The D-xylose-binding protein, XylF, from Thermoanaerobacter ethanolicus 39E: Cloning, molecular analysis, and expression of the structural gene

Journal of Bacteriology

Volumn 180, Issue 14, 1998, Pages 3570-3577

  Erbeznik, Milutin ^a,b   Strobel, Herbert J ^a   Dawson, Karl A ^a   Jones, Chris R ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

^b UNIVERSITY OF KENTUCKY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BINDING PROTEIN; PHOSPHOTRANSFERASE; PROTEIN XYLF; UNCLASSIFIED DRUG; XYLOSE; XYLOSE ISOMERASE; XYLULOSE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; CARBOHYDRATE METABOLISM; ESCHERICHIA COLI; GENE EXPRESSION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; STRUCTURAL GENE; THERMOANAEROBACTER ETHANOLICUS; THERMOPHILIC BACTERIUM;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; POSIBACTERIA; THERMOANAEROBACTER ETHANOLICUS;

EID: 0032448107     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.180.14.3570-3577.1998     Document Type: Article

References (53)

1. Ahlem, C., W. Huisman, G. Neslund, and S. Dahms. 1982. Purification and properties of a periplasmic D-xylose-binding protein from Escherichia coli K-12. J. Biol. Chem. 257:2926-2931.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Ausubel, F. A., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1996. Current protocols in molecular biology. Greene Publishing, New York, N.Y.
4. Bhosale, S. H., M. B. Rao, and V. V. Deshpande. 1996. Molecular and industrial aspects of glucose isomerase. Microbiol. Rev. 60:280-300.
5. Dahl, M. K., J. Degenkolb, and W. Hillen. 1994. Transcription of the xyl operon is controlled in Bacillus sublilis by tandem overlapping operators spaced by four base-pairs. J. Mol. Biol. 243:413-424.
6. Davis, E. O., and P. J. F. Henderson. 1987. The cloning and DNA sequence of the gene xylE for xylose-proton symport in Escherichia coli K12. J. Biol. Chem. 262:13928-13932.
7. Dekker, K., H. Yamagata, K. Sakaguchi, and S. Udaka. 1991. Xylose (glucose) isomerase gene from the thermophilic Clostridium thermohydrosulfuricum; cloning, sequencing, and expression in Escherichia coli. Agric. Biol. Chem. 55:221-227.
8. Erbeznik, M., K. A. Dawson, and H. J. Strobel. 1998. Cloning and characterization of transcription of the xylAB operon from Thermoanaerobacter ethanolicus. J. Bacteriol. 180:1103-1109.
9. Erbeznik, M., C. R. Jones, K. A. Dawson, and H. J. Strobel. 1997. Clostridium thermocellum JW20 (ATCC 31549) is a coculture with Thermoanaerobacter ethanolicus. Appl. Environ. Microbiol. 63:2949-2951.
10. Erbeznik, M., H. J. Strobel, and K. A. Dawson. Unpublished data.
11. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J.-F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. FitzHugh, C. A. Fields, J. D. Gocayne, J. D. Scott, R. Shirley, L.-I. Liu, A. Glodek, J. M. Kelley, J. F. Weidman, C. A. Phillips, T. Spriggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Nguyen, D. M. Saudek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. M. Geoghagen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
12. Furlong, C. E. 1987. Osmotic-shock-sensitive transport systems, p. 768-796. In F. C. Neidhart, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology, vol. 1. American Society for Microbiology, Washington, D.C.
13. Gilkes, N. R., B. Henrissat, D. G. Kilburn, R. C. Miller, Jr., and R. A. J. Warren. 1991. Domains in microbial β-1,4-glycanases: sequence conservation, function, and enzyme families. Microbiol. Rev. 55:303-315.
14. Goodenough, P. W. 1995. A review of protein engineering for the food industry. Mol. Biotechnol. 4:151-166.
15. Graves, M. C., and J. C. Rabinowitz. 1986. In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. J. Biol. Chem. 261:11409-11415.
16. Groarke, J. M., W. C. Mahoney, J. N. Hope, C. E. Furlong, F. T. Robb, H. Zalkin, and M. A. Hermodson. 1983. The amino acid sequence of D-ribose-binding protein from Escherichia coli K12. J. Biol. Chem. 258:12952-12956.
17. Higgins, C. F. 1992. ABC transporters: from microorganisms to man. Annu. Rev. Cell Biol. 8:67-113.
18. Higgins, D. G., and P. M. Sharp. 1989. Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci. 5:151-153.
19. Hogg, R. W., and M. A. Hermodson. 1977. Amino acid sequence of the L-arabinose-binding protein from Escherichia coli B/r. J. Biol. Chem. 252: 5135-5141.
20. Hogg, R. W., C. Voelker, and I. Von Carlowitz. 1991. Nucleotide sequence and analysis of the mgl operon of Escherichia coli K12. Mol. Gen. Genet. 229:453-459.
21. Hueck, C. J., and W. Hillen. 1995. Catabolite repression in Bacillus subtilis: a global regulatory mechanism for the gram-positive bacteria? Mol. Microbiol. 15:395-401.
22. Kemner, J. K., X. Liang, and E. W. Nester. 1997. The Agrobacterium tumefaciens virulence gene chvE is part of a putative ABC-type sugar transport operon. J. Bacteriol. 179:2452-2458.
23. Kreuzer, P., D. Gärtner, R. Allmansberger, and W. Hillen. 1989. Identification and sequence analysis of the Bacillus subtilis W23 xylR gene and xyl operator. J. Bacteriol. 171:3840-3845.
24. Lam, V. M. S., K. R. Daruwalla, P. J. F. Henderson, and M. C. Jones-Mortimer. 1980. Proton-linked D-xylose transport in Escherichia coli. J. Bacteriol. 143:396-402.
25. Lee, C., M. V. Ramesh, and J. G. Zeikus. 1994. Cloning, sequencing and biochemical characterization of xylose isomerase from Thermoanaerobacterium saccharolyticum strain B6A-RI. J. Gen. Microbiol. 139:1227-1234.
26. Lee, S.-P., M. Morikawa, M. Takagi, and T. Imanaka. 1994. Cloning of the aapT gene and characterization of its product, α-amylase-pullulanase (AapT) from thermophilic and alkaliphilic Bacillus sp. strain XAL601. Appl. Environ. Microbiol. 60:3764-3773.
27. Lee, Y.-E., M. Bagdasarian, M. Meng, and J. G. Zeikus. 1990. Catalytic mechanism of xylose (glucose) isomerase from Clostridium thermosulfurogenes. J. Biol. Chem. 265:19082-19090.
28. Lee, Y.-E., M. K. Jain, C. Lee, S. E. Lowe, and J. G. Zeikus. 1993. Taxonomic distinction of saccharolytic thermophilic anaerobes: description of Thermoanaerobacterium xylanolyticum gen. nov., sp. nov., and Thermoanaerobacterium saccharolyticum gen. nov., sp. nov.; reclassification of Thermoanaerobium brockii, Clostridium thermosulfurogenes, and Clostridium thermohydrosulfuricum E100-69 as Thermoanaerobacter brockii comb, nov., Thermoanaerobacterium thermosulfurigenes comb. nov., and Thermoanaerobacter thermohydrosulfuricus comb, nov., respectively; and transfer of Clostridium thermohydrosulfuricum 39E to Thermoanaerobacter ethanolicus. Int. J. Syst. Bacteriol. 43:41-51.
29. Liebl, W., I. Stemplinger, and P. Ruile. 1997. Properties and gene structure of the Thermotoga maritime α-amylase AmyA, a putative lipoprotein of a hyperthermophilic bacterium. J.Bacteriol. 179:941-948.
30. Lokman, B. C., R. J. Leer, R. van Sorge, and P. H. Pouwels. 1994. Promoter analysis and transcriptional regulation of Lactobacillus pentosus genes involved in xylose catabolism. Mol. Gen. Genet. 245:117-125.
31. Meaden, P. G., J. Adose-Opoku, J. Reizer, A. Reizer, Y. A. Lanceman, M. F. Martin, and W. J. Mitchell. 1994. The xylose isomerase-encoding gene (xylA) of Clostridium thermosaccharolyticum: cloning, sequencing and phylogeny of XylA enzymes. Gene 141:97-101.
32. Osborn, M. J., and R. Munson. 1974. Separation of the inner (cytoplasmic) and outer membranes of gram negative bacteria. Methods Enzymol. 31A: 642-653.
33. Pugsley, A. P. 1993. The complete general secretory pathway in gram-negative bacteria. Microbiol. Rev. 57:50-108.
34. Quiocho, F. A. 1990. Atomic structures of periplasmic binding proteins and the high affinity active transport systems in bacteria. Phil. Trans. R. Soc. Lond. B 326:341-351.
35. Rainey, F. A., N. L. Ward, H. W. Morgan, R. Toalster, and E. Stackebrandt. 1993. Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification. J. Bacteriol. 175:4772-4779.
36. Richarme, G., and A. Kepes. 1983. Study of binding protein-ligand interactions by ammonium sulfate-assisted adsorption on cellulose esters filters. Biochim. Biophys. Acta 742:16-24.
37. Rygus, T., A. Scheler, R. Allmansberger, and W. Hillen. 1991. Molecular cloning, structure, promoters and regulatory elements for transcription of the Bacillus megaterium encoded regulon for xylose utilization. Arch. Microbiol. 155:535-542.
38. Sahm, K., M. Matuschek, H. Müller, W. J. Mitchell, and H. Bahl. 1996. Molecular analysis of the amy gene locus of Thermoanaerobacterium thermosulfurigenes EM1 encoding starch-degrading enzymes and a binding protein-dependent maltose transport system. J. Bacteriol. 178:1039-1046.
39. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
40. Schleif, R. 1987. The L-arabinose operon, p. 1473-1481. In F. C. Neidhart, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology, vol. 2. American Society for Microbiology, Washington, D.C.
41. Schlösser, A., T. Kampers, and H. Schrempf. 1997. The Streptomyces ATP-binding component MsiK assists in cellobiose and maltose transport. J. Bacteriol. 179:2092-2095.
42. Schmiedel, D., M. Kintrup, E. Küster, and W. Hillen. 1997. Regulation of expression, genetic organization and substrate specificity of xylose uptake in Bacillus megaterium. Mol. Microbiol. 23:1053-1062.
43. Shamanna, D. K., and K. E. Sanderson. 1979. Genetics and regulation of xylose utilization in Salmonella typhimurium LT2. J. Bacteriol. 139:71-79.
44. Shimoda, N., A. Toyoda-Yamamoto, S. Aoki, and Y. Machida. 1993. Genetic evidence for an interaction between the VirA sensor protein and the ChvE sugar-binding protein of Agrobacterium. J. Biol. Chem. 268:26552-26558.
45. Sizemore, C., B. Wieland, F. Götz, and W. Hillen. 1992. Regulation of Staphylococcus xylosus xylose utilization genes at the molecular level. J. Bacteriol. 174:3042-3048.
46. Sofia, H. J., V. Burland, D. L. Daniels, G. Plunket III, and F. R. Blattner. 1994. Analysis of the Escherichia coli genome. V. DNA sequence region from 76.0 to 81.5 minutes. Nucleic Acids Res. 22:2576-2586.
47. Song, S., and C. Park. 1997. Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator. J. Bacteriol. 179:7025-7032.
48. Sumija, M., E. O. Davis, L. C. Packman, T. P. McDonald, and P. J. F. Henderson. 1995. Molecular genetics of a receptor protein for D-xylose, encoded by the gene xylF in Escherichia coli. Recept. Channels 3:117-128.
49. Sutcliffe, I. C., and R. R. B. Russell. 1995. Lipoproteins of gram-positive bacteria. J. Bacteriol. 177:1123-1128.
50. Tam, R., and M. H. Saier, Jr. 1993. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57:320-346.
51. Vartak, N. B., J. Reizer, A. Reizer, J. T. Gripp, E. A. Groisman, L.-F. Wu, J. M. Tomich, and M. H. Saier, Jr. 1991. Sequence and evolution of the FruR protein of Salmonella typhimurium: a pleiotropic transcriptional regulatory protein possessing both activator and repressor functions which is homologous to the periplasmic ribose-binding protein. Res. Microbiol. 142: 951-963.
52. von Heijne, G. 1989. The structure of signal peptides from bacterial lipoproteins. Protein Eng. 2:531-534.
53. Vyas, N. K., M. N. Vyas, and F. A. Quiocho. 1991. Comparison of the periplasmic receptors for L-arabinose, D-glucose/D-galactose, and D-ribose. J. Biol. Chem. 266:5226-5237.