Novel phosphotransferase system genes revealed by bacterial genome analysis - a gene cluster encoding a unique Enzyme I and the proteins of a fructose-like permease system

References

1. Banki K., Halladay D., Perl A. 1994; Cloning and expression of the human gene for transaldolase. A novel highly repetitive element constitutes an integral part of the coding sequence. J Biol Chem 269:2847–2851
   [Google Scholar]
2. Blattner F. R., Burland V., III Plunkett G., Sofia H. J., Daniels D. L. 1993; Analysis of the Escherichia coli genome. 4. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res 21:5408–5417
   [Google Scholar]
3. Boyd D. A., Cvitkovitch D. G., Hamilton I. R. 1994; Sequence and expression of the genes for HPr (ptsI) and Enzyme I (ptsl) of the phosphoenolpyruvate-dependent phosphotransferase transport system from Streptococcus mutans . Infect Immun 62:1156–1165
   [Google Scholar]
4. Bruchhaus I., Tannich E. 1993; Primary structure of the pyruvate phosphate dikinase in Entamoeba histolytica . Mol Biochem Parasitol 62:153–156
   [Google Scholar]
5. Buck D., Guest J. R. 1989; Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon. Biochem J 260:737–747
   [Google Scholar]
6. Buhr A., Erni B. 1993; Membrane topology of the glucose transporter of Escherichia coli . J Biol Chem 268:11599–11603
   [Google Scholar]
7. Byrne C. R., Monroe R. S., Ward K. A., Kredich N. M. 1988; DNA sequences of the cysK regions of Salmonella typhimurium and Escherichia coli and linkage of the cysK regions to ptsH . J Bacteriol 170:3150–3157
   [Google Scholar]
8. Chen Y. M., Lu Z., Lin E. C. 1989; Constitutive activation of the fucAO operon and silencing of the divergently transcribed fucPLK operon by an IS5 element in Escherichia coli mutants selected for growth on L-l,2-propanediol. J Bacteriol 171:6097–6105
   [Google Scholar]
9. Chin A. M., Sutrina S., Feldheim D. A., Jr Saier M. H. 1987; Genetic expression of Enzyme I activity of the phosphoenolpyruvate : sugar phosphotransferase system in ptsHI deletion strains of Salmonella typhimurium . J Bacteriol 169:894–896
   [Google Scholar]
10. de Crecy-Lagard V., Bouvet O. M., Lejeune P., Danchin A. 1991; Fructose catabolism in Xanthomonas campestris pv campestris. Sequence of the PTS operon, characterization of the fructosespecific enzymes. J Biol Chem 266:18154–18161
    [Google Scholar]
11. De Reuse H., Danchin A. 1988; The ptsH,ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription. J Bacteriol 170:3827–3837
    [Google Scholar]
12. Devereux J., Haeberli P., Smithies N. O. 1984; A comprehensive set of sequence analyses for the VAX. Nucleic Acids Rer 12:387–395
    [Google Scholar]
13. Doolittle R. F. 1986; Of Urfs and Orfs: a Primer on How to Analyse Derived Amino Acid Sequences. Mill Valley, CA: University Science Books;
    [Google Scholar]
14. Feng D.-F., Doolittle R. F. 1990; Progressive alignment and phylogenetic tree construction of protein sequences. Methods Ensymol 183:375–387
    [Google Scholar]
15. Gagnon G., Vadeboncoeur C., Levesque R. C., Frenette M. 1992; Cloning, sequencing and expression in Escherichia coli of the ptsI gene encoding the Enzyme I ofthe phosphoenolpyruvate : sugar phosphotransferase system from Streptococcus saliva- rius . Gene 121:71–88
    [Google Scholar]
16. Geerse R. H. 1989; The phosphoenolpyruvate: fructose phosphotransferase system in Salmonella typhimurium and Escherichia coli. . PhD thesis E. C. Slater Institute for Biochemical Research: University of Amsterdam;
    [Google Scholar]
17. Geerse R. H., Izzo F., Postma P. W. 1989; The PEP:fructose phosphotransferase system in Salmonella typhimurium: FPr combines Enzyme III^Fru and pseudo-HPr activities. Mol & Gen Genet 216:517–525
    [Google Scholar]
18. Givskov M., Olsen L., Molin S. 1988; Cloning and expression in Escherichia coli of the gene for extracellular phospholipase Al from Serratia liquefaciens . J Bacteriol 170:5855–5862
    [Google Scholar]
19. Hall B. G., Yokoyama S., Calhoun D. H. 1983; Role of cryptic genes in microbial evolution. Mol Biol Evol 1:109–124
    [Google Scholar]
20. luchi S., Lin E. C. 1993; Adaptation of Escherichia coli to redox environments by gene expression. Mol Microbiol 9:9–15
    [Google Scholar]
21. Jacobson G. R., Saraceni-Richards C. 1993; The Escherichia coli mannitol permease as a model for transport via the bacterial phosphotransferase system. J. Bioenerg Biomembr 25:621–626
    [Google Scholar]
22. Jacoby J., Hollenberg C. P., Heinisch J. J. 1993; Transaldolase mutants in the yeast Kluyveromyces lactis provide evidence that glucose can be metabolized through the pentose phosphate pathway. Mol Microbiol 10:867–876
    [Google Scholar]
23. Jones D. H. A., Franklin C. H., Thomas C. M. 1994; Molecular analysis of the operon which encodes the RNA polymerase sigma factor σ⁵⁴ of Escherichia coli. . Microbiology 140:1035–1043
    [Google Scholar]
24. Kohlbrecher D., Eisermann R., Hengstenberg W. 1991; Staphylococcal phosphoenolpyruvate-dependent phosphotransferase system: molecular cloning and nucleotide sequence of the Staphylococcus carnosus ptsI gene and expression and complementation studies of the gene product. J Bacteriol 174:2208–2214
    [Google Scholar]
25. Kornberg H. L. 1990; Fructose transport by Escherichia coli . Phil Trans R Soc 326:505–513
    [Google Scholar]
26. Kyte J., Doolittle R. F. 1982; A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132
    [Google Scholar]
27. LiCalsi C., Crocenzi T. S., Freire E., Roseman S. 1991; Sugar transport by the bacterial phosphotransferase system: structural and thermodynamic domains of Enzyme I of Salmonella typhimurium . J Biol Chem 266:19519–19527
    [Google Scholar]
28. Lu Z., Lin E. C. 1989; The nucleotide sequence of Escherichia coli genes for L-fucose dissimilation. Nucleic Acids Res 17:4883–4884
    [Google Scholar]
29. Mallinder P. R., Pritchard A., Moir A. 1992; Cloning and characterization of a gene from Bacillus stearothermophilus var non- diastaticus encoding a glycerol dehydrogenase. Gene 110:9–16
    [Google Scholar]
30. Matsuoka M., Ozeki Y., Yamamoto N., Hirano H., Kano-Murakami Y., Tanaka Y. 1988; Primary structure of maize pyruvate, orthophosphate dikinase as deduced from cDNA sequence. J Biol Chem 263:11080–11083
    [Google Scholar]
31. Niersbach M., Kreuzaler F., Geerse R. H., Postma P. W., Hirsch H. J. 1992; Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase. Mol & Gen Genet 231:332–336
    [Google Scholar]
32. Parker L. L., Hall B. G. 1990; Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli KI2. Genetics 124:455–471
    [Google Scholar]
33. Pearson W. R., Lipman D. J. 1988; Improved tools for biological sequence comparison. Proc. Natl Acad Sci USA 85:2444–2448
    [Google Scholar]
34. Pelliccione N., Jaffin B., Sobel M. E., Krulwich T. A. 1979; Induction of the phosphoenolpyruvate: hexose phosphotransferase system associated with relative anaerobiosis in an obligate aerobe. Eur J Biochem 95:69–75
    [Google Scholar]
35. Peterson S. N., Hu P. C., Bott K. F., Hutchison C. A. 1993; A survey of the Mycoplasma genitalium genome by using random sequencing. J Bacteriol 175:7918–7930
    [Google Scholar]
36. III Plunkett G., Burland V., Daniels D. L., Blattner F. R. 1993; Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res 21:3391–3398
    [Google Scholar]
37. Pocalyko D. J., Carroll L. J., Martin B. M., Babbitt P. C., Dunaway-Mariano D. 1990; Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, Enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs. Biochemistry 29:10757–10765
    [Google Scholar]
38. Postma P., Lengeler J., Jacobson G. R. 1993; Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 57:543–594
    [Google Scholar]
39. Powell B. S., Court D. L., Inada T., Nakamura Y., Michotey V., Cui X., Reizer A., Jr Saier M. H., Reizer J. 1995; Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. EnzymeIIA^Ntr affects growth on organic nitrogen and the conditional lethality of an era^ts mutant. J Biol Chem (in press)
    [Google Scholar]
40. Pries A., Priefert H., Kruger N., Steinbuchel A. 1991; Identification and characterization of two Alcaligenes eutrophus gene loci relevant to the poly (β-hydroxybutyric acid)-leaky phenotype which exhibits homology to ptsH and ptsI of Escherichia coli . J Bacteriol 173:5843–5853
    [Google Scholar]
41. Prior T. I., Kornberg H. L. 1988; Nucleotide sequence of fruA, the gene specifying enzyme II^fru of the phosphoenolpyruvate- dependent sugar phosphotransferase system in Escherichia coli K12. J Gen Microbiol 134:2757–2768
    [Google Scholar]
42. Reizer A., Reizer J. 1994; Progressive multiple alignment of protein sequences and the construction of phylogenetic trees. In Methods in Molecular Biology: Computer Analysis of Sequence Data,Part II pp 319–325 Edited by Griffin A. M., Griffin H. G. Totowa, NJ: Humana Press;
    [Google Scholar]
43. Reizer A., Deutscher J., Jr Saier M. H., Reizer J. 1991a; Analysis of the gluconate (gnt) operon of Bacillus subtilis . Mol Microbiol 5:1081–1089
    [Google Scholar]
44. Reizer A., Pao G. M., Jr Saier M. H. 1991b; Evolutionary relationships among the permease proteins of the bacterial phosphoenolpyruvate:sugar phosphotransferase system. Constructionof phylogenetic trees and possible relatedness to proteins of eukaryotic mitochondria. J Mol Evol 33:179–193
    [Google Scholar]
45. Reizer J., Reizer A., Jr Saier M. H., Jacobson G. R. 1992; A proposed link between nitrogen and carbon metabolism involving protein phosphorylation in bacteria. Protein Sci 1:722–726
    [Google Scholar]
46. Reizer J., Hoischen C., Reizer A., Pham T. N., Jr Saier M. H. 1993; Sequence analyses and evolutionary relationships among the energy-coupling proteins Enzyme I and HPr of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Protein Sci 2:506–521
    [Google Scholar]
47. Reizer J., Michotey V., Reizer A., Jr Saier M. H. 1994a; Novel phosphotransferase system genes revealed by bacterial genome analysis: unique, putative fructose- and glucoside-specific systems. Protein Sci 3:440–450
    [Google Scholar]
48. Reizer J., Reizer A., Kornberg H. L., Jr Saier M. H. 1994b; Sequence of the fruB gene of Escherichia coli encoding the diphosphoryl transfer protein (DTP) of the phosphoenolpyruvate: sugar phosphotransferase system. FEMS Microbiol Lett 118:159–162
    [Google Scholar]
49. Rodel W., Plaga W., Frank R., Knappe J. 1988; Primary structures of Escherichia coli pyruvate formate-lyase and pyruvate formate-lyase-activating enzyme deduced from the DNA nucleotide sequences. Eur J Biochem 177:153–158
    [Google Scholar]
50. Romano A. H., Jr Saier M. H. 1992; Evolution of the bacterial phosphoenolpyruvate:sugar phosphotransferase system. I. Physiologic and organismic considerations. In The Evolution of Metabolic Function pp 171–204 Edited by Mortlock R. P. Boca Raton, FL: CRC Press;
    [Google Scholar]
51. Rosche E., Westhoff P. 1990; Primary structure of pyruvate, orthophosphate dikinase in the dicotyledonous C(4) plant Flaveria trinervia . FEBS Lett 273:116–121
    [Google Scholar]
52. Saffen D. W., Presper K. A., Doering T. L., Roseman S. 1987; Sugar transport by the bacterial phosphotransferase system. Molecular cloning and structural analysis of the Escherichia coli ptsI, ptsl, and crr genes. J Biol Chem 262:16241–16253
    [Google Scholar]
53. Jr Saier M. H. 1977; Bacterial phosphoenolpyruvate:sugar phosphotransferase systems:structural, functional, and evolutionary interrelationships. Bacteriol Rev 41:856–871
    [Google Scholar]
54. Jr Saier M. H., Reizer J. 1992; Proposed uniform nomenclature for the proteins and protein domains of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. J Bacteriol 174:1433–1438
    [Google Scholar]
55. Jr Saier M. H., Reizer J. 1994a; Computational analyses aiding identification and characterization of proteins, genes and operons. In Methods in Molecular Genetics Edited by Jr Adolph MK. W. Orlando, FL: Academic Press (in press);
    [Google Scholar]
56. Jr Saier M. H., Reizer J. 1994b; The bacterial phosphotransferase system: new frontiers 30 years later. Mol Microbiol 13:755–764
    [Google Scholar]
57. Jr Saier M. H., Grenier F. C., Lee C. A., Waygood E. B. 1985; Evidence for the evolutionary relatedness of the proteins of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. J Cell Biochem 27:43–56
    [Google Scholar]
58. Jr Saier ML H., Reizer A., Pao G. M., Wu L.-F., Reizer J., Romano A. H. 1992; Evolution of the bacterial phosphoenolpyruvate : sugar phosphotransferase system. II. Molecular considerations. In The Evolution of Metabolic Function pp. 171–204 Edited by Mortlock R. P. Boca Raton, FL: CRC Press;
    [Google Scholar]
59. Sakai H., Ohta T. 1993; Molecular cloning and nucleotide sequence of the gene for pyruvate kinase of Bacillus stearothermophilus and the production of the enzyme in Escherichia coli. Evidence that the genes for phosphofructokinase and pyruvate kinase constitute an operon. Eur J Biochem 211:851–859
    [Google Scholar]
60. Sawers G., Suppmann B. 1992; Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins. J Bacteriol 174:3474–3478
    [Google Scholar]
61. Schaaff I., Hohmann S., Zimmermann F. K. 1990; Molecular analysis of the structural gene for yeast transaldolase. Eur J Biochem 188:597–603
    [Google Scholar]
62. Sharp P. M., Li W. H. 1987; The codon adaptation index – a measure of directional synonymous codon usage bias, and its potential application. Nucleic Acids Res 15:1281–1295
    [Google Scholar]
63. Smith D. W. 1988; A complete, yet flexible, system for DNA/ protein sequence analysis using VAX/VMS computers. Comput Appl Biosci 4:212
    [Google Scholar]
64. Sugiyama J. E., Mahmoodian S., Jacobson G. R. 1991; Membrane topology analysis of the Escherichia coli mannitol permease by using a nested-deletion method to create mtlA-phoA fusions. Proc Natl Acad Sci USA 88:9603–9607
    [Google Scholar]
65. Sun X., Harder J., Krook M., Jornvall H., Sjoberg B.-M., Reichard P. 1993; A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene. Proc Natl Acad Sci USA 90:577–581
    [Google Scholar]
66. Sutrina S. L., Chin A. M., Esch F., Jr Saier M. H. 1988; Purification and characterization of the fructose-inducible HPr-like protein, FPr, and the fructose-specific Enzyme III of the phosphoenolpyruvate : sugar phosphotransferase system of Salmonella typhimurium . J Biol Chem 263:5061–5069
    [Google Scholar]
67. Titgemeyer F., Reizer J., Reizer A., Tang J., Jr Parr T. R., Jr Saier M. H. 1994; Nucleotide sequence of the region between crr and cysM in Salmonella typhimurium: five novel ORFs including one encoding a putative transcriptional regulator of the phosphotransferase system. DNA Sequence (in press)
    [Google Scholar]
68. Trach K., Chapman J. W., Piggot P., Lecoq D., Hoch J. A. 1988; Complete sequence and transcriptional analysis of the spoOF region of the Bacillus subtilis chromosome. J Bacteriol 170:4194–4208
    [Google Scholar]
69. Truniger V., Boos V. 1994; Mapping and cloning of gldA, the structural gene of the Escherichia coli glycerol dehydrogenase. J Bacteriol 176:1796–1800
    [Google Scholar]
70. Valerie K., Stevens J., Lynch M., Henderson E. E., De-Riel J. K. 1986; Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4. Nucleic Acids Res 14:8637–8654
    [Google Scholar]
71. Varshney U., Hutcheon T., De-Sande J. H. 1988; Sequence analysis, expression, and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung) . J Biol Chem 263:7776–7784
    [Google Scholar]
72. Wagner A. F. V., Frey M., Neugebauer F. A., Schafer W., Knappe J. 1992; The free radical in pyruvate formate-lyase is located on glycine-734. Proc Natl Acad Sci USA 89:996–1000
    [Google Scholar]
73. Wu L.-F., Jr Saier M. H. 1990; Nucleotide sequence of the fruA gene encoding the fructose permease of the Rhodobacter capsulatus phosphotransferase system, and analyses of the deduced protein sequence. J Bacteriol 172:7167–7178
    [Google Scholar]
74. Wu L.-F., Tomich J. M., Jr Saier M. H. 1990; Structure and evolution of a multidomain, multiphosphoryl transfer protein: nucleotide sequence of the fruB(HI) gene in Rhodobacter capsulatus and comparisons with homologous genes from other organisms. J Mol Biol 213:687–703
    [Google Scholar]
75. Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. 1992; Systematic sequencing of the Escherichia coli genome: analysis of the 0–2.4 min region. Nucleic Acids Res 20:3305–3308
    [Google Scholar]