Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: Coordinate action of TbpD and TfbA

BMC Genetics

Volumn 8, Issue , 2007, Pages

  Coker, James A ^a   DasSarma, Shiladitya ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE; TRANSCRIPTION FACTOR; ARCHAEAL PROTEIN; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR B, ARCHAEA; TRANSCRIPTION FACTOR IIB; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CELL VIABILITY; CONTROLLED STUDY; DOWN REGULATION; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENUS; HALOBACTERIUM; HALOPHILIC ARCHAEON; HEAT SHOCK RESPONSE; KNOCKOUT GENE; MULTIGENE FAMILY; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PROKARYOTE; PROMOTER REGION; SCREENING; SEQUENCE ALIGNMENT; TEMPERATURE; TRANSCRIPTOMICS; DNA MICROARRAY; GENE; GENE EXPRESSION REGULATION; GENETICS; PHYLOGENY;

ARCHAEA; EUKARYOTA; HALOBACTERIA; HALOBACTERIUM; HALOBACTERIUM SP. NRC-1; PROKARYOTA;

ARCHAEAL PROTEINS; GENE EXPRESSION REGULATION, ARCHAEAL; GENES, ARCHAEAL; HALOBACTERIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTOR TFIIB; TRANSCRIPTION, GENETIC;

EID: 37049013315     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-8-61     Document Type: Article

References (59)

1. Bell SD Jackson SP Transcription and translation in Archaea: A mosaic of eukaryal and bacterial features Trends Microbiol 1998, 6:222-228 10.1016/ S0966-842X(98)01281-5 9675798
2. Bell SD Jackson SP Mechanism of autoregulation by an archaeal transcriptional repressor J Biol Chem 2000, 275:31624-31629 10.1074/ jbc.M005422200 10900210
3. Reich CI McNeil LK Brace JL Brucker JK Olsen GJ Archaeal RecA homologues: Different response to DNA-damaging agents in mesophilic and thermophilic Archaea Extremophiles 2001, 5:265-275 10.1007/s007920100197 11523896
4. Thomm M Wich G An archaebacterial promoter element for stable RNA genes with homology to the TATA box of higher eukaryotes Nucleic Acids Res 1988, 16:151-163 334618 2448746 10.1093/nar/16.1.151
5. Zillig W Stetter KO Tobien M DNA-dependent RNA polymerase from Halobacterium halobium Eur J Biochem 1978, 91:193-199 10.1111/ j.1432-1033.1978.tb20951.x 720336
6. Littlefield O Korkhin Y Sigler PB The structural basis for the oriented assembly of a TBP/TFB/promoter complex Proc Natl Acad Sci U S A 1999, 96:13668-13673 24122 10570130 10.1073/pnas.96.24.13668
7. Ouhammouch M Geiduschek EP An expanding family of archaeal transcriptional activators Proc Natl Acad Sci U S A 2005, 102:15423-15428 1266154 16230629 10.1073/pnas.0508043102
8. Reiter WD Hudepohl U Zillig W Mutational analysis of an archaebacterial promoter: Essential role of a TATA box for transcription efficiency and start-site selection in vitro Proc Natl Acad Sci U S A 1990, 87:9509-9513 55201 2124695 10.1073/pnas.87.24.9509
9. Goede B Naji S von Kampen O Ilg K Thomm M Protein-protein interactions in the archaeal transcriptional machinery: Binding studies of isolated RNA polymerase subunits and transcription factors J Biol Chem 2006, 281:30581-30592 10.1074/jbc.M605209200 16885163
10. Baliga NS DasSarma S Saturation mutagenesis of the haloarchaeal bop gene promoter: Identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity Mol Microbiol 2000, 36:1175-1183 10.1046/j.1365-2958.2000.01915.x 10844701
11. Baliga NS DasSarma S Saturation mutagenesis of the TATA box and upstream activator sequence in the haloarchaeal bop gene promoter J Bacteriol 1999, 181:2513-2518 93679 10198017
12. Ng WV Kennedy SP Mahairas GG Berquist B Pan M Shukla HD Lasky SR Baliga NS Thorsson V Sbrogna J Swartzell S Weir D Hall J Dahl TA Welti R Goo YA Leithauser B Keller K Cruz R Danson MJ Hough DW Maddocks DG Jablonski PE Krebs MP Angevine CM Dale H Isenbarger TA Peck RF Pohlschroder M Spudich JL Jung KW Alam M Freitas T Hou S Daniels CJ Dennis PP Omer AD Ebhardt H Lowe TM Liang P Riley M Hood L DasSarma S Genome sequence of Halobacterium species NRC-1 Proc Natl Acad Sci USA 2000, 97:12176-12181 17314 11016950 10.1073/pnas.190337797
13. Leffers H Gropp F Lottspeich F Zillig W Garrett RA Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae J Mol Biol 1989, 206:1-17 10.1016/ 0022-2836(89)90519-6 2495365
14. DasSarma S Genome sequence of an extremely halophilic archaeon Microbial Genomes Totowa, NJ, Humana Press, Inc. Fraser T, Read T and Nelson KE 2004:383-399
15. Baliga NS Goo YA Ng WV Hood L Daniels CJ DasSarma S Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol 2000, 36:1184-1185 10.1046/ j.1365-2958.2000.01916.x 10844702
16. Thompson DK Palmer JR Daniels CJ Expression and heat-responsive regulation of a TFIIB homologue from the archaeon Haloferax volcanii Mol Microbiol 1999, 33:1081-1092 10.1046/j.1365-2958.1999.01551.x 10476041
17. Danner S Soppa J Characterization of the distal promoter element of halobacteria in vivo using saturation mutagenesis and selection Mol Microbiol 1996, 19:1265-1276 10.1111/j.1365-2958.1996.tb02471.x 8730868
18. Baliga NS Kennedy SP Ng WV Hood L DasSarma S Genomic and genetic dissection of an archaeal regulon Proc Natl Acad Sci U S A 2001, 98:2521-2525 30170 11226271 10.1073/pnas.051632498
19. Berk AJ TBP-like factors come into focus Cell 2000, 103:5-8 10.1016/ S0092-8674(00)00098-2 11051541
20. Faiger H Ivanchenko M Cohen I Haran TE TBP flanking sequences: Asymmetry of binding, long-range effects and consensus sequences Nucleic Acids Res 2006, 34:104-119 1326239 16407329 10.1093/nar/gkj414
21. Hansen SK Takada S Jacobson RH Lis JT Tjian R Transcription properties of a cell type-specific TATA-binding protein, TRF Cell 1997, 91:71-83 10.1016/S0092-8674(01)80010-6 9335336
22. Holmes MC Tjian R Promoter-selective properties of the TBP-related factor TRF1 Science 2000, 288:867-870 10.1126/science.288.5467.867 10797011
23. DasSarma S Berquist BR Coker JA DasSarma P Muller JA Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1 Saline Systems 2006, 2:3 1447603 16542428 10.1186/1746-1448-2-3
24. DasSarma S Halophilic Archaea Halophiles Plainview, NY, Cold Spring Harbor Laboratory Press DasSarma S and Fleischmann EM 1995
25. DasSarma S DasSarma P Halophiles Encyclopedia of Life Sciences, Wiley Press 2006 http://www.els.net
26. Berquist BR Muller JA DasSarma P DasSarma S Genetic systems for halophilic archaea Methods in Microbiology, Elsevier/Academic Press Oren A and Rainey F 2006:649-680
27. Bergqvist S Williams MA O'Brien R Ladbury JE Halophilic adaptation of protein-DNA interactions Biochem Soc Trans 2003, 31:677-680 10.1042/ BST0310677 12773181
28. Ng WL DasSarma S Minimal replication origin of the 200-kilobase Halobacterium plasmid pNRC100 J Bacteriol 1993, 175:4584-4596 204909 8335618
29. Cline SW Lam WL Charlebois RL Schalkwyk LC Doolittle WF Transformation methods for halophilic archaebacteria Can J Microbiol 1989, 35:148-152 2497937
30. Brochier C Forterre P Gribaldo S Archaeal phylogeny based on proteins of the transcription and translation machineries: Tackling the Methanopyrus kandleri paradox Genome Biol 2004, 5:R17 395767 15003120 10.1186/ gb-2004-5-3-r17
31. Peck RF DasSarma S Krebs MP Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a counterselectable marker Mol Microbiol 2000, 35:667-676 10.1046/j.1365-2958.2000.01739.x 10672188
32. Peck RF Echavarri-Erasun C Johnson EA Ng WV Kennedy SP Hood L DasSarma S Krebs MP brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum J Biol Chem 2001, 276:5739-5744 10.1074/jbc.M009492200 11092896
33. Peck RF Johnson EA Krebs MP Identification of a lycopene beta-cyclase required for bacteriorhodopsin biogenesis in the archaeon Halobacterium salinarum J Bacteriol 2002, 184:2889-2897 135044 12003928 10.1128/ JB.184.11.2889-2897.2002
34. Woodson JD Peck RF Krebs MP Escalante-Semerena JC The cobY gene of the archaeon Halobacterium sp. strain NRC-1 is required for de novo cobamide synthesis J Bacteriol 2003, 185:311-316 141819 12486068 10.1128/ JB.185.1.311-316.2003
35. Woodson JD Zayas CL Escalante-Semerena JC A new pathway for salvaging the coenzyme B12 precursor cobinamide in archaea requires cobinamide-phosphate synthase (CbiB) enzyme activity J Bacteriol 2003, 185:7193-7201 296239 14645280 10.1128/JB.185.24.7193-7201.2003
36. Woodson JD Escalante-Semerena JC CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea Proc Natl Acad Sci U S A 2004, 101:3591-3596 373507 14990804 10.1073/ pnas.0305939101
37. Woodson JD Reynolds AA Escalante-Semerena JC ABC transporter for corrinoids in Halobacterium sp. strain NRC-1 J Bacteriol 2005, 187:5901-5909 1196138 16109931 10.1128/JB.187.17.5901-5909.2005
38. Wang G Kennedy SP Fasiludeen S Rensing C DasSarma S Arsenic resistance in Halobacterium sp. strain NRC-1 examined by using an improved gene knockout system J Bacteriol 2004, 186:3187-3194 400623 15126481 10.1128/ JB.186.10.3187-3194.2004
39. Baliga NS Bjork SJ Bonneau R Pan M Iloanusi C Kottemann MC Hood L DiRuggiero J Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1 Genome Res 2004, 14:1025-1035 419780 15140832 10.1101/gr.1993504
40. Baliga NS Pan M Goo YA Yi EC Goodlett DR Dimitrov K Shannon P Aebersold R Ng WV Hood L Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach Proc Natl Acad Sci U S A 2002, 99:14913-14918 137519 12403819 10.1073/pnas.192558999
41. McCready S Muller JA Boubriak I Berquist BR Ng WL DasSarma S UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1 Saline Systems 2005, 1:3 1224876 16176594 10.1186/1746-1448-1-3
42. Müller JA DasSarma S Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: Dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors J Bacteriol 2005, 187:1659-1667 1064022 15716436 10.1128/JB.187.5.1659-1667.2005
43. Coker JA Dassarma P Kumar J Müller JA Dassarma S Transcriptional profiling of the model Archaeon Halobacterium sp. NRC-1: Responses to changes in salinity and temperature Saline Systems 2007, 3:6 1971269 17651475 10.1186/1746-1448-3-6
44. Narberhaus F Alpha-crystallin-type heat shock proteins: Socializing minichaperones in the context of a multichaperone network Microbiol Mol Biol Rev 2002, 66:64-93 120782 11875128 10.1128/MMBR.66.1.64-93.2002
45. Shukla HD Proteomic analysis of acidic chaperones, and stress proteins in extreme halophile Halobacterium NRC-1: A comparative proteomic approach to study heat shock response Proteome Sci 2006, 4:6 1475562 16623945 10.1186/1477-5956-4-6
46. Wettach J Gohl HP Tschochner H Thomm M Functional interaction of yeast and human TATA-binding proteins with an archaeal RNA polymerase and promoter Proc Natl Acad Sci U S A 1995, 92:472-476 42762 7831313 10.1073/ pnas.92.2.472
47. Madon J Zillig W A form of the DNA-dependent RNA polymerase of Halobacterium halobium, containing an additional component, is able to transcribe native DNA Eur J Biochem 1983, 133:471-474 10.1111/ j.1432-1033.1983.tb07487.x 6852054
48. Cashikar AG Schirmer EC Hattendorf DA Glover JR Ramakrishnan MS Ware DM Lindquist SL Defining a pathway of communication from the C-terminal peptide binding domain to the N-terminal ATPase domain in a AAA protein Mol Cell 2002, 9:751-760 10.1016/S1097-2765(02)00499-9 11983167
49. Haslbeck M Walke S Stromer T Ehrnsperger M White HE Chen S Saibil HR Buchner J Hsp26: A temperature-regulated chaperone EMBO J 1999, 18:6744-6751 1171736 10581247 10.1093/emboj/18.23.6744
50. Klunker D Haas B Hirtreiter A Figueiredo L Naylor DJ Pfeifer G Muller V Deppenmeier U Gottschalk G Hartl FU Hayer-Hartl M Coexistence of group I and group II chaperonins in the archaeon Methanosarcina mazei J Biol Chem 2003, 278:33256-33267 10.1074/jbc.M302018200 12796498
51. Chapman E Farr GW Usaite R Furtak K Fenton WA Chaudhuri TK Hondorp ER Matthews RG Wolf SG Yates JR Pypaert M Horwich AL Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL Proc Natl Acad Sci U S A 2006, 103:15800-15805 1613232 17043235 10.1073/pnas.0607534103
52. Daniels CJ McKee AH Doolittle WF Archaebacterial heat-shock proteins EMBO J 1984, 3:745-749 557420 16453513
53. Bartfai R Balduf C Hilton T Rathmann Y Hadzhiev Y Tora L Orban L Muller F TBP2, a vertebrate-specific member of the TBP family, is required in embryonic development of zebrafish Curr Biol 2004, 14:593-598 10.1016/ j.cub.2004.03.034 15062100
54. Santangelo TJ Cubonova L James CL Reeve JN TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro J Mol Biol 2007, 367:344-357 10.1016/j.jmb.2006.12.069 17275836
55. Facciotti MT Reiss DJ Pan M Kaur A Vuthoori M Bonneau R Shannon P Srivastava A Donohoe SM Hood LE Baliga NS General transcription factor specified global gene regulation in archaea Proc Natl Acad Sci U S A 2007, 104:4630-4635 1838652 17360575 10.1073/pnas.0611663104
56. Hughes TR Mao M Jones AR Burchard J Marton MJ Shannon KW Lefkowitz SM Ziman M Schelter JM Meyer MR Kobayashi S Davis C Dai H He YD Stephaniants SB Cavet G Walker WL West A Coffey E Shoemaker DD Stoughton R Blanchard AP Friend SH Linsley PS Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer Nat Biotechnol 2001, 19:342-347 10.1038/86730 11283592
57. Wang X Seed B Selection of oligonucleotide probes for protein coding sequences Bioinformatics 2003, 19:796-802 10.1093/bioinformatics/btg086 12724288
58. Cleveland WS Robust locally weighted regression and smoothing scatterplots J Am Stat Assoc 1979, 74:829-839 10.2307/2286407
59. Quackenbush J Microarray data normalization and transformation Nat Genet 2002, 32(Suppl):496-501 10.1038/ng1032 12454644