A histidine gene cluster of the hyperthermophile Thermotoga maritima: Sequence analysis and evolutionary significance

Extremophiles

Volumn 2, Issue 4, 1998, Pages 379-389

  Thoma, Ralf ^a   Schwander, Martin ^a   Liebl, Wolfgang ^b,c   Kirschner, Kasper ^a   Sterner, Reinhard ^a,c  

^a UNIVERSITY OF BASEL   (Switzerland)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

( )8 Barrel enzymes; Histidine operon; Phosphate binding site Protein thermostability; Salt bridges

Indexed keywords

GENE SEQUENCING; GENETIC ANALYSIS;

ALDOSE-KETOSE ISOMERASES; AMINO ACID SEQUENCE; AMINOHYDROLASES; BASE SEQUENCE; BINDING SITES; CLONING, MOLECULAR; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENES, BACTERIAL; HISTIDINE; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHOSPHATES; SEQUENCE ANALYSIS; THERMOTOGA MARITIMA;

BACTERIA (MICROORGANISMS); ENTEROBACTERIA; THERMOTOGA MARITIMA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0032211977     PISSN: 14310651     EISSN: None     Source Type: Journal    
DOI: 10.1007/s007920050082     Document Type: Article

References (54)

1. Achenbach-Richter L, Gupta R, Stetter KO, Woese CR (1987) Were the original eubacteria thermophiles? Syst Appl Microbiol 9:34-39
2. Alifano P, Rivellini F, Limauro D, Bruni CB, Caromagno MS (1991) A consensus motif common to all rho-dependent prokaryotic transcription terminators. Cell 64:553-563
3. Alifano P, Fani R, Liò P, Lazcano A, Bazzicalupo M, Calomagno MS, Bruni CB (1996) Histidine biosynthetic pathway and genes: structure, regulation, and evolution. Microbiol Rev 60:44-69
4. Beckler GS, Reeve JN (1986) Conservation of primary structure in the hisI gene of the archaebacterium Methanococcus vannielii, the eubacterium Escherichia coli and the eucaryote Saccharomyces cerevisiae. Mol Gen Genet 204:133-140
5. Bork P, Gellerich J, Groth H, Hooft R, Martin F (1995) Divergent evolution of a β/α-barrel subclass: detection of numerous phosphate-binding sites by motif search. Protein Sci 4:268-274
6. Brändén C-I (1991) The TIM barrel - the most frequently occurring folding motif in proteins. Curr Opin Struct Biol 1:978-983
7. Broach JR (1981) Genes of Saccharomyces cerevisiae. In: strathern JN, Jones EW, Broach JR (eds) The molecular biology of the yeast Saccharomyces. Life cycle and inheritance. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 653-727
8. Broom JE, Hill DF, Hughes G, Jones WA, McNaughton JC, Stockwell PA, Petersen GB (1995) Sequence of a transposon identified as Tn1000. DNA Seq 5:185-189
9. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, Fitzgerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Weidman JF, Fuhrmann JL, Nguyen D, Utterback TR, Kelly JM, Peterson JD, Sadow PW, Hanna MC, Cotton MD, Roberts KM, Hurst MA, Kaine BP, Borodovsky M, Klenk HP, Fraser CM, Smith HO, Woese CR, Venter JC (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073
10. Carlomagno MS, Chiariotti L, Alifano P, Nappo AG, Bruni CB (1988) Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons. J Mol Biol 203:585-606
11. dFDEHI gene cluster from the archeon Sulfolobus solfataricus P2. J Bacteriol 179:4429-4432
12. D'Aubenton-Carafa Y, Brody E, Thermes C (1990) Prediction of rho-independent Escherichia coli transcription terminators. J Mol Biol 216:835-858
13. Delorme C, Ehrlich SD, Renault P (1992) Histidine biosynthesis genes in Lactococcus lactis susbsp. lactis. J Bacteriol 174:6571-6579
14. Dower WJ, Miller JF, Ragsdale CW (1988) High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16:6127-6145
15. Eder J, Kirschner K (1992) Stable substructures of eightfold βα-barrel proteins: fragment complementation of phosphoribosylanthranilate isomerase. Biochemistry 31:3617-3625
16. Fani R, Bazzicalupo M, Damiani G, Bianchi A, Schipani C, Sgaramella V, Polsinelli M (1989) Cloning of histidine genes of Azospirillum brasilense: organization of the ABFH gene cluster and nucleotide sequence of the hisB gene. Mol Gen Genet 216:224-229
17. Fani R, Liò P, Chiarelli I, Bazzicalupo M (1994) The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. J Mol Evol 38:489-495
18. Fani R, Liò P, Lazcano A (1995) Molecular evolution of the histidine biosynthetic pathway. J Mol Evol 41:760-774
19. Farber GK, Petsko GA (1990) The evolution of α/β barrel enzymes. Trends Biochem Sci 15:228-234
20. Fink GR (1964) Gene-enzyme relations in histidine biosynthesis in yeast. Science 146:525-527
21. Goldschmidt EP, Cater MS, Matney TS, Butler MA, Greene A (1970) Genetic analysis of the histidine operon in Escherichia coli K12. Genetics 66:219-229
22. Gorman JA, Hu AS (1969) The separation and partial characterization of L-histidinol phosphatase and an alkaline phosphatase of Saccharomyces cerevisiae. J Biol Chem 244:1645-1650
23. Grisolia V, Ricco A, Bruni CB (1983) Structure and function of the internal promotor (hisBp) of the Escherichia coli K-12 histidine operon. J Bacteriol 155:1288-1296
24. Hennig M, Schlesier B, Dauter Z, Pfeffer S, Betzel C, Höhne WE, Wilson KS (1992) A TIM barrel protein without enzymatic activity? FEBS Lett 306:80-84
25. Hennig M, Darimont B, Sterner R, Kirschner K, Jansonius JN (1995) 2.0 Å structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinants of protein stability. Structure (Lond) 3:1295-1306
26. Hennig M, Sterner R, Kirschner K, Jansonius JN (1997) Crystal structure at 2.0 Å resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability. Biochemistry 36:6009-6016
27. Hinnebusch AG, Fink GR (1983) Repeated DNA sequences upstream from HISI also occur at several other co-regulated genes in Saccharomyces cerevisiae. J Biol Chem 258:5238-5247
28. Jaenicke R (1996) Stability and folding of ultrastable proteins: eye lens crystallins and enzymes from thermophiles. FASEB J 10:84-92
29. Kawamura T, Ishimoto N, Ito E (1982) UDP-N-acetyl-D-glucosamine 2-epimerase from Escherichia coli. Methods Enzymol 83:515-519
30. Kelly CA, Nishiyama M, Ohnishi Y, Beppu T, Birktoft JJ (1993) Determinants of protein thermostability observed in the 1.9-Å crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. Biochemistry 32:3913-3922
31. Knöchel TR, Hennig M, Merz A, Darimont B, Kirschner K, Jansonius JN (1996) The crystal structure of indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus in three different crystal forms: effects of ionic strength. J Mol Biol 262:502-515
32. Korndörfer I, Steipe B, Huber R, Tomschy A, Jaenicke R (1995) The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 Å resolution. J Mol Biol 246:511-521
33. Lim JH, Yu YG, Choi IG, Ryu JR, Ahn BY, Kim SH, Han YS (1997) Cloning and expression of Superoxide dismutase from Aquifex pyrophilus, a hyperthermophilic bacterium. FEBS Lett 406:142-146
34. Limauro D, Avitabile A, Cappellano C, Puglia AM, Bruni CB (1990) Cloning and characterization of the histidine biosynthetic gene cluster of Streptomyces coelicolor A3(2). Gene (Amst) 90:31-41
35. Macedo-Ribeiro S, Darimont B, Sterner R, Huber R (1996) Small structural changes account for the high thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima. Structure (Lond) 4:1291-1301
36. Matney TS, Goldschmidt EP, Erwin NS, Scroggs A (1964) A preliminary map of genomic sites for F-attachment in Escherichia coli K12. Biochem Biophys Res Commun 17:278-281
37. Miles EW, Yutani K, Ogasahara K (1982) Guanidine hydrochloride induced unfolding of the alpha subunit of tryptophan synthase and of the two alpha proteolytic fragments: evidence for stepwise unfolding of the two alpha domains. Biochemistry 21:2586-2592
38. Ostendorp R, Liebl W, Schurig H, Jaenicke R (1993) The L-lactate dehydrogenase gene of the hyperthermophilic bacterium Thermotoga maritima cloned by complementation in Escherichia coli. Eur J Biochem 216:709-715
39. Perutz MF, Raidt H (1975) Strereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature (Lond) 275:256-259
40. Reardon D, Farber GK (1995) The structure and evolution of α/β barrel proteins. FASEB J 9:497-503
41. Rost B, Sander C (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72
42. Samhrook J, Fritsch EE, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor, NY
43. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467
44. 8-barrel proteins of tryptophan biosynthesis in hyperthermophile Thermotoga maritima. EMBO J 14:4395-4402
45. Struhl K (1985) Nucleotide sequence and transcritional mapping of the yeast pet56-his3-ded1 gene region. Nucleic Acids Res 13:8587-8601
46. Tanner JJ, Hecht RM, Krause KL (1996) Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 2.5 Å resolution. Biochemistry 35:2597-2609
47. Vogt G, Woell S, Argos P (1997) Protein thermal stability, hydrogen bonds, and ion pairs. J Mol Biol 269:631-643
48. Wilmanns M, Hyde CC, Davies DR, Kirschner K, Jansonius JN (1991) Structural conservation in parallel β/α-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry 30:9161-9169
49. Wilmanns M, Eisenberg D (1993) Three-dimensional profiles from residue-pair preferences: identification of sequences with β/α-barrel fold. Proc Natl Acad Sci USA 90:1379-1383
50. Wilmanns M, Eisenberg D (1995) Inverse protein folding by residue pair preference profile method: estimating the correctness of alignments of structurally compatible sequences. Protein Eng 8:627-639
51. Winkler ME (1996) Biosynthesis of histidine. In: neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Renikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, vol 1. American Society for Microbiology, Washington, DC, pp 485-505
52. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea. Bacteria and Eucarya. Proc Natl Acad Sci USA 87:4576-4579
53. Yip KS, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, Sedelnikova SE, Engel PC, Pasquo A, Chiaraluce R, Consalvi V (1995) The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure (Lond) 3:1147-1158
54. Zalkin H, Smith JL (1998) Enzymes utilizing glutamine as an amide donor. Adv Enzymol Relat Areas Mol Biol 72:87-144