A transcriptional-switch model for Slr1738-controlled gene expression in the cyanobacterium Synechocystis

BMC Structural Biology

Volumn 12, Issue , 2012, Pages

  Garcin, Paul ^a   Delalande, Olivier ^a   Zhang, Ju Yuan ^a   Cassier Chauvat, Corinne ^a,b   Chauvat, Franck ^a   Boulard, Yves ^a  

^a SERVICE DE CHIMIE BIOORGANIQUE ET DE MARQUAGE   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; CYANOBACTERIUM; DNA STRUCTURE; GENE EXPRESSION; GENETIC TRANSCRIPTION; OXIDATIVE STRESS; PROTEIN DNA INTERACTION; SEQUENCE HOMOLOGY; SLR1738 GENE; SYNECHOCYSTIS; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; GC RICH SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; HOMEOSTASIS; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE;

SYNECHOCYSTIS; SYNECHOCYSTIS SP.;

BACTERIAL DNA; BACTERIAL PROTEIN; IRON;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; DNA, BACTERIAL; GC RICH SEQUENCE; GENE EXPRESSION REGULATION, BACTERIAL; HOMEOSTASIS; IRON; MODELS, GENETIC; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OXIDATIVE STRESS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; SYNECHOCYSTIS; TRANSCRIPTION, GENETIC;

EID: 84862790110     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-12-1     Document Type: Article

References (70)

1. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? Pabo CO, Nekludova L, J Mol Biol 2000 301 597 624 10.1006/jmbi.2000.3918 10966773
2. Recent progress and future directions in protein-protein docking. Ritchie DW, Curr Protein Pept Sci 2008 9 1 15 10.2174/138920308783565741 18336319
3. Iron and metal regulation in bacteria. Hantke K, Curr Opin Microbiol 2001 4 172 177 10.1016/S1369-5274(00)00184-3 11282473 (Pubitemid 32294419)
4. Functional specialization within the Fur family of metalloregulators. Lee J-W, Helmann JD, Biometals 2007 20 485 499 10.1007/s10534-006-9070-7 17216355 (Pubitemid 46776584)
5. PerR vs OhrR: selective peroxide sensing in Bacillus subtilis. Duarte V, Latour J-M, Mol Biosyst 2010 6 316 323 10.1039/b915042k 20094649
6. The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation. Lee JW, Helmann JD, Nature 2006 440 363 367 10.1038/nature04537 16541078
7. Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis. Traore DAK, El Ghazouani A, Ilango S, Dupuy J, Jacquamet L, Ferrer J-L, Caux-Thang C, Duarte V, Latour J-M, Mol Microbiol 2006 61 1211 1219 10.1111/j.1365-2958.2006.05313.x 16925555 (Pubitemid 44215422)
8. Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding. Jacquamet L, Traore DAK, Ferrer JL, Proux O, Testemale D, Hazemann JL, Nazarenko E, El Ghazouani A, Caux-Thang C, Duarte V, Latour JM, Mol Microbiol 2009 73 20 31 10.1111/j.1365-2958.2009.06753.x 19508285
9. The origin of atmospheric oxygen on Earth: the innovation of oxygenic photosynthesis. Dismukes GC, Klimov VV, Baranov SV, Kozlov YN, DasGupta J, Tyryshkin A, Proc Natl Acad Sci USA 2001 98 2170 2175 10.1073/pnas.061514798 11226211 (Pubitemid 32209454)
10. Applications of cyanobacteria in biotechnology. Abed RMM, Dobretsov S, Sudesh K, J Appl Microbiol 2009 106 1 12 10.1111/j.1365-2672.2008.03918.x 19191979
11. Aquatic phototrophs: efficient alternatives to land-based crops for biofuels. Dismukes GC, Carrieri D, Bennette N, Ananyev GM, Posewitz MC, Curr Opin Biotechnol 2008 19 235 240 10.1016/j.copbio.2008.05.007 18539450
12. Panning for chemical gold: marine bacteria as a source of new therapeutics. Williams PG, Trends Biotechnol 2009 27 45 52 10.1016/j.tibtech. 2008.10.005 19022511
13. Oxidative stress in cyanobacteria. Latifi A, Ruiz M, Zhang C-C, FEMS Microbiol Rev 2009 33 258 278 10.1111/j.1574-6976.2008.00134.x 18834454
14. Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator. Houot L, Floutier M, Marteyn B, Michaut M, Picciocchi A, Legrain P, Aude J-C, Cassier-Chauvat C, Chauvat F, BMC Genomics 2007 8 350 10.1186/1471-2164-8-350 17910763
15. Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Kobayashi M, Ishizuka T, Katayama M, Kanehisa M, Bhattacharyya-Pakrasi M, Pakrasi HB, Ikeuchi M, Plant Cell Physiol 2004 45 290 299 10.1093/pcp/pch034 15047877 (Pubitemid 38473457)
16. Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. strain PCC 6803. Li H, Singh AK, McIntyre LM, Sherman LA, J Bacteriol 2004 186 3331 3345 10.1128/JB.186.11.3331- 3345.2004 15150218 (Pubitemid 38661528)
17. Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. Singh AK, Elvitigala T, Cameron JC, Ghosh BK, Bhattacharyya-Pakrasi M, Pakrasi HB, BMC Syst Biol 2010 4 105 20678200
18. A conjugative plasmid vector for promoter analysis in several cyanobacteria of the genera Synechococcus and Synechocystis. Marraccini P, Bulteau S, Cassier-Chauvat C, Mermet-Bouvier P, Chauvat F, Plant Mol Biol 1993 23 905 909 10.1007/BF00021546 8251644 (Pubitemid 2021271)
19. Promoter element spacing controls basal expression and light inducibility of the cyanobacterial secA gene. Mazouni K, Bulteau S, Cassier-Chauvat C, Chauvat F, Mol Microbiol 1998 30 1113 1122 10.1046/j.1365-2958.1998.01145.x 9988485 (Pubitemid 28550132)
20. Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator. Pohl E, Haller JC, Mijovilovich A, Meyer-Klaucke W, Garman E, Vasil ML, Mol Microbiol 2003 47 903 915 10.1046/j.1365-2958.2003.03337.x 12581348 (Pubitemid 36232790)
21. Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Stote RH, Karplus M, Proteins 1995 23 12 31 10.1002/prot. 340230104 8539245
22. A metallothionein containing a zinc finger within a four-metal cluster protects a bacterium from zinc toxicity. Blindauer CA, Harrison MD, Parkinson JA, Robinson AK, Cavet JS, Robinson NJ, Sadler PJ, Proc Natl Acad Sci USA 2001 98 9593 9598 10.1073/pnas.171120098 11493688 (Pubitemid 32769348)
23. A metallothionein containing a zinc finger within a four-metal cluster protects a bacterium from zinc toxicity. Blindauer CA, Harrison MD, Parkinson JA, Robinson AK, Cavet JS, Robinson NJ, Sadler PJ, Proc Natl Acad Sci USA 2001 98 9593 9598 10.1073/pnas.171120098 11493688 (Pubitemid 32769348)
24. Ferric uptake regulation protein acts as a repressor, employing iron (II) as a cofactor to bind the operator of an iron transport operon in Escherichia coli. Bagg A, Neilands JB, Biochemistry 1987 26 5471 5477 10.1021/bi00391a039 2823881
25. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA, AMBER 9 University of California, San Francisco 2006
26. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE III, Acc Chem Res 2000 33 889 897 10.1021/ar000033j 11123888 (Pubitemid 32056774)
27. MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. Gohlke H, Case DA, Converging free energy estimates, J Comput Chem 2004 25 238 250 10.1002/jcc.10379 14648622
28. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. Masukawa KM, Kollman PA, Kuntz ID, J Med Chem 2003 46 5628 5637 10.1021/jm030060q 14667217 (Pubitemid 37543314)
29. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. Wang J, Morin P, Wang W, Kollman PA, J Am Chem Soc 2001 123 5221 5230 10.1021/ja003834q 11457384 (Pubitemid 32910665)
30. Reduced surface: an efficient way to compute molecular surfaces. Sanner MF, Olson AJ, Spehner JC, Biopolymers 1996 38 305 320 10.1002/(SICI)1097- 0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y 8906967
31. Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information. Pellegrini-Calace M, Thornton JM, Nucleic Acids Res 2005 33 2129 2140 10.1093/nar/gki349 15831786 (Pubitemid 41439881)
32. On the transcriptional regulation of methicillin resistance: MecI repressor in complex with its operator. Garcia-Castellanos R, Mallorqui-Fernandez G, Marrero A, Potempa J, Coll M, Gomis-Ruth FX, J Biol Chem 2004 279 17888 17896 10.1074/jbc.M313123200 14960592 (Pubitemid 38560557)
33. Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Hong M, Fuangthong M, Helmann JD, Brennan RG, Mol Cell 2005 20 131 141 10.1016/j.molcel.2005.09.013 16209951 (Pubitemid 41396568)
34. Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain. Pohl E, Holmes RK, Hol WG, J Mol Biol 1999 292 653 667 10.1006/jmbi.1999.3073 10497029 (Pubitemid 29457326)
35. Crystal structure of an IdeR-DNA complex reveals a conformational change in activated IdeR for base-specific interactions. Wisedchaisri G, Holmes RK, Hol WGJ, J Mol Biol 2004 342 1155 1169 10.1016/j.jmb.2004.07.083 15351642 (Pubitemid 39207894)
36. Characterization of the DNA-binding site in the ferric uptake regulator protein from Escherichia coli by UV crosslinking and mass spectrometry. Tiss A, Barre O, Michaud-Soret I, Forest E, FEBS Lett 2005 579 5454 5460 10.1016/j.febslet.2005.08.067 16212958 (Pubitemid 41455614)
37. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S, DNA Res 1996 3 185 209 10.1093/dnares/3.3.185 8905238 (Pubitemid 126682796)
38. A conjugative plasmid vector for promoter analysis in several cyanobacteria of the genera Synechococcus and Synechocystis. Marraccini P, Bulteau S, Cassier-Chauvat C, Mermet-Bouvier P, Chauvat F, Plant Mol Biol 1993 23 905 909 10.1007/BF00021546 8251644 (Pubitemid 2021271)
39. Function and regulation of the cyanobacterial genes lexA, recA and ruvB: LexA is critical to the survival of cells facing inorganic carbon starvation. Domain F, Houot L, Chauvat F, Cassier-Chauvat C, Mol Microbiol 2004 53 65 80 10.1111/j.1365-2958.2004.04100.x 15225304 (Pubitemid 38901380)
40. Unravelling the regulatory function of FurA in Anabaena sp. PCC 7120 through 2-D DIGE proteomic analysis. Gonzalez A, Bes MT, Peleato ML, Fillat MF, J Proteomics 2011 74 660 671 10.1016/j.jprot.2011.02.001 21315197
41. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Pribnow D, Proc Natl Acad Sci USA 1975 72 784 788 10.1073/pnas.72.3. 784 1093168
42. Amplification of 5' end cDNA with 'new RACE'. Scotto-Lavino E, Du G, Frohman MA, Nat Protoc 2006 1 3056 3061 17406568
43. The gene ssl3076 encodes a protein mediating the salt-induced expression of ggpS for the biosynthesis of the compatible solute glucosylglycerol in Synechocystis sp. strain PCC 6803. Klahn S, Hohne A, Simon E, Hagemann M, J Bacteriol 2010 192 4403 4412 10.1128/JB.00481-10 20601470
44. The carbon metabolism-controlled Synechocystis gap2 gene harbours a conserved enhancer element and a Gram-positive-like -16 promoter box retained in some chloroplast genes. Figge RM, Cassier-Chauvat C, Chauvat F, Cerff R, Mol Microbiol 2000 36 44 54 10.1046/j.1365-2958.2000.01806.x 10760162 (Pubitemid 30195387)
45. Expression and regulation of the crucial plant-like ferredoxin of cyanobacteria. Mazouni K, Domain F, Chauvat F, Cassier-Chauvat C, Mol Microbiol 2003 49 1019 1029 10.1046/j.1365-2958.2003.03609.x 12890025 (Pubitemid 36981346)
46. Unusual regulatory elements for iron deficiency induction of the idiA gene of Synechococcus elongatus PCC 7942. Michel KP, Pistorius EK, Golden SS, J Bacteriol 2001 183 5015 5024 10.1128/JB.183.17.5015-5024.2001 11489854 (Pubitemid 32750929)
47. Escherichia coli and Salmonella. Records MT, Reznikoff WS, Craig ML, McQuade KL, Schlax PJ, Neidhardt American Society for Microbiology, Washington DC, Ingraham FC, Lin JL, Magasanik ECC, Reznikoff B, Riley WS, Schaechter M, Umbarger HE, 1996 792 820
48. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. Barne KA, Bown JA, Busby SJ, Minchin SD, Embo J 1997 16 4034 4040 10.1093/emboj/16.13. 4034 9233812 (Pubitemid 27281018)
49. Structural changes of Escherichia coli ferric uptake regulator during metal-dependent dimerization and activation explored by NMR and X-ray crystallography. Pecqueur L, D'Autreaux B, Dupuy J, Nicolet Y, Jacquamet L, Brutscher B, Michaud-Soret I, Bersch B, J Biol Chem 2006 281 21286 21295 10.1074/jbc.M601278200 16690618 (Pubitemid 44121126)
50. The helix-turn-helix DNA binding motif. Brennan RG, Matthews BW, J Biol Chem 1989 264 1903 1906 2644244 (Pubitemid 19057656)
51. Secondary structure of the ETS domain places murine Ets-1 in the superfamily of winged helix-turn-helix DNA-binding proteins. Donaldson LW, Petersen JM, Graves BJ, McIntosh LP, Biochemistry 1994 33 13509 13516 10.1021/bi00250a001 7947760 (Pubitemid 24381911)
52. Structural dynamics and functional domains of the fur protein. Coy M, Neilands JB, Biochemistry 1991 30 8201 8210 10.1021/bi00247a016 1868094
53. Electrospray ionization mass spectrometry analysis of the apo- and metal-substituted forms of the Fur protein. Michaud-Soret I, Adrait A, Jaquinod M, Forest E, Touati D, Latour JM, FEBS Lett 1997 413 473 476 10.1016/S0014-5793(97)00963-0 9303558 (Pubitemid 27371486)
54. Recognition of DNA by three ferric uptake regulator (Fur) homologs in Bacillus subtilis. Fuangthong M, Helmann JD, J Bacteriol 2003 185 6348 6357 10.1128/JB.185.21.6348-6357.2003 14563870 (Pubitemid 37305535)
55. Helical parameters, fluctuations, alternative hydrogen bonding, and bending in oligonucleotides containing a mismatched base-pair by NOESY distance restrained and distance free molecular dynamics. Cognet JAH, Boulard Y, Fazakerley GV, Journal of Molecular Biology 1995 246 209 226 10.1006/jmbi.1994.0077 7853398
56. Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water. Roll C, Ketterlé C, Faibis V, Fazakerley GV, Boulard Y, Biochemistry 1998 37 4059 4070 10.1021/bi972377w 9521727 (Pubitemid 28166427)
57. Solution structures of an oligonucleotide containing a N-(2'-deoxy - D-erythropentofuranosyl)formamide-guanine base pair by NMR and molecular dynamics studies. Maufrais C, Fazakerley GV, Guy A, Cadet J, Boulard Y, Biochemistry 2000 39 5614 5621 10.1021/bi9928849 10820035 (Pubitemid 30257104)
58. Structural study of DNA duplex containing a N-(2'-deoxy - D-erythropentofuranosyl)-formamide frameshifts by NMR and restrained molecular dynamics. Maufrais C, Fazakerley GV, Cadet J, Boulard Y, Nucleic Acids Research 2003 31 1 11 10.1093/nar/gkg120 12519937 (Pubitemid 36150323)
59. NMR Assessment of the global shape of a non-labeled DNA dodecamer containing a tandem of G-T mismatches. Alvarez Salgado F, Desvaux H, Boulard Y, Magnetic Resonance in Chemistry 2006 44 1081 1089 10.1002/mrc.1902 16972306 (Pubitemid 44861607)
60. DNA conformations and their sequence preferences. Svozil D, Kalina J, Omelka M, Schneider B, Nucleic Acids Res 2008 36 3690 3706 10.1093/nar/gkn260 18477633 (Pubitemid 351917531)
61. 3DNA: a software package for the analysis, rebuilding and visualization of the three-dimensional nucleic acid structures. Lu X-J, Olson WK, Nucleic Acids Research 20031 31 5108 5121 (Pubitemid 37441878)
62. Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence. Baichoo N, Helmann JD, J Bacteriol 2002 184 5826 5832 10.1128/JB.184.21.5826-5832.2002 12374814 (Pubitemid 35168229)
63. Operator sequences of the aerobactin operon of plasmid ColV-K30 binding the ferric uptake regulation (fur) repressor. de Lorenzo V, Wee S, Herrero M, Neilands JB, J Bacteriol 1987 169 2624 2630 3294800 (Pubitemid 17104324)
64. Binding of the fur (ferric uptake regulator) repressor of Escherichia coli to arrays of the GATAAT sequence. Escolar L, Perez-Martin J, de Lorenzo V, J Mol Biol 1998 283 537 547 10.1006/jmbi.1998.2119 9784364 (Pubitemid 28486718)
65. Fur-DNA interactions at the bidirectional fepDGC-entS promoter region in Escherichia coli. Lavrrar JL, Christoffersen CA, McIntosh MA, J Mol Biol 2002 322 983 995 10.1016/S0022-2836(02)00849-5 12367523 (Pubitemid 35266507)
66. Architecture of a fur binding site: a comparative analysis. Lavrrar JL, McIntosh MA, J Bacteriol 2003 185 2194 2202 10.1128/JB.185.7.2194-2202.2003 12644489 (Pubitemid 36367200)
67. Hubbard SJ, Thornton JM, NACCESS 1993
68. Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. Singh AK, Elvitigala T, Cameron JC, Ghosh BK, Bhattacharyya-Pakrasi M, Pakrasi HB, BMC Syst Biol 2010 4 105 20678200
69. Oligomerization properties of FurA from cyanobacterium Anabaena sp. 7120: Direct visualization by in situ atomic force microscopy under different redox conditions. Lostao A, Peleato ML, Gomez-Moreno C, Fillat MF, Biochim Biophys Acta 2010 1804 1723 1729 20417733
70. Evidence of an unusually long operator for the fur repressor in the aerobactin promoter of Escherichia coli. Escolar L, Perez-Martin J, de Lorenzo V, J Biol Chem 2000 275 24709 24714 10.1074/jbc.M002839200 10833520 (Pubitemid 30626572)