Comparative genomic analyses of the bacterial phosphotransferase system

Microbiology and Molecular Biology Reviews

Volumn 69, Issue 4, 2005, Pages 608-634

  Barabote, Ravi D ^a   Saier Jr , Milton H ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2 PROPANOL; BACTERIAL ENZYME; HYBRID PROTEIN; PHOSPHOTRANSFERASE;

BACTERIAL GENETICS; BACTERIAL GENOME; ENZYME PHOSPHORYLATION; ENZYME SUBSTRATE; GENOME; GRAM POSITIVE BACTERIUM; NONHUMAN; PHYLOGENY; PROTEIN DOMAIN; PROTEOBACTERIA; REVIEW; SPIROCHETE; STRAIN DIFFERENCE; TAXONOMY;

GENOME, BACTERIAL; GENOMICS; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE SYSTEM; PHOSPHORYLATION; PHOSPHOTRANSFERASES; PROTEIN STRUCTURE, TERTIARY;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; POSIBACTERIA; PROTEOBACTERIA; SPIROCHAETALES;

EID: 29144518548     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/MMBR.69.4.608-634.2005     Document Type: Review

References (114)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Austin, S., M. Buck, W. Cannon, T. Eydmann, and R. Dixon. 1994. Purification and in vitro activities of the native nitrogen fixation control proteins NifA and NifL. J. Bacteriol. 176:3460-3465.
3. Bächler, C. 2004. Catalysis and transcription control by the dihydroxyacetone kinase of Escherichia coli Ph.D. thesis. University of Berne, Berne, Switzerland.
4. Bächler, C., K. Flükiger-Brühwiler, P. Schneider, P. Bähler, and B. Erni. 2005. From ATP as substrate to ADP as coenzyme. Functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases. J. Biol. Chem. 280:18321-18325.
5. Bao, Q., Y. Tian, W. Li, Z. Xu, Z. Xuan, S. Hu, W. Dong, J. Yang, Y. Chen, Y. Xue, Y. Xu, X. Lai, L. Huang, X. Dong, Y. Ma, L. Ling, H. Tan, R. Chen, J. Wang, J. Yu, and H. Yang. 2002. A complete sequence of the T. tengcongensis genome. Genome Res. 12:689-700.
6. Bertram, R., M. Schlicht, K. Mahr, H. Nothaft, M. H. Saier, Jr., and F. Titgemeyer. 2004. In silico and transcriptional analysis of carbohydrate uptake systems of Streptomyces coelicolor A3(2). J. Bacteriol. 186:1362-1373.
7. Boël, G., I. Mijakovic, A. Mazé, S. Poncet, M.-K. Taha, M. Larribe, E. Darbon, A. Khemiri, A. Galinier, and J. Deutscher. 2003. Transcription regulators potentially controlled by HPr kinase/phosphorylase in gram-negative bacteria. J. Mol. Microbiol. Biotechnol. 5:206-215.
8. Brown, N. O., J. V. Stoyanov, S. P. Kidd, and J. L. Hobman. 2003. The MerR family of transcriptional regulators. FEMS Microbiol. Rev. 27:145-163.
9. Brüggemann, H., A. Henne, F. Hoster, H. Liesegang, A. Wiezer, A. Strittmatter, S. Hujer, P. Durre, and G. Gottschalk. 2004. The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science 305:671-673.
10. Busch, W. and M. H. Saier, Jr. 2002. The transporter classification (TC) system, 2002. CRC Crit. Rev. Biochem. Mol. Biol. 37:287-337.
11. Canback, B., I. Tamas, and S. G. Andersson. 2004. A phylogenetic study of endosymbiotic bacteria. Mol. Biol. Evol. 21:1110-1122.
12. 54 Pu promoter of Pseudomonas putida. J. Bacteriol. 182:956-960.
13. Chang, A. B., R. Lin, W. K. Studley, C. V. Tran, and M. H. Saier, Jr. 2004. Phylogeny as a guide to structure and function of membrane transport proteins. Mol. Membr. Biol. 21:171-181.
14. Chassy, B. M., and C. A. Alpert. 1989. Molecular characterization of the plasmid-encoded lactose-PTS of Lactobacillus casei.. FEMS Microbiol. Rev. 5:157-165.
15. Connelly, J. C., and D. R. Leach. 1996. The sbcC and sbcD genes of Escherichia coli encode a nuclease involved in palindrome inviability and genetic recombination. Genes Cells 1:285-291.
16. Debarbouille, M., I. Martin-Verstraete, A. Klier, and G. Rapoport. 1991. The transcriptional regulator LevR of Bacillus subtilis has domains homologous to both sigma 54- and phosphotransferase system-dependent regulators. Proc. Natl. Acad. Sci. USA 88:2212-2216.
17. de Crécy-Lagard, V., O. M. M. Bouvet, P. Legeune, and A. Danchin. 1991. Fructose catabolism in Xanthomonas campestris pv. Campestris. Sequence of the PTS operon, characterization of the fructose-specific enzymes. J. Biol. Chem. 266:18154-18161.
18. Deutscher, J., B. Pevec, K. Beyreuther, H. H. Kiltz, and W. Hengstenberg. 1986. Streptococcal phosphoenolpyruvate-sugar phosphotransferase system: amino acid sequence and site of ATP-dependent phosphorylation of HPr. Biochemistry 25:6543-6551.
19. Deutscher, J., and M. H. Saier, Jr. 1983. ATP-dependent protein kinase-catalyzed phosphorylation of a seryl residue in HPr, the phosphoryl carrier protein of the phosphotransferase system in Streptococcus pyogenes. Proc. Natl. Acad. Sci. USA 80:6790-6795.
20. Doudoroff, M., W. Z. Hassid, E. W. Putman, and A. L. Potter. 1949. Direct utilization of maltose by Escherichia coli.. J. Biol. Chem. 179:921-934.
21. Fraser, C. M., J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton, R. D. Fleischmann, C. J. Bult, A. R. Kerlavage, G. Sutton, J. M. Kelley, J. L. Fritchman, J. F. Weidman, K. V. Small, M. Sandusky, J. Fuhrmann, D. Nguyen, T. R. Utterback, D. M. Saudek, C. A. Phillips, J. M. Merrick, J.-F. Tomb, B. A. Dougherty, K. F. Bott, P.-C. Hu, T. S. Lucier, S. N. Peterson, H. O. Smith, C. A. Hutchinson III, and J. C. Venter. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397-403.
22. Garcia-Alles, L. F., C. Siebold, T. L. Nyffeler, K. Flükiger- Bruhwiler, P. Schneider, H. B. Burgi, U. Baumann, and B. Erni. 2004. Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism. Biochemistry 43:13037-13045.
23. Gonzalez, C. F., A. J. Stonestrom, G. L. Lorca, and M. H. Saier, Jr. 2005. Biochemical characterization of phosphoryl transfer involving HPr of the phosphoenolpyruvate-dependent phosphotransferase system in Treponema denticola, an organism that lacks PTS permeases. Biochemistry 44:598-608.
24. Greenberg, D. B., J. Stülke, and M. H. Saier, Jr. 2002. Domain analysis of transcriptional regulators bearing PTS-regulatory domains. Res. Microbiol. 153:519-526.
25. Gutknecht, R., R. Beutler, L. F. Garcia-Alles, U. Baumann, and B. Erni. 2001. The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor. EMBO J. 20:2480-2486.
26. Halbedel, S., C. Hames, and J. Stülke. 2004. In vivo activity of enzymatic and regulatory components of the phosphoenolpyruvate:sugar phosphotransferase system in Mycoplasma pneumoniae. J. Bacteriol. 186:7936-7943.
27. Higgins, C. F. 1992. ABC transporters: from microorganisms to man. Annu. Rev. Cell Biol. 8:67-113.
28. Hoischen, C., J. Reizer, A. Dijkstra, S. Rottem, and M. H. Saier, Jr. 1993. Presence of protein constituents of the gram-positive bacterial phosphotransferase regulatory system in Acholeplasma laidlawii. J. Bacteriol. 175: 6599-6604.
29. Hu, K.-Y., and M. H. Saier, Jr. 2002. Phylogeny of phosphoryl transfer proteins of the phosphoenolpyruvate-dependent sugar transporting phosphotransferase system. Res. Microbiol. 153:405-415.
30. Huang, K., G. Kapadia, P. P. Zhu, A. Peterkofsky, and O. Herzberg. 1998. A promiscuous binding surface: crystal structure of the IIA domain of the glucose-specific permease from Mycoplasma capricolum.. Structure 6:697-710.
31. Huber, R., T. A. Langworthy, H. König, M. Thomm, C. R. Woese, U. B. Sleytr, and K. O. Stetter. 1986. Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C. Arch. Microbiol. 144:324-333.
32. Huber, R., and K. O. Stetter. 1992. The order Thermotogales, p. 3809-3815. In A. Balows et al. (ed.). The prokaryotes: a handbook on the biology of bacteria. Ecophysiology, isolation, identification, applications, 2nd ed., vol. 4. Springer, Berlin, Germany.
33. Hvorup, R. N., A. B. Chang, and M. H. Saier, Jr. 2003. Bioinformatic analyses of homologues of the bacterial L-ascorbate PTS permeases. J. Mol. Microbiol. Biotechnol. 6:191-205.
34. Jessberger, R. 2002. The many functions of SMC proteins in chromosome dynamics. Nat. Rev. Mol. Cell Biol. 3:767-778.
35. Ntr and aspartokinase to regulate bacterial oligopeptide transport. J. Biol. Chem. 276:21311-21316.
36. Glc in Escherichia coli. J. Biol. Chem. 279:31613-31621.
37. Kristich, C. J., G. D. Glekas, and G. W. Ordal. 2003. The conserved cytoplasmic module of the transmembrane chemoreceptor McpC mediates carbohydrate chemotaxis in Bacillus subtilis. Mol. Microbiol. 47:1353-1366.
38. Kundig, W., S. Ghosh, and S. Roseman. 1964. Phosphate bound to histidine in a protein as an intermediate in a novel phosphotransferase system. Proc. Natl. Acad. Sci. USA 52:1067-1074.
39. Lengeler, J. W., and K. Jahreis. 1996. Phosphotransferase systems or PTSs as carbohydrate transport and as signal transduction systems, p. 573-598. In W. N. Konings et al. (ed.), Handbook of biological physics, vol. 2. Elsevier Science B.V., Amsterdam, The Netherlands.
40. Liao, D. I., E. Silverton, Y. J. Seok, B. R. Lee, A. Peterkofsky, and D. R. Davies. 1996. The first step in sugar transport: crystal structure of the amino terminal domain of enzyme 1 of the E. coli PEP:sugar phosphotransferase system and a model of the phosphotransfer complex with HPr. Structure 4:861-872.
41. Makarova, K. S., L. Aravind, Y. I. Wolf, R. L. Tatusov, K. W. Minton, E. V. Koonin, and M. J. Daly. 2001. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65:44-79.
42. Marchler-Bauer, A., and S. H. Bryant. 2004. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 32:W327-W331.
43. Martin-Lluesma, S., V. M. Stucke, and E. A. Nigg. 2002. Role of Hec1 in spindle checkpoint signaling and kinetochore recruitment of Mad1/Mad2. Science 297:2267-2270.
44. Meier, T. I., R. B. Peery, K. A. McAllister, and G. Zhao. 2000. Era GTPase of Escherichia coli: binding to 16S rRNA and modulation of GTPase activity by RNA and carbohydrates. Microbiology 146:1071-1083.
45. Merrick, M. J. 1993. In a class of its own-the RNA polymerase sigma factor sigma 54 (sigma N). Mol. Microbiol. 10:903-909.
46. 54-dependent promoters. Mol. Microbiol. 3:1765-1775.
47. Merrick, M. J., and R. A. Edwards. 1995. Nitrogen control in bacteria. Microbiol. Rev. 59:604-622.
48. Merzbacher, M., C. Detsch, W. Hillen, and J. Stülke. 2004. Mycoplasma pneumoniae HPr kinase/phosphorylase. Eur. J. Biochem. 271:367-374.
49. Mijakovic, I., S. Poncet, A. Galinier, V. Monedero, S. Fieulaine, J. Janin, S. Nessler, J. A. Marquez, K. Scheffzek, S. Hasenbein, W. Hengstenberg, and J. Deutscher. 2002. Pyrophosphate-producing protein dephosphorylation by HPr kinase/phosphorylase: a relic of early life? Proc. Natl. Acad. Sci. USA 99:13442-13447.
50. Mitchell, W. J., J. Reizer, C. Herring, C. Hoischen, and M. H. Saier, Jr. 1993. Identification of a phosphoenolpyruvate:fructose phosphotransferase system (fructose-1-P forming) in Listeria monocytogenes. J. Bacteriol. 175: 2756-2761.
51. Moran, N. A. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583-586.
52. Nelson, K. E., R. A. Clayton, S. R. Gill, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, W. C. Nelson, K. A. Ketchum, L. McDonald, T. R. Utterback, J. A. Malek, K. D. Linher, M. M. Garrett, A. M. Stewart, M. D. Cotton, M. S. Pratt, C. A. Phillips, D. Richardson, J. Heidelberg, G. G. Sutton, R. D. Fleischmann, J. A. Eisen, O. White, S. L. Salzberg, H. O. Smith, J. C. Venter, and C. M. Fraser. 1999. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermologa maritima. Nature 399:323-329.
53. Nessler, S., S. Fieulaine, S. Poncet, A. Galinier, J. Deutscher, and J. Janin. 2003. HPr kinase/phosphorylase, the sensor enzyme of catabolite repression in gram-positive bacteria: structural aspects of the enzyme and the complex with its protein substrate. J. Bacteriol. 185:4003-4010.
54. O'Toole, R., D. L. Milton, P. Horstedt, and H. Wolf-Watz. 1997. RpoN of the fish pathogen Vibrio (Listonella) anguillarum is essential for flagellum production and virulence by the water-borne but not intraperitoneal route of inoculation. Microbiology 143:3849-3859.
55. Pao, S. S., I. T. Paulsen, and M. H. Saier, Jr. 1998. The major facilitator superfamily. Microbiol. Mol. Biol. Rev. 62:1-32.
56. Paulsen, I. T., J. Reizer, R. Z. Jin, E. C. Lin, and M. H. Saier, Jr. 2000. Functional genomic studies of dihydroxyacetone utilization in Escherichia coli. Microbiology 146:2343-2344.
57. Paulsen, I. T., M. K. Sliwinski, and M. H. Saier, Jr. 1998. Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. J. Mol. Biol. 277:573-592.
58. Peterkofsky, A., G. Wang, D. S. Garrett, B. R. Lee, Y. J. Seek, and G. M. Clore. 2001. Three-dimensional structures of protein-protein complexes in the E. coli PTS. J. Mol. Microbiol. Biotechnol. 3:347-354.
59. Pieper, U., G. Kapadia, P. P. Zhu, A. Peterkofsky, and O. Herzberg. 1995. Structural evidence for the evolutionary divergence of mycoplasma from gram-positive bacteria: the histidine-containing phosphocarrier protein. Structure 3:781-790.
60. + symport by phosphoenolpyruvate- dependent enzyme I/HPr-mediated phosphorylation. Proc. Natl. Acad. Sci. USA 92:778-782.
61. Poolman, B., T. J. Royer, S. E. Mainzer, and B. F. Schmidt. 1989. Lactose transport system of Streptococcus thermophilus: a hybrid protein with homology to the melibiose carrier and enzyme III of phosphoenolpyruvate-dependent phosphotransferase systems. J. Bacteriol. 171:244-253.
62. Postma, P. W., J. W. Lengeler, and G. R. Jacobson. 1996. Phosphoenolpyruvate: carbohydrate phosphotransferase systems, p. 1149-1174. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, D.C.
63. Powell, B. S., D. L. Court, T. Inada, Y. Nakamura, V. Michotey, X. Cui, A. Reizer, M. H. Saier, Jr., and J. Reizer. 1995. Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. J. Biol. Chem. 270:4822-4839.
64. Pries, A., H. Priefert, N. Kruger, and A. Steinbuchel. 1991. Identification and characterization of two Alcaligenes eutrophus gene loci relevant to the poly(β-hydroxybutyric acid)-leaky phenotype which exhibit homology to ptsH and ptsI of Escherichia coli. J. Bacteriol. 173:5843-5853.
65. Ntr from Escherichia coli: a novel enzyme of the phosphoenolpyruvate-dependent phosphotransferase system exhibiting strict specificity for its phosphoryl acceptor, NPr. J. Biol. Chem. 274:26185-26191.
66. Reizer, J., C. Hoischen, F. Titgemeyer, C. Rivolta, R. Rabus, J. Stülke, D. Karamata, M. H. Saier, Jr., and W. Hillen. 1998. A novel protein kinase that controls carbon catabolite repression in bacteria. Mol. Microbiol. 27: 1157-1169.
67. Reizer, J., A. Reizer, H. L. Kornberg, and M. H. Saier, Jr. 1994. 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.
68. Reizer, J., A. Reizer, M. J. Lagrou, K. R. Folger, C. K. Stover, and M. H. Saier, Jr. 1999. Novel phosphotransferase systems revealed by bacterial genome analysis: the complete repertoire of pts genes in Pseudomonas aeruginosa. J. Mol. Microbiol. Biotechnol. 1:289-293.
69. Reizer, J., A. Reizer, M. J. Merrick, G. Plunkett III, D. J. Rose, and M. H. Saier, Jr. 1996. Novel phosphotransferase-encoding genes revealed by analysis of the Escherichia coli genome: a chimeric gene encoding an enzyme I homologue that possesses a putative sensory transduction domain. Gene 181:103-108.
70. Reizer, J., A. Reizer, M. H. Saier, Jr., and G. R. Jacobson. 1992. A proposed link between nitrogen and carbon metabolism involving protein phosphorylation in bacteria. Protein Sci. 1:722-726.
71. Reizer, J., A. Reizer, M. Yamada, and M. H. Saier, Jr. 1998. The glucitol permease of Escherichia coli: a tripartite permease of the phosphotransferase system. Microbiology 144:1463-1464.
72. Reizer, J., and M. H. Saier, Jr. 1997. Modular multidomain phosphoryl transfer proteins of bacteria. Curr. Opin. Struct. Biol. 7:407-415.
73. Reizer, J., B. Schneider, A. Reizer, and M. H. Saier, Jr. 1999. A hybrid response regulator possessing a PEP-dependent phosphorylation domain. Microbiology 145:987-989.
74. Reyes-Ramirez, F., R. Little, and R. Dixon. 2001. Role of Escherichia coli nitrogen regulatory genes in the nitrogen response of the Azotobacter vinelandii NifL-NifA complex. J. Bacteriol. 183:3076-3082.
75. Saier, M. H., Jr. 1977. Bacterial phosphoenolpyruvate:sugar phosphotransferase systems: structural, functional, and evolutionary interrelationships. Bacteriol. Rev. 41:856-871.
76. Saier, M. H., Jr. 1989. Protein phosphorylation and allosteric control of inducer exclusion and catabolite repression by the bacterial phosphoenolpyruvate:sugar phosphotransferase system. Microbiol. Rev. 53:109-120.
77. Saier, M. H., Jr. 2000. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. 64:354-411.
78. Saier, M. H., Jr., S. Chauvaux, G. M. Cook, J. Deutscher, I. T. Paulsen, J. Reizer, and J.-J. Ye. 1996. Catabolite repression and inducer control in gram-positive bacteria. Microbiology 142:217-230.
79. Saier, M. H., Jr., S. Chauvaux, J. Deutscher, J. Reizer, and J.-J. Ye. 1995. Protein phosphorylation and the regulation of carbon metabolism in gram-negative versus gram-positive bacteria. Trends Biochem. Sci. 20:267-271.
80. Saier, M. H., Jr., B. U. Feucht, and S. Roseman. 1971. Phosphoenolpyruvate-dependent fructose phosphorylation in photosynthetic bacteria. J. Biol. Chem. 246:7819-7821.
81. Saier, M. H., Jr., R. N. Hvorup, and R. D. Barabote. 2005. Evolution of the bacterial phosphotransferase system: from carriers and enzymes to group translocators. Biochem. Soc. Trans. 33:220-224.
82. 14C] mannitol catalyzed by the enzyme II complexes of the phosphoenolpyruvate:mannitol phosphotransferase systems in Spirochaeta aurantia and Salmonella typhimurium. J. Biol. Chem. 251:3834-3837.
83. Saier, M. H., Jr., M. J. Newman, and A. W. Rephaeli. 1977. Properties of a phosphoenol-pyruvate:mannitol phosphotransferase system in Spirochaeta aurantia. J. Biol. Chem. 252:8890-8898.
84. Saier, M. H., Jr., and J. Reizer. 1994. The bacterial phosphotransferase system: new frontiers 30 years later. Mol. Microbiol. 13:755-764.
85. Saier, M. H., Jr., and J. T. Staley. 1977. Phosphoenolpyruvate:sugar phosphotransferase system in Ancalomicrobium adetum. J. Bacteriol. 131:716-718.
86. Saier, M. H., Jr., R. Tam, A. Reizer, and J. Reizer. 1994. Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport. Mol. Microbiol. 11:841-847.
87. Saier, M. H., Jr., P. Werner, and M. Müller. 1989. Insertion of proteins into bacterial membranes: mechanism, characteristics and comparisons with the eukaryotic process. Microbiol. Rev. 53:333-366.
88. Schmid, K., M. Schupfner, and R. Schmitt. 1982. Plasmid-mediated uptake and metabolism of sucrose by Escherichia coli K-12. J. Bacteriol. 151:68-76.
89. Schmidt, A. J., D. A. Ryjenkov, and M. Gomelsky. 2005. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J. Bacteriol. 187:4774-4781.
90. Segura, D., and G. Espin. 1998. Mutational inactivation of a gene homologous to Escherichia coli ptsP affects poly-β-hydroxybutyrate accumulation and nitrogen fixation in Azotobacter vinelandii. J. Bacteriol. 180:4790-4798.
91. Seok, Y. J., M. Sondej, P. Badawi, M. S. Lewis, M. C. Briggs, H. Jaffe, and A. Peterkofsky. 1997. High affinity binding and allosteric regulation of Escherichia coli glycogen phosphorylase by the histidine phosphocarrier protein, HPr. J. Biol. Chem. 272:26511-26521.
92. Sharma, A., and A. Mondragon. 1995. DNA topoisomerases. Curr. Opin. Struct. Biol. 5:39-47.
93. Siebold, C., I. Arnold, L. F. Garcia-Alles, U. Baumann, and B. Erni. 2003. Crystal structure of the Citrobacter freundii dihydroxyacetone kinase reveals an eight-stranded alpha-helical barrel ATP-binding domain. J. Biol. Chem. 278:48236-48244.
94. Siebold, C., L. F. Garcia-Alles, B. Erni, and U. Baumann. 2003. A mechanism of covalent substrate binding in the X-ray structure of subunit K of the Escherichia coli dihydroxyacetone kinase. Proc. Natl. Acad. Sci. USA 100:8188-8192.
95. Simm, R., M. Morr, A. Kader, M. Kimtz, and U. Romling. 2004. GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility. Mol. Microbiol. 53:1123-1134.
96. Simoni, R. D., M. Levinthal, F. D. Kundig, W. Kundig, B. Anderson, P. E. Hartman, and S. Roseman. 1967. Genetic evidence for the role of a bacterial phosphotransferase system in sugar transport. 58:1963-1970.
97. Stonestrom, A., R. D. Barabote, C. Gonzalez, and M. H. Saier, Jr. 2005. Bioinformatic analyses of bacterial HPr kinase homologues. Res. Microbiol. 156:443-451.
98. Stülke, J. 2002. Control of transcription termination in bacteria by RNA-binding proteins that modulate RNA structures. Arch. Microbiol. 177:433-440.
99. Stülke, J., M. Arnaud, G. Rapoport, and I. Martin-Verstraete. 1998. PRD-a protein domain involved in PTS-dependent induction and carbon catabolite repression of catabolic operons in bacteria. Mol. Microbiol. 28: 865-874.
100. Stülke, J., and W. Hillen. 1998. Coupling physiology and gene regulation in bacteria: the phosphotransferase sugar uptake system delivers the signals. Naturwissenschaften 85:583-592.
101. Tchieu, J. H., V. Norris, J. S. Edwards, and M. H. Saier, Jr. 2001. The complete phosphotransferase system in Escherichia coli.. J. Mol. Microbiol. Biotechnol. 3:329-346.
102. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
103. Titgemeyer, F., K. Jahreis, R. Ebner, and J. W. Lengeler. 1996. Molecular analysis of the scrA and scrB genes from Klebsiella pneumoniae and plasmid pUR400, which encode the sucrose transport protein enzyme II Scr of the phosphotransferase system and a sucrose-6-phosphate invertase. Mol. Gen. Genet. 250:197-206.
104. Titgemeyer, F., J. Walkenhorst, X. Cui, J. Reizer, and M. H. Saier, Jr. 1994. Proteins of the phosphoenolpyruvate:sugar phosphotransferase system in Streptomyces: possible involvement in the regulation of antibiotic production. Res. Microbiol. 145:89-92.
105. Ueda, K., A. Yamashita, J. Ishikawa, M. Shimada, T. O. Watsuji, K. Morimura, H. Ikeda, M. Hattori, and T. Beppu. 2004. Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res. 32:4937-4944.
106. van Tilbeurgh, H., and N. Declerck. 2001. Structural insights into the regulation of bacterial signalling proteins containing PRDs. Curr. Opin. Struct. Biol. 11:685-693.
107. Wassmann, K., V. Liberal, and R. Benezra. 2003. Mad2 phosphorylation regulates its association with Mad1 and the APC/C. EMBO J. 22:797-806.
108. Welch, R. A., V. Burland, G. Plunkett III, P. Redford, P. Roesch, D. Rasko, E. L. Buckles, S. R. Liou, A. Boutin, J. Hackett, D. Stroud, G. F. Mayhew, D. J. Rose, S. Zhou, D. C. Schwartz, N. T. Perna, H. L. Mobley, M. S. Donnenberg, and F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Eschericnia coli. Proc. Natl. Acad. Sci. USA 99:17020-17024.
109. White, O., J. A. Eisen, J. F. Heidelberg, E. K. Hickey, J. D. Peterson, R. J. Dodson, D. H. Haft, M. L. Gwinn, W. C. Nelson, D. L. Richardson, K. S. Moffat, H. Qin, L. Jiang, W. Pamphile, M. Crosby, M. Shen, J. J. Vamathevan, P. Lam, L. McDonald, T. Utterback, C. Zalewski, K. S. Makarova, L. Aravind, M. J. Daly, K. W. Minton, R. D. Fleischmann, K. A. Ketchum, K. E. Nelson, S. Salzberg, H. O. Smith, J. C. Venter, and C. M. Fraser. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286:1571-1577.
110. Wu, L.-F., J. M. Tomich, and M. H. Saier, Jr. 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.
111. Yamada, M., and M. H. Saier, Jr. 1987. Glucitol-specific enzymes of the phospho-transferase system in Escherichia coli. Nucleotide sequence of the gut operon. J. Biol. Chem. 262:5455-5463.
112. Yu, P. L., R. A. Hodge, and X. P. Li. 1990. In vitro expression of Lac-PTS and tagatose 1,6-bisphosphate aldolase genes from Lactococcus lactis subsp. cremoris plasmid pDI-21. Appl. Microbiol. Biotechnol. 33:677-679.
113. Zhai, Y., J. Tchieu, and M. H. Saier, Jr. 2002. A web-based Tree View (TV) program for the visualization of phylogenetic trees. J. Mol. Microbiol. Biotechnol. 4:69-70.
114. Zuniga, M., I. Comas, R. Linaje, V. Monedero, M. J. Yebra, C. D. Esteban, J. Deutscher, G. Perez-Martinez, and F. Gonzalez-Candelas. 2005. Horizontal gene transfer in the molecular evolution of mannose PTS transporters. Mol. Biol. Evol. 22:1673-1685.