| [1] Lee SJ. Hydroxylation of methane through component interactions in soluble methane monooxygenases. J Microbiol. 2016 Apr;54(4):277-82. doi: 10.1007/s12275-016-5642-6. Epub 2016 Apr 1. Review. PubMed PMID: 27033202. |
| [2] Wajjwalkul W, Sukmak M, Amavisit P, Sukpuaram T, La-ard A. MOLECULAR CHARACTERIZATION OF FLAB FOR LEPTOSPIRA IDENTIFICATION. Southeast Asian J Trop Med Public Health. 2015 Mar;46(2):262-7. PubMed PMID: 26513929. |
| [3] McDonald C, Jovanovic G, Ces O, Buck M. Membrane Stored Curvature Elastic Stress Modulates Recruitment of Maintenance Proteins PspA and Vipp1. MBio. 2015 Sep 1;6(5):e01188-15. doi: 10.1128/mBio.01188-15. PubMed PMID: 26330516; PubMed Central PMCID: PMC4556811. |
| [4] Gallarato LA, Sánchez DG, Olvera L, Primo ED, Garrido MN, Beassoni PR, Morett E, Lisa AT. Exopolyphosphatase of Pseudomonas aeruginosa is essential for the production of virulence factors, and its expression is controlled by NtrC and PhoB acting at two interspaced promoters. Microbiology. 2014 Feb;160(Pt 2):406-17. doi: 10.1099/mic.0.074773-0. Epub 2013 Nov 25. PubMed PMID: 24275100. |
| [5] Noar JD, Bruno-Bárcena JM. Complete Genome Sequences of Azotobacter vinelandii Wild-Type Strain CA and Tungsten-Tolerant Mutant Strain CA6. Genome Announc. 2013 Jun 27;1(3). pii: e00313-13. doi: 10.1128/genomeA.00313-13. PubMed PMID: 23792740; PubMed Central PMCID: PMC3675510. |
| [6] Galardini M, Pini F, Bazzicalupo M, Biondi EG, Mengoni A. Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti. Genome Biol Evol. 2013;5(3):542-58. doi: 10.1093/gbe/evt027. PubMed PMID: 23431003; PubMed Central PMCID: PMC3622305. |
| [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013 Jan;41(Database issue):D203-13. doi: 10.1093/nar/gks1201. Epub 2012 Nov 29. PubMed PMID: 23203884; PubMed Central PMCID: PMC3531196. |
| [8] de Oliveira Cunha C, Goda Zuleta LF, Paula de Almeida LG, Prioli Ciapina L, Lustrino Borges W, Pitard RM, Baldani JI, Straliotto R, de Faria SM, Hungria M, Sousa Cavada B, Mercante FM, Ribeiro de Vasconcelos AT. Complete genome sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a heat-tolerant, nitrogen-fixing symbiont of Mimosa flocculosa. J Bacteriol. 2012 Dec;194(23):6675-6. doi: 10.1128/JB.01821-12. PubMed PMID: 23144415; PubMed Central PMCID: PMC3497515. |
| [9] Liebner S, Svenning MM. Environmental transcription of mmoX by methane-oxidizing Proteobacteria in a subarctic Palsa Peatland. Appl Environ Microbiol. 2013 Jan;79(2):701-6. doi: 10.1128/AEM.02292-12. Epub 2012 Oct 26. PubMed PMID: 23104418; PubMed Central PMCID: PMC3553753. |
| [10] Ma L, Zhang Y, Yan X, Guo L, Wang L, Qiu J, Yang R, Zhou D. Expression of the type VI secretion system 1 component Hcp1 is indirectly repressed by OpaR in Vibrio parahaemolyticus. ScientificWorldJournal. 2012;2012:982140. doi: 10.1100/2012/982140. Epub 2012 Jul 31. PubMed PMID: 22924031; PubMed Central PMCID: PMC3417189. |
| [11] Kabisch J, Thürmer A, Hübel T, Popper L, Daniel R, Schweder T. Characterization and optimization of Bacillus subtilis ATCC 6051 as an expression host. J Biotechnol. 2013 Jan 20;163(2):97-104. doi: 10.1016/j.jbiotec.2012.06.034. Epub 2012 Jul 10. PubMed PMID: 22789474. |
| [12] Romeo A, Sonnleitner E, Sorger-Domenigg T, Nakano M, Eisenhaber B, Bläsi U. Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon. Microbiology. 2012 Jun;158(Pt 6):1543-52. doi: 10.1099/mic.0.053850-0. Epub 2012 Apr 5. PubMed PMID: 22493305. |
| [13] Shin SH, Kim S, Kim JY, Lee S, Um Y, Oh MK, Kim YR, Lee J, Yang KS. Complete genome sequence of Klebsiella oxytoca KCTC 1686, used in production of 2,3-butanediol. J Bacteriol. 2012 May;194(9):2371-2. doi: 10.1128/JB.00026-12. PubMed PMID: 22493189; PubMed Central PMCID: PMC3347058. |
| [14] Taniyama K, Itoh H, Takuwa A, Sasaki Y, Yajima S, Toyofuku M, Nomura N, Takaya N. Group X aldehyde dehydrogenases of Pseudomonas aeruginosa PAO1 degrade hydrazones. J Bacteriol. 2012 Mar;194(6):1447-56. doi: 10.1128/JB.06590-11. Epub 2012 Jan 20. PubMed PMID: 22267508; PubMed Central PMCID: PMC3294850. |
| [15] Lonjers ZT, Dickson EL, Chu TP, Kreutz JE, Neacsu FA, Anders KR, Shepherd JN. Identification of a new gene required for the biosynthesis of rhodoquinone in Rhodospirillum rubrum. J Bacteriol. 2012 Mar;194(5):965-71. doi: 10.1128/JB.06319-11. Epub 2011 Dec 22. PubMed PMID: 22194448; PubMed Central PMCID: PMC3294814. |
| [16] Hu W, Yang Z, Lux R, Zhao M, Wang J, He X, Shi W. Direct visualization of the interaction between pilin and exopolysaccharides of Myxococcus xanthus with eGFP-fused PilA protein. FEMS Microbiol Lett. 2012 Jan;326(1):23-30. doi: 10.1111/j.1574-6968.2011.02430.x. Epub 2011 Oct 21. PubMed PMID: 22092602; PubMed Central PMCID: PMC3454480. |
| [17] Yu H, Yuan M, Lu W, Yang J, Dai S, Li Q, Yang Z, Dong J, Sun L, Deng Z, Zhang W, Chen M, Ping S, Han Y, Zhan Y, Yan Y, Jin Q, Lin M. Complete genome sequence of the nitrogen-fixing and rhizosphere-associated bacterium Pseudomonas stutzeri strain DSM4166. J Bacteriol. 2011 Jul;193(13):3422-3. doi: 10.1128/JB.05039-11. Epub 2011 Apr 22. PubMed PMID: 21515765; PubMed Central PMCID: PMC3133286. |
| [18] Yang Z, Hu W, Chen K, Wang J, Lux R, Zhou ZH, Shi W. Alanine 32 in PilA is important for PilA stability and type IV pili function in Myxococcus xanthus. Microbiology. 2011 Jul;157(Pt 7):1920-8. doi: 10.1099/mic.0.049684-0. Epub 2011 Apr 14. PubMed PMID: 21493683; PubMed Central PMCID: PMC3167889. |
| [19] Faulds-Pain A, Birchall C, Aldridge C, Smith WD, Grimaldi G, Nakamura S, Miyata T, Gray J, Li G, Tang JX, Namba K, Minamino T, Aldridge PD. Flagellin redundancy in Caulobacter crescentus and its implications for flagellar filament assembly. J Bacteriol. 2011 Jun;193(11):2695-707. doi: 10.1128/JB.01172-10. Epub 2011 Mar 25. PubMed PMID: 21441504; PubMed Central PMCID: PMC3133132. |
| [20] Massimelli MJ, Sánchez DG, Buchieri MV, Olvera L, Beassoni PR, Schweizer HP, Morett E, Lisa AT. Choline catabolism, σ⁵⁴ factor and NtrC are required for the full expression of the Pseudomonas aeruginosa phosphorylcholine phosphatase gene. Microbiol Res. 2011 Jul 20;166(5):380-90. doi: 10.1016/j.micres.2010.07.004. Epub 2010 Oct 12. PubMed PMID: 20869215. |
| [21] Peng Z, Yan Y, Xu Y, Takeo M, Yu H, Zhao Z, Zhan Y, Zhang W, Lin M, Chen M. Improvement of an E. coli bioreporter for monitoring trace amounts of phenol by deletion of the inducible sigma54-dependent promoter. Biotechnol Lett. 2010 Sep;32(9):1265-70. doi: 10.1007/s10529-010-0317-6. Epub 2010 Jun 9. PubMed PMID: 20533077. |
| [22] Lu YK, Marden J, Han M, Swingley WD, Mastrian SD, Chowdhury SR, Hao J, Helmy T, Kim S, Kurdoglu AA, Matthies HJ, Rollo D, Stothard P, Blankenship RE, Bauer CE, Touchman JW. Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum. BMC Genomics. 2010 May 25;11:325. doi: 10.1186/1471-2164-11-325. PubMed PMID: 20500872; PubMed Central PMCID: PMC2890560. |
| [23] Marks ME, Castro-Rojas CM, Teiling C, Du L, Kapatral V, Walunas TL, Crosson S. The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol. 2010 Jul;192(14):3678-88. doi: 10.1128/JB.00255-10. Epub 2010 May 14. PubMed PMID: 20472802; PubMed Central PMCID: PMC2897358. |
| [24] Yang Z, Lux R, Hu W, Hu C, Shi W. PilA localization affects extracellular polysaccharide production and fruiting body formation in Myxococcus xanthus. Mol Microbiol. 2010 Jun;76(6):1500-13. doi: 10.1111/j.1365-2958.2010.07180.x. Epub 2010 Apr 23. PubMed PMID: 20444090; PubMed Central PMCID: PMC2935901. |
| [25] Burrows PC, Joly N, Buck M. A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9376-81. doi: 10.1073/pnas.1001188107. Epub 2010 May 3. PubMed PMID: 20439713; PubMed Central PMCID: PMC2889110. |
| [26] Strnad H, Lapidus A, Paces J, Ulbrich P, Vlcek C, Paces V, Haselkorn R. Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol. 2010 Jul;192(13):3545-6. doi: 10.1128/JB.00366-10. Epub 2010 Apr 23. PubMed PMID: 20418398; PubMed Central PMCID: PMC2897665. |
| [27] Zhao K, Liu M, Burgess RR. Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis. Nucleic Acids Res. 2010 Mar;38(4):1273-83. doi: 10.1093/nar/gkp1123. Epub 2009 Dec 6. PubMed PMID: 19969540; PubMed Central PMCID: PMC2831329. |
| [28] Juárez JF, Zamarro MT, Barragán MJ, Blázquez B, Boll M, Kuntze K, García JL, Díaz E, Carmona M. Identification of the Geobacter metallireducens bamVW two-component system, involved in transcriptional regulation of aromatic degradation. Appl Environ Microbiol. 2010 Jan;76(1):383-5. doi: 10.1128/AEM.02255-09. Epub 2009 Nov 13. PubMed PMID: 19915033; PubMed Central PMCID: PMC2798620. |
| [29] Reichenbach B, Göpel Y, Görke B. Dual control by perfectly overlapping sigma 54- and sigma 70- promoters adjusts small RNA GlmY expression to different environmental signals. Mol Microbiol. 2009 Dec;74(5):1054-70. doi: 10.1111/j.1365-2958.2009.06918.x. Epub 2009 Oct 27. PubMed PMID: 19843219. |
| [30] Koskenkorva-Frank TS, Kallio PT. Induction of Pseudomonas aeruginosa fhp and fhpR by reactive oxygen species. Can J Microbiol. 2009 Jun;55(6):657-63. doi: 10.1139/w09-024. PubMed PMID: 19767835. |
| [31] Zhang N, Joly N, Burrows PC, Jovanovic M, Wigneshweraraj SR, Buck M. The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins. Nucleic Acids Res. 2009 Oct;37(18):5981-92. doi: 10.1093/nar/gkp658. Epub 2009 Aug 19. PubMed PMID: 19692583; PubMed Central PMCID: PMC2764435. |
| [32] Papa R, Rippa V, Duilio A. Identification of the transcription factor responsible for L-malate-dependent regulation in the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. FEMS Microbiol Lett. 2009 Jun;295(2):177-86. doi: 10.1111/j.1574-6968.2009.01589.x. PubMed PMID: 19646180. |
| [33] Xiao Y, Wigneshweraraj SR, Weinzierl R, Wang YP, Buck M. Construction and functional analyses of a comprehensive sigma54 site-directed mutant library using alanine-cysteine mutagenesis. Nucleic Acids Res. 2009 Jul;37(13):4482-97. doi: 10.1093/nar/gkp419. Epub 2009 May 27. PubMed PMID: 19474350; PubMed Central PMCID: PMC2715252. |
| [34] Du BZ, Zeng W, Tao CM, Kang M, Liu M, Zhang ZR, Jia WX. [The influence of lysogenic phage on biofilm formation of Pseudomonas aeruginosa]. Sichuan Da Xue Xue Bao Yi Xue Ban. 2008 Nov;39(6):886-9. Chinese. PubMed PMID: 19253818. |
| [35] Bernardo LM, Johansson LU, Skärfstad E, Shingler V. sigma54-promoter discrimination and regulation by ppGpp and DksA. J Biol Chem. 2009 Jan 9;284(2):828-38. doi: 10.1074/jbc.M807707200. Epub 2008 Nov 13. PubMed PMID: 19008221. |
| [36] Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, Hancock RE, Brinkman FS. Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res. 2009 Jan;37(Database issue):D483-8. doi: 10.1093/nar/gkn861. Epub 2008 Oct 31. PubMed PMID: 18978025; PubMed Central PMCID: PMC2686508. |
| [37] de la Riva L, Badia J, Aguilar J, Bender RA, Baldoma L. The hpx genetic system for hypoxanthine assimilation as a nitrogen source in Klebsiella pneumoniae: gene organization and transcriptional regulation. J Bacteriol. 2008 Dec;190(24):7892-903. doi: 10.1128/JB.01022-08. Epub 2008 Oct 10. PubMed PMID: 18849434; PubMed Central PMCID: PMC2593211. |
| [38] Chung GT, Yoo JS, Oh HB, Lee YS, Cha SH, Kim SJ, Yoo CK. Complete genome sequence of Neisseria gonorrhoeae NCCP11945. J Bacteriol. 2008 Sep;190(17):6035-6. doi: 10.1128/JB.00566-08. Epub 2008 Jun 27. PubMed PMID: 18586945; PubMed Central PMCID: PMC2519540. |
| [39] da Silva Neto JF, Koide T, Abe CM, Gomes SL, Marques MV. Role of sigma54 in the regulation of genes involved in type I and type IV pili biogenesis in Xylella fastidiosa. Arch Microbiol. 2008 Mar;189(3):249-61. Epub 2007 Nov 6. PubMed PMID: 17985115. |
| [40] Leech AJ, Sprinkle A, Wood L, Wozniak DJ, Ohman DE. The NtrC family regulator AlgB, which controls alginate biosynthesis in mucoid Pseudomonas aeruginosa, binds directly to the algD promoter. J Bacteriol. 2008 Jan;190(2):581-9. Epub 2007 Nov 2. PubMed PMID: 17981963; PubMed Central PMCID: PMC2223705. |
| [41] Matta MK, Lioliou EE, Panagiotidis CH, Kyriakidis DA, Panagiotidis CA. Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon. J Bacteriol. 2007 Sep;189(17):6324-32. Epub 2007 Jul 6. PubMed PMID: 17616594; PubMed Central PMCID: PMC1951910. |
| [42] Janaszak A, Majczak W, Nadratowska B, Szalewska-Palasz A, Konopa G, Taylor A. A sigma54-dependent promoter in the regulatory region of the Escherichia coli rpoH gene. Microbiology. 2007 Jan;153(Pt 1):111-23. PubMed PMID: 17185540. |
| [43] Dago AE, Wigneshweraraj SR, Buck M, Morett E. A role for the conserved GAFTGA motif of AAA+ transcription activators in sensing promoter DNA conformation. J Biol Chem. 2007 Jan 12;282(2):1087-97. Epub 2006 Nov 6. PubMed PMID: 17090527. |
| [44] Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB. Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5. Epub 2006 Oct 2. Erratum in: Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19605. Eisen, J [corrected to Eisen, J A]. PubMed PMID: 17015832; PubMed Central PMCID: PMC1622800. |
| [45] Cirz RT, O'Neill BM, Hammond JA, Head SR, Romesberg FE. Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin. J Bacteriol. 2006 Oct;188(20):7101-10. PubMed PMID: 17015649; PubMed Central PMCID: PMC1636241. |
| [46] Leach RN, Gell C, Wigneshweraraj S, Buck M, Smith A, Stockley PG. Mapping ATP-dependent activation at a sigma54 promoter. J Biol Chem. 2006 Nov 3;281(44):33717-26. Epub 2006 Aug 22. PubMed PMID: 16926155. |
| [47] Bonner PJ, Black WP, Yang Z, Shimkets LJ. FibA and PilA act cooperatively during fruiting body formation of Myxococcus xanthus. Mol Microbiol. 2006 Sep;61(5):1283-93. PubMed PMID: 16925559. |
| [48] Regni C, Shackelford GS, Beamer LJ. Complexes of the enzyme phosphomannomutase/phosphoglucomutase with a slow substrate and an inhibitor. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Aug 1;62(Pt 8):722-6. Epub 2006 Jul 24. PubMed PMID: 16880541; PubMed Central PMCID: PMC2242917. |
| [49] Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods. 2006 Aug;3(8):623-8. PubMed PMID: 16862137. |
| [50] Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS, Mauchline TH, East AK, Quail MA, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol. 2006;7(4):R34. Epub 2006 Apr 26. Review. PubMed PMID: 16640791; PubMed Central PMCID: PMC1557990. |
| [51] Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, Cleland C, Dimitrijevic M, Doggett NA, Fawcett JJ, Glavina T, Goodwin LA, Green LD, Hill KK, Hitchcock P, Jackson PJ, Keim P, Kewalramani AR, Longmire J, Lucas S, Malfatti S, McMurry K, Meincke LJ, Misra M, Moseman BL, Mundt M, Munk AC, Okinaka RT, Parson-Quintana B, Reilly LP, Richardson P, Robinson DL, Rubin E, Saunders E, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Ticknor LO, Wills PL, Brettin TS, Gilna P. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. J Bacteriol. 2006 May;188(9):3382-90. Erratum in: J Bacteriol. 2006 Nov;188(21):7711. Brown, Nancy [added]; Green, Lance D [added]. PubMed PMID: 16621833; PubMed Central PMCID: PMC1447445. |
| [52] Delamarre SC, Batt CA. Comparative study of promoters for the production of polyhydroxyalkanoates in recombinant strains of Wautersia eutropha. Appl Microbiol Biotechnol. 2006 Aug;71(5):668-79. Epub 2005 Dec 15. PubMed PMID: 16362422. |
| [53] Kimmel JL, Tipton PA. Inactivation of GDP-mannose dehydrogenase from Pseudomonas aeruginosa by penicillic acid identifies a critical active site loop. Arch Biochem Biophys. 2005 Sep 15;441(2):132-40. PubMed PMID: 16111644. |
| [54] Li B, Brown EW, D'Agostino C, Leclerc JE, Cebula TA. Structure and distribution of the phosphoprotein phosphatase genes, prpA and prpB, among Shigella subgroups. Microbiology. 2005 Aug;151(Pt 8):2671-83. PubMed PMID: 16079345. |
| [55] Palmer KL, Mashburn LM, Singh PK, Whiteley M. Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology. J Bacteriol. 2005 Aug;187(15):5267-77. PubMed PMID: 16030221; PubMed Central PMCID: PMC1196007. |
| [56] Joly B, Pierre M, Auvin S, Colin F, Gottrand F, Guery B, Husson MO. Relative expression of Pseudomonas aeruginosa virulence genes analyzed by a real time RT-PCR method during lung infection in rats. FEMS Microbiol Lett. 2005 Feb 1;243(1):271-8. Erratum in: FEMS Microbiol Lett. 2005 Sep 1;250(1):173. Béatrice, Joly [corrected to Joly, Béatrice]; Maud, Pierre [corrected to Pierre, Maud]; Stéphane, Auvin [corrected to Auvin, Stéphane]; Franc Cois, Collet [corrected to Colin, Franc]; Frédéric, Gottrand [corrected to Gottrand, Frédéric]; Benoit, Guery [corrected to Guery, Benoit]. PubMed PMID: 15668029. |
| [57] Tucker N, D'autréaux B, Spiro S, Dixon R. DNA binding properties of the Escherichia coli nitric oxide sensor NorR: towards an understanding of the regulation of flavorubredoxin expression. Biochem Soc Trans. 2005 Feb;33(Pt 1):181-3. PubMed PMID: 15667300. |
| [58] Lloyd LJ, Jones SE, Jovanovic G, Gyaneshwar P, Rolfe MD, Thompson A, Hinton JC, Buck M. Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein G (PspG). J Biol Chem. 2004 Dec 31;279(53):55707-14. Epub 2004 Oct 13. PubMed PMID: 15485810. |
| [59] Burrows PC, Severinov K, Buck M, Wigneshweraraj SR. Reorganisation of an RNA polymerase-promoter DNA complex for DNA melting. EMBO J. 2004 Oct 27;23(21):4253-63. Epub 2004 Oct 7. PubMed PMID: 15470504; PubMed Central PMCID: PMC524386. |
| [60] Bordes P, Wigneshweraraj SR, Chaney M, Dago AE, 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 Oct;54(2):489-506. PubMed PMID: 15469519. |
| [61] Tucker NP, D'Autréaux B, Studholme DJ, Spiro S, Dixon R. DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria. J Bacteriol. 2004 Oct;186(19):6656-60. PubMed PMID: 15375149; PubMed Central PMCID: PMC516610. |
| [62] Cannon WV, Schumacher J, Buck M. Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein. Nucleic Acids Res. 2004 Aug 27;32(15):4596-608. Print 2004. PubMed PMID: 15333692; PubMed Central PMCID: PMC516047. |
| [63] Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EG. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res. 2003 Nov 15;31(22):6435-43. PubMed PMID: 14602901; PubMed Central PMCID: PMC275561. |
| [64] Medina G, Juárez K, Díaz R, Soberón-Chávez G. Transcriptional regulation of Pseudomonas aeruginosa rhlR, encoding a quorum-sensing regulatory protein. Microbiology. 2003 Nov;149(Pt 11):3073-81. PubMed PMID: 14600219. |
| [65] Gimenez R, Nuñez MF, Badia J, Aguilar J, Baldoma L. The gene yjcG, cotranscribed with the gene acs, encodes an acetate permease in Escherichia coli. J Bacteriol. 2003 Nov;185(21):6448-55. PubMed PMID: 14563880; PubMed Central PMCID: PMC219408. |
| [66] Huerta AM, Collado-Vides J. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol. 2003 Oct 17;333(2):261-78. PubMed PMID: 14529615. |
| [67] Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G. Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis. J Mol Biol. 2003 Sep 12;332(2):369-83. PubMed PMID: 12948488. |
| [68] Samsonova NN, Smirnov SV, Altman IB, Ptitsyn LR. Molecular cloning and characterization of Escherichia coli K12 ygjG gene. BMC Microbiol. 2003 Jan 31;3(1):2. PubMed PMID: 12617754; PubMed Central PMCID: PMC150594. |
| [69] Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K, Kohara M, Matsumoto M, Shimpo S, Tsuruoka H, Wada T, Yamada M, Tabata S. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 (supplement). DNA Res. 2002 Dec 31;9(6):225-56. PubMed PMID: 12597279. |
| [70] Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K, Kohara M, Matsumoto M, Shimpo S, Tsuruoka H, Wada T, Yamada M, Tabata S. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 2002 Dec 31;9(6):189-97. PubMed PMID: 12597275. |
| [71] Navarro-Lloréns JM, Martínez-García E, Tormo A. Enterobacter cloacae rpoS promoter and gene organization. Arch Microbiol. 2002 Dec;179(1):33-41. Epub 2002 Oct 31. PubMed PMID: 12471502. |
| [72] Skibinski DA, Golby P, Chang YS, Sargent F, Hoffman R, Harper R, Guest JR, Attwood MM, Berks BC, Andrews SC. Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR. J Bacteriol. 2002 Dec;184(23):6642-53. PubMed PMID: 12426353; PubMed Central PMCID: PMC135417. |
| [73] Jyot J, Dasgupta N, Ramphal R. FleQ, the major flagellar gene regulator in Pseudomonas aeruginosa, binds to enhancer sites located either upstream or atypically downstream of the RpoN binding site. J Bacteriol. 2002 Oct;184(19):5251-60. PubMed PMID: 12218010; PubMed Central PMCID: PMC135358. |
| [74] Kiupakis AK, Reitzer L. ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli. J Bacteriol. 2002 Jun;184(11):2940-50. PubMed PMID: 12003934; PubMed Central PMCID: PMC135064. |
| [75] Hutcheson SW, Bretz J, Sussan T, Jin S, Pak K. Enhancer-binding proteins HrpR and HrpS interact to regulate hrp-encoded type III protein secretion in Pseudomonas syringae strains. J Bacteriol. 2001 Oct;183(19):5589-98. PubMed PMID: 11544221; PubMed Central PMCID: PMC95450. |
| [76] Tian ZX, Li QS, Buck M, Kolb A, Wang YP. The CRP-cAMP complex and downregulation of the glnAp2 promoter provides a novel regulatory linkage between carbon metabolism and nitrogen assimilation in Escherichia coli. Mol Microbiol. 2001 Aug;41(4):911-24. PubMed PMID: 11532153. |
| [77] Reitzer L, Schneider BL. Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli. Microbiol Mol Biol Rev. 2001 Sep;65(3):422-44, table of contents. Review. PubMed PMID: 11528004; PubMed Central PMCID: PMC99035. |
| [78] Kuczyńska-Wisńik D, Laskowska E, Taylor A. Transcription of the ibpB heat-shock gene is under control of sigma(32)- and sigma(54)-promoters, a third regulon of heat-shock response. Biochem Biophys Res Commun. 2001 Jun 1;284(1):57-64. PubMed PMID: 11374870. |
| [79] Egener T, Martin DE, Sarkar A, Reinhold-Hurek B. Role of a ferredoxin gene cotranscribed with the nifHDK operon in N(2) fixation and nitrogenase "switch-off" of Azoarcus sp. strain BH72. J Bacteriol. 2001 Jun;183(12):3752-60. PubMed PMID: 11371540; PubMed Central PMCID: PMC95253. |
| [80] Ali NO, Bignon J, Rapoport G, Debarbouille M. Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. J Bacteriol. 2001 Apr;183(8):2497-504. PubMed PMID: 11274109; PubMed Central PMCID: PMC95166. |
| [81] Leonhartsberger S, Huber A, Lottspeich F, Böck A. The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system. J Mol Biol. 2001 Mar 16;307(1):93-105. PubMed PMID: 11243806. |
| [82] Göttfert M, Röthlisberger S, Kündig C, Beck C, Marty R, Hennecke H. Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J Bacteriol. 2001 Feb;183(4):1405-12. PubMed PMID: 11157954; PubMed Central PMCID: PMC95015. |
| [83] Masepohl B, Kaiser B, Isakovic N, Richard CL, Kranz RG, Klipp W. Urea utilization in the phototrophic bacterium Rhodobacter capsulatus is regulated by the transcriptional activator NtrC. J Bacteriol. 2001 Jan;183(2):637-43. PubMed PMID: 11133958; PubMed Central PMCID: PMC94920. |
| [84] Ikegami A, Nakasone K, Kato C, Nakamura Y, Yoshikawa I, Usami R, Horikoshi K. Glutamine synthetase gene expression at elevated hydrostatic pressure in a deep-sea piezophilic Shewanella violacea. FEMS Microbiol Lett. 2000 Nov 1;192(1):91-5. PubMed PMID: 11040434. |
| [85] Poggio S, Aguilar C, Osorio A, González-Pedrajo B, Dreyfus G, Camarena L. sigma(54) Promoters control expression of genes encoding the hook and basal body complex in Rhodobacter sphaeroides. J Bacteriol. 2000 Oct;182(20):5787-92. PubMed PMID: 11004178; PubMed Central PMCID: PMC94701. |
| [86] Kersulyte D, Mukhopadhyay AK, Shirai M, Nakazawa T, Berg DE. Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori. J Bacteriol. 2000 Oct;182(19):5300-8. PubMed PMID: 10986230; PubMed Central PMCID: PMC110970. |
| [87] Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 2000 Aug 3;406(6795):477-83. PubMed PMID: 10952301. |
| [88] Kumari S, Beatty CM, Browning DF, Busby SJ, Simel EJ, Hovel-Miner G, Wolfe AJ. Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol. 2000 Aug;182(15):4173-9. PubMed PMID: 10894724; PubMed Central PMCID: PMC101899. |
| [89] Palacios S, Escalante-Semerena JC. prpR, ntrA, and ihf functions are required for expression of the prpBCDE operon, encoding enzymes that catabolize propionate in Salmonella enterica serovar typhimurium LT2. J Bacteriol. 2000 Feb;182(4):905-10. PubMed PMID: 10648513; PubMed Central PMCID: PMC94363. |
| [90] Barrios H, Valderrama B, Morett E. Compilation and analysis of sigma(54)-dependent promoter sequences. Nucleic Acids Res. 1999 Nov 15;27(22):4305-13. PubMed PMID: 10536136; PubMed Central PMCID: PMC148710. |
| [91] Janausch IG, Unden G. The dcuD (former yhcL) gene product of escherichia coli as a member of the DcuC family of C4-dicarboxylate carriers: lack of evident expression. Arch Microbiol. 1999 Oct;172(4):219-26. PubMed PMID: 10525738. |
| [92] Pallen M. RpoN-dependent transcription of rpoH? Mol Microbiol. 1999 Jan;31(1):393. PubMed PMID: 9987139. |
| [93] Genschik P, Drabikowski K, Filipowicz W. Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon. J Biol Chem. 1998 Sep 25;273(39):25516-26. PubMed PMID: 9738023. |
| [94] Fraley CD, Kim JH, McCann MP, Matin A. The Escherichia coli starvation gene cstC is involved in amino acid catabolism. J Bacteriol. 1998 Aug;180(16):4287-90. PubMed PMID: 9696780; PubMed Central PMCID: PMC107428. |
| [95] Muse WB, Bender RA. The nac (nitrogen assimilation control) gene from Escherichia coli. J Bacteriol. 1998 Mar;180(5):1166-73. PubMed PMID: 9495755; PubMed Central PMCID: PMC107004. |
| [96] Pearson JP, Pesci EC, Iglewski BH. Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes. J Bacteriol. 1997 Sep;179(18):5756-67. PubMed PMID: 9294432; PubMed Central PMCID: PMC179464. |
| [97] Kinsella N, Guerry P, Cooney J, Trust TJ. The flgE gene of Campylobacter coli is under the control of the alternative sigma factor sigma54. J Bacteriol. 1997 Aug;179(15):4647-53. PubMed PMID: 9244248; PubMed Central PMCID: PMC179307. |
| [98] Michel-Reydellet N, Desnoues N, Elmerich C, Kaminski PA. Characterization of Azorhizobium caulinodans glnB and glnA genes: involvement of the P(II) protein in symbiotic nitrogen fixation. J Bacteriol. 1997 Jun;179(11):3580-7. PubMed PMID: 9171403; PubMed Central PMCID: PMC179151. |
| [99] van Heeswijk WC, Hoving S, Molenaar D, Stegeman B, Kahn D, Westerhoff HV. An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli. Mol Microbiol. 1996 Jul;21(1):133-46. PubMed PMID: 8843440. |
| [100] Maier T, Binder U, Böck A. Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism. Arch Microbiol. 1996 May;165(5):333-41. PubMed PMID: 8661925. |
| [101] Gardan R, Rapoport G, Débarbouillé M. Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J Mol Biol. 1995 Jun 23;249(5):843-56. PubMed PMID: 7540694. |
| [102] Schlensog V, Lutz S, Böck A. Purification and DNA-binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli. J Biol Chem. 1994 Jul 29;269(30):19590-6. PubMed PMID: 8034727. |
| [103] Cebolla A, Ruiz-Berraquero F, Palomares AJ. Analysis of the expression from Rhizobium meliloti fix-promoters in other Rhizobium backgrounds. Microbiology. 1994 Mar;140 ( Pt 3):443-53. PubMed PMID: 8012569. |
| [104] de Zamaroczy M, Paquelin A, Elmerich C. Functional organization of the glnB-glnA cluster of Azospirillum brasilense. J Bacteriol. 1993 May;175(9):2507-15. PubMed PMID: 8097514; PubMed Central PMCID: PMC204551. |
| [105] Zielinski NA, Maharaj R, Roychoudhury S, Danganan CE, Hendrickson W, Chakrabarty AM. Alginate synthesis in Pseudomonas aeruginosa: environmental regulation of the algC promoter. J Bacteriol. 1992 Dec;174(23):7680-8. PubMed PMID: 1447138; PubMed Central PMCID: PMC207481. |
| [106] Santero E, Hoover TR, North AK, Berger DK, Porter SC, Kustu S. Role of integration host factor in stimulating transcription from the sigma 54-dependent nifH promoter. J Mol Biol. 1992 Oct 5;227(3):602-20. PubMed PMID: 1404379. |
| [107] Timm A, Steinbüchel A. Cloning and molecular analysis of the poly(3-hydroxyalkanoic acid) gene locus of Pseudomonas aeruginosa PAO1. Eur J Biochem. 1992 Oct 1;209(1):15-30. PubMed PMID: 1396693. |
| [108] Martin-Verstraete I, Débarbouillé M, Klier A, Rapoport G. Mutagenesis of the Bacillus subtilis "-12, -24" promoter of the levanase operon and evidence for the existence of an upstream activating sequence. J Mol Biol. 1992 Jul 5;226(1):85-99. PubMed PMID: 1619665. |
| [109] Ingmer H, Atlung T. Expression and regulation of a dnaA homologue isolated from Pseudomonas putida. Mol Gen Genet. 1992 Apr;232(3):431-9. PubMed PMID: 1588913. |
| [110] Foster-Hartnett D, Kranz RG. Analysis of the promoters and upstream sequences of nifA1 and nifA2 in Rhodobacter capsulatus; activation requires ntrC but not rpoN. Mol Microbiol. 1992 Apr;6(8):1049-60. PubMed PMID: 1374828. |
| [111] Popham D, Keener J, Kustu S. Purification of the alternative sigma factor, sigma 54, from Salmonella typhimurium and characterization of sigma 54-holoenzyme. J Biol Chem. 1991 Oct 15;266(29):19510-8. PubMed PMID: 1918063. |
| [112] Weiner L, Brissette JL, Model P. Stress-induced expression of the Escherichia coli phage shock protein operon is dependent on sigma 54 and modulated by positive and negative feedback mechanisms. Genes Dev. 1991 Oct;5(10):1912-23. PubMed PMID: 1717346. |
| [113] Guerry P, Alm RA, Power ME, Logan SM, Trust TJ. Role of two flagellin genes in Campylobacter motility. J Bacteriol. 1991 Aug;173(15):4757-64. PubMed PMID: 1856171; PubMed Central PMCID: PMC208154. |
| [114] Romeo JM, Zusman DR. Transcription of the myxobacterial hemagglutinin gene is mediated by a sigma 54-like promoter and a cis-acting upstream regulatory region of DNA. J Bacteriol. 1991 May;173(9):2969-76. PubMed PMID: 1850403; PubMed Central PMCID: PMC207880. |
| [115] Lutz S, Jacobi A, Schlensog V, Böhm R, Sawers G, Böck A. Molecular characterization of an operon (hyp) necessary for the activity of the three hydrogenase isoenzymes in Escherichia coli. Mol Microbiol. 1991 Jan;5(1):123-35. PubMed PMID: 1849603. |
| [116] Hoover TR, Santero E, Porter S, Kustu S. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell. 1990 Oct 5;63(1):11-22. PubMed PMID: 2208275. |
| [117] Martin-Verstraete I, Débarbouillé M, Klier A, Rapoport G. Levanase operon of Bacillus subtilis includes a fructose-specific phosphotransferase system regulating the expression of the operon. J Mol Biol. 1990 Aug 5;214(3):657-71. PubMed PMID: 2117666. |
| [118] Su W, Porter S, Kustu S, Echols H. DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5504-8. PubMed PMID: 2164685; PubMed Central PMCID: PMC54353. |
| [119] Lutz S, Böhm R, Beier A, Böck A. Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli. Mol Microbiol. 1990 Jan;4(1):13-20. PubMed PMID: 2181234. |
| [120] de Zamaroczy M, Delorme F, Elmerich C. Regulation of transcription and promoter mapping of the structural genes for nitrogenase (nifHDK) of Azospirillum brasilense Sp7. Mol Gen Genet. 1989 Dec;220(1):88-94. PubMed PMID: 2608030. |
| [121] Reitzer LJ, Movsas B, Magasanik B. Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase. J Bacteriol. 1989 Oct;171(10):5512-22. PubMed PMID: 2571609; PubMed Central PMCID: PMC210391. |
| [122] Popham DL, Szeto D, Keener J, Kustu S. Function of a bacterial activator protein that binds to transcriptional enhancers. Science. 1989 Feb 3;243(4891):629-35. PubMed PMID: 2563595. |
| [123] Gubler M, Zürcher T, Hennecke H. The Bradyrhizobium japonicum fixBCX operon: identification of fixX and of a 5' mRNA region affecting the level of the fixBCX transcript. Mol Microbiol. 1989 Feb;3(2):141-8. PubMed PMID: 2503674. |
| [124] Nees DW, Stein PA, Ludwig RA. The Azorhizobium caulinodans nifA gene: identification of upstream-activating sequences including a new element, the 'anaerobox'. Nucleic Acids Res. 1988 Oct 25;16(20):9839-53. PubMed PMID: 3186446; PubMed Central PMCID: PMC338782. |
| [125] Joerger RD, Bishop PE. Nucleotide sequence and genetic analysis of the nifB-nifQ region from Azotobacter vinelandii. J Bacteriol. 1988 Apr;170(4):1475-87. PubMed PMID: 2450865; PubMed Central PMCID: PMC210991. |
| [126] Thöny B, Fischer HM, Anthamatten D, Bruderer T, Hennecke H. The symbiotic nitrogen fixation regulatory operon (fixRnifA) of Bradyrhizobium japonicum is expressed aerobically and is subject to a novel, nifA-independent type of activation. Nucleic Acids Res. 1987 Oct 26;15(20):8479-99. PubMed PMID: 3313281; PubMed Central PMCID: PMC306372. |
| [127] Ninfa AJ, Reitzer LJ, Magasanik B. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers. Cell. 1987 Sep 25;50(7):1039-46. PubMed PMID: 3304660. |
| [128] Schmitz G, Dürre P, Mullenbach G, Ames GF. Nitrogen regulation of transport operons: analysis of promoters argTr and dhuA. Mol Gen Genet. 1987 Sep;209(2):403-7. PubMed PMID: 3118148. |
| [129] Birkmann A, Zinoni F, Sawers G, Böck A. Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli. Arch Microbiol. 1987 Jun;148(1):44-51. PubMed PMID: 2443100. |
| [130] Nohno T, Saito T. Two transcriptional start sites found in the promoter region of Escherichia coli glutamine permease operon, glnHPQ. Nucleic Acids Res. 1987 Mar 25;15(6):2777. PubMed PMID: 3550701; PubMed Central PMCID: PMC340687. |
| [131] Yun AC, Szalay AA. Structural genes of dinitrogenase and dinitrogenase reductase are transcribed from two separate promoters in the broad host range cowpea Rhizobium strain IRc78. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7358-62. PubMed PMID: 16578778; PubMed Central PMCID: PMC392145. |
| [132] Dixon R. Tandem promoters determine regulation of the Klebsiella pneumoniae glutamine synthetase (glnA) gene. Nucleic Acids Res. 1984 Oct 25;12(20):7811-30. PubMed PMID: 6149519; PubMed Central PMCID: PMC320202. |
| [133] Osorio AV, Servín-González L, Rocha M, Covarrubias AA, Bastarrachea F. cis-Dominant, glutamine synthetase constitutive mutations of Escherichia coli independent of activation by the glnG and glnF products. Mol Gen Genet. 1984;194(1-2):114-23. PubMed PMID: 6145084. |