y., Kortkhonjia E., Kim T., Chowdhury S., Wigneshweraraj S., Irschik H., Jansen R., Nixon B.T., Knight J., Weiss S., Ebright R.H. Opening and closing of the bacterial RNA polymerase clamp. Science 2012, 337:591-595.
36. Chaney M., Grande R., Wigneshweraraj S.R., Cannon W., Casaz P., Gallegos M.T., Schumacher J., Jones S., Elderkin S., Dago A.E., Morett E., Buck M. Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action. Genes Dev. 2001, 15:2282-2294.
37. Charity J.C., Blalock L.T., Costante-Hamm M.M., Kasper D.L., Dove S.L. Small molecule control of virulence gene expression in Francisella tularensis. PLoS Pathog. 2009, 5:e1000641.
38. Chater K.F., Chandra G. The use of the rare UUA codon to define expression "space" for genes involved in secondary metabolism, development and environmental adaptation in streptomyces. J. Microbiol. 2008, 46:1-11.
39. Chatterji D., Fujita N., Ishihama A. The mediator for stringent control, ppGpp, binds to the beta-subunit of Escherichia coli RNA polymerase. Genes Cells 1998, 3:279-287.
40. Chaudhary A.K., Dhakal D., Sohng J.K. An insight into the "-omics" based engineering of Streptomycetes for secondary metabolite overproduction. Biomed. Res. Int. 2013, 2013:968518.
41. Chopra I. Bacterial RNA polymerase: a promising target for the discovery of new antimicrobial agents. Curr. Opin. Investig. Drugs 2007, 8:600-607.
42. Ciampi M.S., Alifano P., Nappo A.G., Bruni C.B., Carlomagno M.S. Features of the rho-dependent transcription termination polar element within the hisG cistron of Salmonella typhimurium. J. Bacteriol. 1989, 171:4472-4478.
43. Cox J.S., Chen B., McNeil M., Jacobs W.R. Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice. Nature 1999, 402:79-83.
44. Cramer P., Bushnell D.A., Fu J., Gnatt A.L., Maier-Davis B., Thompson N.E., Burgess R.R., Edwards A.M., David P.R., Kornberg R.D. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 2000, 288:640-649.
45. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 2001, 292:1863-1876.
46. Cui L., Isii T., Fukuda M., Ochiai T., Neoh H.M., Camargo I.L., Watanabe Y., Shoji M., Hishinuma T., Hiramatsu K. An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus. Antimicrob. Agents Chemother. 2010, 54:5222-5233.
47. Daddi G., Lucchesi M., Mancini P., Termine A. The virulence of Mycobacterium tuberculosis strains resistant to rifampicin (Preliminary note). Ann. Ist. Carlo Forlanini 1969, 29:29-33.
48. Dalebroux Z.D., Svensson S.L., Gaynor E.C., Swanson M.S. ppGpp conjures bacterial virulence. Microbiol. Mol. Biol. Rev. 2010, 74:171-199.
49. Dalebroux Z.D., Swanson M.S. ppGpp: magic beyond RNA polymerase. Nat. Rev. Microbiol. 2012, 10:203-212.
50. Darst S.A. New inhibitors targeting bacterial RNA polymerase. Trends Biochem. Sci. 2004, 29:159-160.
51. Das R., Loss S., Li J., Waugh D.S., Tarasov S., Wingfield P.T., Byrd R.A., Altieri A.S. Structural biophysics of the NusB:NusE antitermination complex. J. Mol. Biol. 2008, 376:705-720.
52. de Knegt G.J., Bruning O., ten Kate M.T., de Jong M., van Belkum A., Endtz H.P., Breit T.M., Bakker-Woudenberg I.A., de Steenwinkel J.E. Rifampicin-induced transcriptome response in rifampicin-resistant Mycobacterium tuberculosis. Tuberculosis 2013, 93:96-101.
53. di Mauro E., Synder L., Marino P., Lamberti A., Coppo A., Tocchini-Valentini G.P. Rifampicin sensitivity of the components of DNA-dependent RNA polymerase. Nature 1969, 222:533-537.
54. Donahue J.P., Turnbough C.L. Characterization of transcriptional initiation from promoters P1 and P2 of the pyrBI operon of Escherichia coli K12. J. Biol. Chem. 1990, 265:19091-19099.
55. Durfee T., Hansen A.-M., Zhi H., Blattner F.R., Jin D.J. Transcription profiling of the stringent response in Escherichia coli. J. Bacteriol. 2008, 190:1084-1096.
56. Ebright R.H. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 2000, 304:687-698.
57. Edwards A.N., Patterson-Fortin L.M., Vakulskas C.A., Mercante J.W., Potrykus K., Vinella D., Camacho M.I., Fields J.A., Thompson S.A., Georgellis D., Cashel M., Babitzke P., Romeo T. Circuitry linking the Csr and stringent response global regulatory systems. Mol. Microbiol. 2011, 80:1561-1580.
58. Elena S.F., Ekunwe L., Hajela N., Oden S.A., Lenski R.E. Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 1998, 102/103:349-358.
59. Ezekiel D.H., Hutchins J.E. Mutations affecting RNA polymerase associated with rifampicin resistance in Escherichia coli. Nature 1968, 220:276-277.
60. Fernández-Moreno M.A., Caballero J.L., Hopwood D.A., Malpartida F. The act cluster contains regulatory and antibiotic export genes, direct targets for translational control by the bldA tRNA gene of Streptomyces. Cell 1991, 66:769-780.
61. Fish R.N., Kane C.M. Promoting elongation with transcript cleavage stimulatory factors. Biochim. Biophys. Acta 2002, 1577:287-307.
62. Fisher M.A., Grimm D., Henion A.K., Elias A.F., Stewart P.E., Rosa P.A., Gherardini F.C. Borrelia burgdorferi sigma54 is required for mammalian infection and vector transmission but not for tick colonization. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:5162-5167.
63. Gagneux S., Long C.D., Small P.M., Van T., Schoolnik G.K., Bohannan B.J. The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science 2006, 312:1944-1946.
64. Gallant J., Irr J., Cashel M. The mechanism of amino acid control of guanylate and adenylate biosynthesis. J. Biol. Chem. 1971, 246:5812-5816.
65. Gallegos M., Cannon W., Buck M. Functions of the sigma(54) region I in trans and implications for transcription activation. J. Biol. Chem. 1999, 274:25285-25290.
66. Gao W., Cameron D.R., Davies J.K., Kostoulias X., Stepnell J., Tuck K.L., Yeaman M.R., Peleg A.Y., Stinear T.P., Howden B.P. The RpoB H481Y rifampicin resistance mutation and an active stringent response reduce virulence and increase resistance to innate immune responses in Staphylococcus aureus. J. Infect. Dis. 2013, 207:929-939.
67. Garzoni C., Kelley W.L. Return of the Trojan horse: intracellular phenotype switching and immune evasion by Staphylococcus aureus. EMBO Mol. Med. 2011, 3:115-117.
68. Gatewood M.L., Jones G.H. (p)ppGpp inhibits polynucleotide phosphorylase from streptomyces but not from Escherichia coli and increases the stability of bulk mRNA in Streptomyces coelicolor. J. Bacteriol. 2010, 192:4275-4280.
69. Gnatt A., Cramer P., Fu J., Bushnell D., Kornberg R. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3Å resolution. Science 2001, 292:1876-1882.
70. Gourse R.L., Ross W., Gaal T. Ups and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 2000, 37:687-695.
71. Gruber T.M., Gross C.A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 2003, 57:441-466.
72. Gupta A.K., Katoch V.M., Chauhan D.S., Sharma R., Singh M., Venkatesan K., Sharma V.D. Microarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. Microb. Drug Resist. 2010, 16:21-28.
73. Haugen S.P., Ross W., Gourse R.L. Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat. Rev. Microbiol. 2008, 6:507-519.
74. Heisler L.M., Feng G., Jin D.J., Gross C.A., Landick R. Amino acid substitutions in the two largest subunits of Escherichia coli RNA polymerase that suppress a defective Rho termination factor affect different parts of the transcription complex. J. Biol. Chem. 1996, 271:14572-14583.
75. Helmann J.D. RNA polymerase: a nexus of gene regulation. Methods 2009, 47:1-5.
76. Hirata A., Klein B.J., Murakami K.S. The X-ray crystal structure of RNA polymerase from Archaea. Nature 2008, 451:851-854.
77. Hu H., Ochi K. Novel approach for improving the productivity of antibiotic-producing strains by inducing combined resistant mutations. Appl. Environ. Microbiol. 2001, 67:1885-1892.
78. Hu H., Zhang Q., Ochi K. Activation of antibiotic biosynthesis by specified mutations in the rpoB gene (encoding the RNA polymerase beta subunit) of Streptomyces lividans. J. Bacteriol. 2002, 184:3984-3991.
79. Inaoka T., Ochi K. Scandium stimulates the production of amylase and bacilysin in Bacillus subtilis. Appl. Environ. Microbiol. 2011, 77:8181-8183.
80. Inaoka T., Takahashi K., Yada H., Yoshida M., Ochi K. RNA polymerase mutation activates the production of a dormant antibiotic 3,3'-neotrehalosadiamine via an autoinduction mechanism in Bacillus subtilis. J. Biol. Chem. 2004, 279:3885-3892.
81. Ingham C.J., Furneaux P.A. Mutations in the β subunit of the Bacillus subtilis RNA polymerase that confer both rifampicin resistance and hypersensitivity to NusG. Microbiology 2000, 146:3041-3049.
82. Irschik H., Jansen R., Gerth K., Hofle G., Reichenbach H. The sorangicins: novel and powerful inhibitors of eubacterial RNA polymerase isolated from myxobacteria. J. Antibiot. (Tokyo) 1987, 40:7-13.
83. Ishikawa J., Chiba K., Kurita H., Satoh H. Contribution of rpoB2 RNA polymerase beta subunit gene to rifampin resistance in Nocardia species. Antimicrob. Agents Chemother. 2006, 50:1342-1346.
84. Jansen R., Wray V., Irschik H., Reichenbach H., Hofle G. Isolation and spectroscopic structure elucidation of sorangicin A, a new type of macrolide-polyether antibiotic from gliding bacteria. Tetrahedron Lett. 1985, 26:6031-6034.
85. Jin D.J., Gross C.A. Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance. J. Mol. Biol. 1988, 202:45-58.
86. Jin D.J., Gross C.A. Characterization of the pleiotropic phenotypes of rifampicin-resistant rpoB mutants of Escherichia coli. J. Bacteriol. 1989, 171:5229-5231.
87. Jin D.J., Gross C.A. RpoB8, a rifampicin-resistant termination-proficient RNA polymerase, has an increased Km for purine nucleotides during transcription elongation. J. Biol. Chem. 1991, 266:14478-14485.
88. Jin D.J., Cashel M., Friedman D.I., Nakamaru Y., Walter W.A., Gross C.A. Effects of rifampicin resistant rpoB mutations on antitermination and interaction with nusA in Escherichia coli. J. Mol. Biol. 1988, 204:247-261.
89. Jin D.J., Walter W., Gross C.A. Characterization of the termination phenotypes of rifampicin resistant rpoB mutants in Escherichia coli. J. Mol. Biol. 1988, 202:245-263.
90. Kasai K., Nishizawa T., Takahashi K., Hosaka T., Aoki H., Ochi K. Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus. J. Bacteriol. 2006, 188:7111-7122.
91. Kawai K., Wang G., Okamoto S., Ochi K. The rare earth, scandium, causes antibiotic overproduction in Streptomyces spp. FEMS Microbiol. Lett. 2007, 274:311-315.
92. Kawamura F., Wang F.L., Doi R.H. Catabolite-resistant sporulation (crsA) mutations in the Bacillus subtilis RNA polymerase 43 gene (rpoD) can suppress and be suppressed by mutations in the spoO genes. Proc. Natl. Acad. Sci. U.S.A. 1985, 82:8124-8128.
93. Khesin R.B., Gorlenko Z.M., Shemyakin M.F., Stvolinsky S.L., Mindlin S.Z., Ilyina T.S. Studies on the functions of the RNA polymerase components by means of mutations. Mol. Gen. Genet. 1969, 105:243-261.
94. Kirksey M.A., Tischler A.D., Siméone R., Hisert K.B., Uplekar S., Guilhot C., McKinney J.D. Spontaneous phthiocerol dimycocerosate-deficient variants of Mycobacterium tuberculosis are susceptible to gamma interferon-mediated immunity. Infect. Immun. 2011, 79:2829-2838.
95. Korzheva N., Mustaev A., Kozlov M., Malhotra A., Nikiforov V., Goldfarb A., Darst S.A. A structural model of transcription elongation. Science 2000, 289:619-625.
96. Krásný L., Gourse R.L. An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation. EMBO J. 2004, 23:4473-4483.
97. Kriel A., Bittner A.N., Kim S.H., Liu K., Tehranchi A.K., Zou W.Y., Rendon S., Chen R., Tu B.P., Wang J.D. Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance. Mol. Cell 2012, 48:231-241.
98. Lai C., Xu J., Tozawa Y., Okamoto-Hosoya Y., Yao X., Ochi K. Genetic and physiological characterization of rpoB mutations that activate antibiotic production in Streptomyces lividans. Microbiology 2002, 148:3365-3373.
99. Landick R. RNA polymerase clamps down. Cell 2001, 105:567-570.
100. Landick R., Stewart J., Lee D.N. Amino acid changes in conserved regions of the beta-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination. Genes Dev. 1990, 4:1623-1636.
101. Lavitola A., Bucci C., Salvatore P., Maresca G., Bruni C.B., Alifano P. Intracistronic transcription termination in polysialyltransferase gene (siaD) affects phase variation in Neisseria meningitidis. Mol. Microbiol. 1999, 33:119-127.
102. Lechevalier M.P., Prauser H., Labeda D.P., Ruan J.S. Two genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int. J. Syst. Bacteriol. 1986, 36:29-37.
103. Lisitsyn N.A., Sverdlov E.D., Moiseyeva E.P., Danilevskaya O.N., Nikiforov V.G. Mutation to rifampicin resistance at the beginning of the RNA polymerase beta subunit gene in Escherichia coli. Mol. Gen. Genet. 1984, 196:173-174.
104. Lopez J.M., Dromerick A., Freese E. Response of guanosine 5'-triphosphate concentration to nutritional changes and its significance for Bacillus subtilis sporulation. J. Bacteriol. 1981, 146:605-613.
105. Louw G.E., Warren R.M., Gey van Pittius N.C., Leon R., Jimenez A., Hernandez-Pando R., McEvoy C.R., Grobbelaar M., Murray M., van Helden P.D., Victor T.C. Rifampicin reduces susceptibility to ofloxacin in rifampicin-resistant Mycobacterium tuberculosis through efflux. Am. J. Respir. Crit. Care Med. 2011, 184:269-276.
106. Mallik P., Paul B.J., Rutherford S.T., Gourse R.L., Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J. Bacteriol. 2006, 188:5775-5782.
107. Manten A., Van Wijngaarden L.J. Development of drug resistance to rifampicin. Chemotherapy 1969, 14:93-100.
108. Martínez-Costa O.H., Arias P., Romero N.M., Parro V., Mellado R.P., Malpartida F. A relA/spoT homologous gene from Streptomyces coelicolor A3(2) controls antibiotic biosynthetic genes. J. Biol. Chem. 1996, 271:10627-10634.
109. Matsuo M., Hishinuma T., Katayama Y., Cui L., Kapi M., Hiramatsu K. Mutation of RNA polymerase beta subunit (rpoB) promotes hVISA-to-VISA phenotypic conversion of strain Mu3. Antimicrob. Agents Chemother. 2011, 55:4188-4195.
110. Maughan H., Galeano B., Nicholson W.L. Novel rpoB mutations conferring rifampin resistance on Bacillus subtilis: global effects on growth, competence, sporulation, and germination. J. Bacteriol. 2004, 186:2481-2486.
111. Merrikh H., Ferrazzoli A.E., Bougdour A., Olivier-Mason A., Lovett S.T. A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:611-616.
112. Miloso M., Limauro D., Alifano P., Rivellini F., Lavitola A., Gulletta E., Bruni C.B. Characterization of the rho genes of Neisseria gonorrhoeae and Salmonella typhimurium. J. Bacteriol. 1993, 175:8030-8037.
113. Moeller R., Vlašić I., Reitz G., Nicholson W.L. Role of altered rpoB alleles in Bacillus subtilis sporulation and spore resistance to heat, hydrogen peroxide, formaldehyde, and glutaraldehyde. Arch. Microbiol. 2012, 194:759-767.
114. Monaco C., Talà A., Spinosa M.R., Progida C., De Nitto E., Gaballo A., Bruni C.B., Bucci C., Alifano P. Identification of a meningococcal l-glutamate ABC transporter operon essential for growth in low-sodium environments. Infect. Immun. 2006, 74:1725-1740.
115. Mooney R.A., Artsimovitch I., Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 1998, 180:3265-3275.
116. Morgan W.D., Bear D.G., Litchman B.L., von Hippel P.H. RNA sequence and secondary structure requirements for Rho-dependent transcription termination. Nucleic Acids Res. 1985, 13:3739-3754.
117. Murakami K.S., Darst S.A. Bacterial RNA polymerases: the whole story. Curr. Opin. Struct. Biol. 2003, 13:31-39.
118. Murakami K., Masuda S., Darst S. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4Å resolution. Science 2002, 296:1280-1284.
119. Murakami K., Masuda S., Campbell E., Muzzin O., Darst S. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 2002, 296:1285-1290.
120. Murray H.D., Schneider D.A., Gourse R.L. Control of rRNA expression by small molecules is dynamic and nonredundant. Mol. Cell 2003, 12:125-134.
121. Murry J.P., Pandey A.K., Sassetti C.M., Rubin E.J. Phthiocerol dimycocerosate transport is required for resisting interferon-gamma-independent immunity. J. Infect. Dis. 2009, 200:774-782.
122. Mustaev A., Kashlev M., Lee J.Y., Polyakov A., Lebedev A., Zalenskaya K., Grachev M., Goldfarb M., Nikiforov A.V. Mapping of the priming substrate contacts in the active center of Escherichia coli RNA polymerase. J. Biol. Chem. 1991, 266:23927-23931.
123. Mustaev A., Kozlov M., Markovtsov V., Zaychikov E., Denissova L., Goldfarb A. Modular organization of the catalytic center of RNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:6641-6645.
124. Nanamiya H., Fugono N., Asai K., Doi R.H., Kawamura F. Suppression of temperature-sensitive sporulation mutation in the Bacillus subtilis sigA gene by rpoB mutation. FEMS Microbiol. Lett. 2000, 192:237-241.
125. Neri A., Mignogna G., Fazio C., Giorgi A., Schininà M.E., Stefanelli P. Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed. BMC Microbiol. 2010, 10:246.
126. Nudler E., Gottesman M. Transcription termination and anti-termination in E. coli. Genes Cells 2002, 7:755-768.
127. Ochi K. From microbial differentiation to ribosome engineering. Biosci. Biotechnol. Biochem. 2007, 71:1373-1386.
128. Ochi K. Metabolic initiation of differentiation and secondary metabolism by Streptomyces griseus: significance of the stringent response (ppGpp) and GTP content in relation to A factor. J. Bacteriol. 1987, 169:3608-3616.
129. Ochi K., Hosaka T. New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters. Appl. Microbiol. Biotechnol. 2013, 97:87-98.
130. Ochi K., Okamoto S., Tozawa S., Inaoka Y., Hosaka T., Xu T., Kurosawa J.K. Ribosome engineering and secondary metabolite production. Adv. Appl. Microbiol. 2004, 56:155-184.
131. Ochi K., Tanaka Y., Tojo S. Activating the expression of bacterial cryptic genes by rpoB mutations in RNA polymerase or by rare earth elements. J. Ind. Microbiol. Biotechnol. 2014, 41:403-414.
132. Ohnishi Y., Yamazaki H., Kato J.Y., Tomono A., Horinouchi S. AdpA, a central transcriptional regulator in the A-factor regulatory cascade that leads to morphological development and secondary metabolism in Streptomyces griseus. Biosci. Biotechnol. Biochem. 2005, 69:431-439.
133. O'Neill A., Oliva B., Storey C., Hoyle A., Fishwick C., Chopra I. RNA polymerase inhibitors with activity against rifampin-resistant mutants of Staphylococcus aureus. Antimicrob. Agents Chemother. 2000, 44:3163-3166.
134. O'Neill A.J., Huovinen T., Fishwick C.W., Chopra I. Molecular genetic and structural modeling studies of Staphylococcus aureus RNA polymerase and the fitness of rifampin resistance genotypes in relation to clinical prevalence. Antimicrob. Agents Chemother. 2006, 50:298-309.
135. Ovchinnikov Y., Monastyrskaya G.S., Gubanov V.V., Lipkin V.M., Sverdlov E.D., Kiver I.F., Bass I.A., Mindlin S.Z., Danilevskaya O.N., Khesin R.B. Primary structure of Escherichia coli RNA polymerase nucleotide substitution in the beta subunit gene of the rifampicin resistant rpoB255 mutant. Mol. Gen. Genet. 1981, 184:536-538.
136. Ovchinnikov Y.A., Monastyrskaya G.S., Guriev S.O., Kalinina N.F., Sverdlov E.D., Gragerov A.I., Bass I.A., Kiver I.F., Moiseyeva E.P., Igumnov V.N., Mindlin S.Z., Nikiforov V.G., Khesin R.B. RNA polymerase rifampicin resistance mutations in Escherichia coli: sequence changes and dominance. Mol. Gen. Genet. 1983, 190:344-348.
137. Paget M.S.B., Helmann J.D. The sigma70 family of sigma factors. Genome Biol. 2003, 4(1):203.
138. Pagliarulo C., Salvatore P., De Vitis L.R., Colicchio R., Monaco C., Tredici M., Talà A., Bardaro M., Lavitola A., Bruni C.B., Alifano P. Regulation and differential expression of gdhA encoding NADP-specific glutamate dehydrogenase in Neisseria meningitidis clinical isolates. Mol. Microbiol. 2004, 51:1757-1772.
139. Paul B.J., Barker M.M., Ross W., Schneider D.A., Webb C., Foster J.W., Gourse R.L. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 2004, 118:311-322.
140. Peano C., Talà A., Corti G., Pasanisi D., Durante M., Mita G., Bicciato S., De Bellis G., Alifano P. Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain. Microb. Cell Fact. 2012, 11:32.
141. Perederina A., Svetlov V., Vassylyeva M.N., Tahirov T.H., Yokoyama S., Artsimovitch I., Vassylyev D.G. Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription. Cell 2004, 118:297-309.
142. Perkins A.E., Nicholson W.L. Uncovering new metabolic capabilities of Bacillus subtilis using phenotype profiling of rifampin-resistant rpoB mutants. J. Bacteriol. 2008, 190:807-814.
143. Potrykus K., Cashel M. (p)ppGpp: still magical?. Annu. Rev. Microbiol. 2008, 62:35-51.
144. Queck S.Y., Jameson-Lee M., Villaruz A.E., Bach T.H., Khan B.A., Sturdevant D.E., Ricklefs S., Li M., Otto M.M. RNAIII-independent target gene control by the agr quorum-sensing system: insight into the evolution of virulence regulation in Staphylococcus aureus. Mol. Cell 2008, 32:150-158.
145. Rao F., See R.Y., Zhang D., Toh D.C., Ji Q., Liang Z.X. YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity. J. Biol. Chem. 2010, 285:473-482.
146. Rappas M., Bose D., Zhang X. Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription. Curr. Opin. Struct. Biol. 2007, 17:110-116.
147. Reed M.B., Domenech P., Manca C., Su H., Barczak A.K., Kreiswirth B.N., Kaplan G., Barry C.E. A glycolipid of hypervirulent tuberculosis strains that inhibits the innate immune response. Nature 2004, 431:84-87.
148. Retzlaff L., Distler J. The regulator of streptomycin gene expression, StrR, of Streptomyces griseus is a DNA binding activator protein with multiple recognition sites. Mol. Microbiol. 1995, 18:151-162.
149. Reynolds M.G. Compensatory evolution in rifampin-resistant Escherichia coli. Genetics 2000, 156:1471-1481.
150. Richardson J.P. Preventing the synthesis of unused transcripts by Rho factor. Cell 1991, 64:1047-1049.
151. Richardson J.P., Greenblatt J.L. Control of RNA chain elongation and termination. Escherichia coli and Salmonella: Cellular and Molecular Biology 1996, 822-848. ASM Press, Washington, DC. 2nd ed. F.C. Neidhardt (Ed.).
152. Rivellini F., Alifano P., Piscitelli C., Blasi V., Bruni C.B., Carlomagno M.S. A cytosine-over guanosine-rich sequence in RNA activates rho-dependent transcription termination. Mol. Microbiol. 1991, 5:3049-3054.
153. Roberts J., Park J.S. Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr. Opin. Microbiol. 2004, 7:120-125.
154. Rommele G., Wirz G., Solf R., Vosbeck K., Gruner J., Wehrli W. Resistance of Escherichia coli to rifampicin and sorangicin A-a comparison. J. Antibiot. (Tokyo) 1990, 43:88-91.
155. Ross W., Verntas C.E., Sanchez-Vazquez P., Gaal T., Gourse R.L. The magic spot: a ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation. Mol. Cell 2013, 50:420-429.
156. Saito M., Katayama Y., Hishinuma T., Iwamoto A., Aiba Y., Kuwahara-Arai K., Cui L., Matsuo M., Aritaka N., Hiramatsu K. Slow VISA' (sVISA), a novel phenotype of vancomycin resistance, obtained in vitro from hVISA. Antimicrob. Agents Chemother. 2014, 58:5024-5035.
157. Saito N., Xu J., Hosaka T., Okamoto S., Aoki H., Bibb M.J., Ochi K. EshA accentuates ppGpp accumulation and is conditionally required for antibiotic production in Streptomyces coelicolor A3(2). J. Bacteriol. 2006, 188:4952-4961.
158. Schumacher J., Zhang X., Jones S., Bordes P., Buck M. ATP-dependent transcriptional activation by bacterial PspF AAA1 protein. J. Mol. Biol. 2004, 338:863-875.
159. Severinov K., Soushko M., Goldfarb A., Nikiforov V. Rifampicin region revisited. New rifampicin-resistant and streptolydigin-resistant mutants in the beta subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 1993, 268:14820-14825.
160. Current Topics in Microbiology and Immunology 1996, Academic Press, New York. T. Shinnick (Ed.).
161. Siculella L., Damiano F., di Summa R., Tredici S.M., Alduina R., Gnoni G.V., Alifano P. Guanosine 5'-diphosphate 3'-diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a 'rare' actinomycete. Mol. Microbiol. 2010, 77:716-729.
162. Singer M., Jin D.J., Walter W.A., Gross C.A. Genetic evidence for the interaction between cluster I and cluster III rifampicin resistant mutations. J. Mol. Biol. 1993, 231:1-5.
163. Sonenshein A.L. CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria. Curr. Opin. Microbiol. 2005, 8:203-207.
164. Squires C.L., Zaporojets D. Proteins shared by the transcription and translation machines. Annu. Rev. Microbiol. 2000, 54:775-798.
165. Stagno J.R., Altieri A.S., Bubunenko M., Tarasov S.G., Li J., Court D.L., Byrd R.A., Ji X. Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination. Nucleic Acids Res. 2011, 39:7803-7815.
166. Stephanopoulos G., Alper H., Moxley J. Exploiting biological complexity for strain improvement through systems biology. Nat. Biotechnol. 2004, 22:1261-1267.
167. Sukhodolets M.V., Cabrera J.E., Zhi H., Jin D.J. RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription. Genes Dev. 2001, 15:3330-3341.
168. Sun Y.H., Bakshi S., Chalmers R., Tang C.M. Functional genomics of Neisseria meningitidis pathogenesis. Nat. Med. 2000, 6:1269-1273.
169. Tagami S., Sekine S., Kumarevel T., Hino N., Murayama Y., Kamegamori S., Yamamoto M., Sakamoto K., Yokoyama S. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature 2010, 468:978-982.
170. Taha M.K., Zarantonelli M.L., Ruckly C., Giorgini D., Alonso J.M. Rifampin-resistant Neisseria meningitidis. Emerg. Infect. Dis. 2006, 12:859-860.
171. Takano E., Bibb M.J. The stringent response, ppGpp and antibiotic production in Streptomyces coelicolor A3(2). Actinomycetologica 1994, 8:1-10.
172. Talà A., Monaco C., Nagorska K., Exley R.M., Corbett A., Zychlinsky A., Alifano P., Tang C.M. Glutamate utilization promotes meningococcal survival in vivo through avoidance of the neutrophil oxidative burst. Mol. Microbiol. 2011, 81:1330-1342.
173. Talà A., Wang G., Zemanova M., Okamoto S., Ochi K., Alifano P. Activation of dormant bacterial genes by Nonomuraea sp. strain ATCC 39727 mutant-type RNA polymerase. J. Bacteriol. 2009, 191:805-814.
174. Tamehiro N., Hosaka T., Xu J., Hu H., Otake N., Ochi K. Innovative approach for improvement of an antibiotic-overproducing industrial strain of Streptomyces albus. Appl. Environ. Microbiol. 2003, 69:6412-6417.
175. Tanaka Y., Hosaka T., Ochi K. Rare earth elements activate the secondary metabolite-biosynthetic gene clusters in Streptomyces coelicolor A3(2). J. Antibiot. (Tokyo) 2010, 63:477-481.
176. Tanaka Y., Kasahara K., Hirose Y., Murakami K., Kugimiya R., Ochi K. Activation and products of the cryptic secondary metabolite biosynthetic gene clusters by rifampin resistance (rpoB) mutations in actinomycetes. J. Bacteriol. 2013, 195:2959-2970.
177. Tavormina P.L., Landick R., Gross C.A. Isolation, purification and in vitro characterization of recessive-lethal-mutant RNA polymerases from Escherichia coli. J. Bacteriol. 1996, 178:5263-5271.
178. Tocchini-Valentini G.P., Marino P., Colvill A.J. Mutant of E. coli containing an altered DNA-dependent RNA polymerase. Nature 1968, 220:275-276.
179. Toulokhonov I.I., Shulgina I., Hernandez V.J. Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N terminus of the beta'-subunit. J. Biol. Chem. 2001, 276:1220-1225.
180. Trivedi O.A., Arora P., Vats A., Ansari M.Z., Tickoo R., Sridharan V., Mohanty D., Gokhale R.S. Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Mol. Cell 2005, 17:631-643.
181. Traxler M.F., Summers S.M., Nguyen H.-T., Zacharia V.M., Hightower G.A., Smith J.T., Conway T. The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli. Mol. Microbiol. 2008, 68:1128-1148.
182. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6Å resolution. Nature 2002, 417:712-719.
183. Vassylyev D.G., Vassylyeva M.N., Perederina A., Tahirov T.H., Artsimovitch I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 2007, 448:157-162.
184. Vattanaviboon P., Sukchawalit R., Jearanaikoon P., Chuchottaworn C., Ponglikitmongkol M. Analysis of RNA polymerase gene mutation in three isolates of rifampicin resistant Mycobacterium tuberculosis. Southeast Asian J. Trop. Med. Public Health 1995, 26(Suppl. 1):333-336.
185. Vigliotta G., Tredici S.M., Damiano F., Montinaro M.R., Pulimeno R., di Summa R., Massardo D.R., Gnoni G.V., Alifano P. Natural merodiploidy involving duplicated rpoB alleles affects secondary metabolism in a producer actinomycete. Mol. Microbiol. 2005, 55:396-412.
186. Villain-Guillot P., Bastide L., Gualtieri M., Leonetti J. Progress in targeting bacterial transcription. Drug Discov. Today 2007, 12:200-208.
187. Vrentas C.E., Gaal T., Berkmen M.B., Rutherford S.T., Haugen S.P., Vassylyev D.G., Ross W., Gourse R.L. Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J. Mol. Biol. 2008, 377:551-564.
188. Wang G., Hosaka T., Ochi K. Dramatic activation of antibiotic production in Streptomyces coelicolor by cumulative drug resistance mutations. Appl. Environ. Microbiol. 2008, 74:2834-2840.
189. Wang G., Tanaka Y., Ochi K. The G243D mutation (afsB mutation) in the principal sigma factor sigma HrdB alters intracellular ppGpp level and antibiotic production in Streptomyces coelicolor A3(2). Microbiology 2010, 156:2384-2392.
190. Watanabe Y., Cui L., Katayama Y., Kozue K., Hiramatsu K. Impact of rpoB mutations on reduced vancomycin susceptibility in Staphylococcus aureus. J. Clin. Microbiol. 2011, 49:2680-2684.
191. Westover K.D., Bushnell D.A., Kornberg R.D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 2004, 119:481-489.
192. Wichelhaus T.A., Böddinghaus B., Besier S., Schäfer V., Brade V., Ludwig A. Biological cost of rifampin resistance from the perspective of Staphylococcus aureus. Antimicrob. Agents Chemother. 2002, 46:3381-3385.
193. Wigneshweraraj S., Bose D., Burrows P.C., Joly N., Schumacher J., Rappas M., Pape T., Zhang X., Stockley P., Severinov K., Buck M. Modus operandi of the bacterial RNA polymerase containing the sigma(54) promoter-specificity factor. Mol. Microbiol. 2008, 68:538-546.
194. Wilson K.S., von Hippel P.H. Stability of Escherichia coli transcription complexes near an intrinsic terminator. J. Mol. Biol. 1994, 244:36-51.
195. Witte G., Hartung S., Buttner K., Hopfner K.P. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol. Cell 2008, 30:167-178.
196. Xu H., Hoover T.R. Transcriptional regulation at a distance in bacteria. Curr. Opin. Microbiol. 2001, 4:138-144.
197. Xu C., Liu L., Zhang Z., Jin D., Qiu J., Chen M. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl. Microbiol. Biotechnol. 2013, 97:519-539.
198. Xu J., Tozawa Y., Lai C., Hayashi H., Ochi K. A rifampicin resistance mutation in the rpoB gene confers ppGpp-independent antibiotic production in Streptomyces coelicolor A3 (2). Mol. Genet. Genomics 2002, 268:179-189.
199. Xu M., Zhou Y., Goldstein B., Jin D. Cross-resistance of Escherichia coli RNA polymerases conferring rifampin resistance to different antibiotics. J. Bacteriol. 2005, 187:2783-2792.
200. Yang X., Ishiguro E.E. Temperature-sensitive growth and decreased thermotolerance associated with relA mutations in Escherichia coli. J. Bacteriol. 2003, 185:5765-5771.
201. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3Å resolution. Cell 1999, 98:811-824.
202. Zhang X., Chaney M., Wigneshweraraj S., Schumacher J., Bordes P., Cannon W., Buck M. Mechanochemical ATPases and transcriptional activation. Mol. Microbiol. 2002, 45:895-903.
203. Zhang Y., Feng Y., Chatterjee S., Tuske S., Ho M.X., Arnold E., Ebright R.H. Structural basis of transcription initiation. Science 2012, 338:1076-1080.
204. Zhao G., Weatherspoon N., Kong W., Curtiss R., Shi Y. A dual-signal regulatory circuit activates transcription of a set of divergent operons in Salmonella typhimurium. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:20924-20929.
205. Zhou Y.N., Jin D.J. The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like stringent RNA polymerases in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:2908-2913.
206. Zuo Y., Wang Y., Steitz T.A. The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex. Mol. Cell 2013, 50:430-436.