1887

Chapter 19 : Purine, Pyrimidine, and Pyridine Nucleotide Metabolism

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817992/9781555812058_Chap19-1.gif /docserver/preview/fulltext/10.1128/9781555817992/9781555812058_Chap19-2.gif

Abstract:

A fairly complete description of the genes involved in the de novo synthesis of purine and pyrimidine nucleotides and of the pyridine nucleotide coenzymes in is now available. Of the enzymes for de novo synthesis of inosine monophosphate (IMP), most are similar in to those in other organisms, including . Genes encoding functions involved in purine transport, salvage, and interconversion are scattered on the chromosome of . Binding of PyrR to the specific RNA site is promoted by uridine monophosphate (UMP) and uridie triphosphate (UTP) and is antagonized by 5-phospho-d-ribosyl-α, 1-pyrophosphate (PRPP), which places transcriptional attenuation under the feedback control of the end products of the pathway and provides for activation of nucleotide biosynthesis by the metabolite PRPP, as also seen in the purine biosynthetic pathway. dihydroorotate (DHO) dehydrogenase is composed of two subunits, PyrDI and PyrDII, which are homologues of PyrDb and PyrK, respectively. This is the only DHO dehydrogenase produced by , where it is clear that the pyrDI gene is essential for pyrimidine biosynthesis and that deletion of the pyrDII gene results in pyrimidine bradytrophy. The protein YqeJ, with 33% amino acid sequence identity to NadD, is likely to encode nicotinate mononucleotide adenyltransferase. NAD is phosphorylated by ATP and NAD kinase to form NADP, but the corresponding gene from B. subtilis has not been annotated.

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

De novo purine nucleotide biosynthesis in the pathway to IMP.

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

De novo purine nucleotide biosynthesis in synthesis of GMP and AMP.

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Purine transport, salvage, and interconversion in . Gene designations are , adenylosuccinate lyase; phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase; , adenylosuccinate synthetase; , IMP dehydrogenase; , GMP synthetase; adenine phosphoribosyltransferase; , hypoxanthine-guanine phosphoribosyltransferase; xanthine phosphoribosyltransferase; guaC, GMP reductase; adenosine/deoxyadenosine phosphorylase; , guanosine/deoxyguanosine-inosine/deoxyinosine phosphorylase; deoxycytidine-deoxyadenosine kinase; , deoxyguanosine kinase; adenine deaminase; , hypoxanthine/guanine permease; adenylate kinase; nucleoside diphosphophokinase; , ribonucleotide reductase; putative guanylate kinase; xanthine pennease; ( ), putative adenine transport system. Dashed lines indicate steps catalyzed by multiple enzymes.

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

De novo pyrimidine nucleotide biosynthesis in and , thymidylate synthases A and B; , thymidylate kinase. For other gene designations, see Fig. 3 .

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Formation of pyrimidine deoxynucleotides in

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6
FIGURE 6

Mechanism of the regulation of the operon in by transcriptional attenuation. Numbered arrows refer to self-complementary segments of mRNA that form secondary structures functional in attenuation. In the absence of PyrR binding, segments 1 and 2 base pair to form the antiterminator structure (lower left). This structure prevents base pairing of segment 3 with segment 4, thus preventing formation of the terminator structure (lower right) and allowing transcription of downstream genes. Binding of PyrR to a specific sequence (crosshatched bars), called the anti-antiterminator or binding loop, is promoted by UMP and/or UTP. PyrR binding stabilizes the anti-antiterminator stem-loop, disrupts the antiterminator, and permits formation of the terminator, reducing transcription of downstream genes. Binding of PRPP to PyrR antagonizes the action of UMP/UTP. Three attenuation sites are located within the and operons, but the operon has two attenuation sites ( ), and the operon has only one ( ).

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 7
FIGURE 7

Pyrimidine transport, salvage, and interconversion in

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 8
FIGURE 8

Biosynthesis of NAD in

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817992.chap19
1. Andersen, P. S.,, P. J. G. Jansen,, and K. Hammer. 1994. Two different dihydroorotate dehydrogenases in Lactococus lactis. J. Bacteriol. 176: 3975 3982.
2. Andersen, P. S.,, J. Martinussen,, and K. Hammer. 1996. Sequence analysis and identification of the pyrK-pyrDb-pyrF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis. J. Bacteriol. 178: 5005 5012.
2a.. Andersen, R. B.,, and J. Neuhard. 2001. Deoxynucleoside kinases encoded by the yaaG and yaaF genes of Bacillus subtilis. Substrate specificity and kinetic analysis of de-oxyguanosine kinase with UTP as the preferred phosphate donor. J. Biol. Chem. 276: 5518 5524.
3. Appleby, T. C.,, C. Kinsland,, T. P. Begley,, and S. E. Ealick. 2000. The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase. Proc. Natl. Acad. Sci. USA 97: 2005 2010.
4. Arnvig, K.,, B. Hove-Jensen,, and R. L. Switzer. 1990. Purification and properties of phosphoribosyl-diphosphate synthetase from Bacillus subtilis. Eur. J. Biochem. 192: 195 200.
5. Bentsen, A. K.,, T. A. Larsen,, A. Kadziola,, S. Larsen,, and K. W. Harlow. 1996. Overexpression of Bacillus subtilis phosphoribosylpyrophosphate synthetase and crystallization and preliminary X-ray characterization of the free enzyme and its substrate-effector complexes. Proteins 24: 238 246.
6. Blattner, F. R., et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453 1474.
7. Bolotin, A.,, S. Mauger,, K. Malarme,, S. D. Ehrlich,, and A. Sorokin. 1999. Low-redundancy sequencing of the entire Lactococcus lactis IL 1403 genome. Antonie Leeuwenhoek 76: 27 76.
8. Bonner, E. R.,, J. N. D'EIia,, and R. L. Switzer. Unpublished data.
9.[Reference deleted].
10. Cantoni, R.,, M. Branzoni,, J. Labo,, M. Rizzi,, and G. Riccardi. 1998. The MTCY428.08 gene of Mycobacterium tuberculosis codes for NAD + synthetase. J. Bacteriol. 180: 3218 3221.
11. Chen, S.,, D. R. Tomchick,, D. Wolle,, P. Hu,, J. L. Smith,, R. L. Switzer,, and H. Zalkin. 1997. Mechanism of the synergistic end-product regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase by nucleotides. Biochemistry 36: 10718 10726.
12. Christiansen, L. C.,, S. Schou,, P. Nygaard,, and H. H. Saxild. 1997. Xanthine metabolism in Bacillus subtilis: characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism. J. Bacteriol. 179: 2540 2550.
13. Cole, S. T., et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537 544.
14. Curnow, A. W.,, K. W. Hong,, R. Yuan,, S. I. Kim,, O. Martins,, W. Winkler,, T. M. Henkin,, and D. Soli. 1997. Glu-tRNA Gln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl. Acad. Sci. USA 94: 11819 11826.
15. Eads, J. C.,, D. Ozturk,, T. B. Wexler,, C. Grubmeyer,, and J. C. Sacchettini. 1997. A new function for a common fold: the crystal structure of quinolinic acid phosphoribosyltransferase. Structure 5: 47 58.
16. Ebbole, D. J.,, and H. Zalkin. 1987. Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide biosynthesis. J. Biol. Chem. 262: 8274 8287.
17. Ebbole, D. J., andH. Zalkin. 1988. Detection of pur operon-attenuated mRNA and accumulated degradation intermediates in Bacillus subtilis. J. Biol. Chem. 263: 10894 10902.
18. Ebbole, D. J.,, and H. Zalkin. 1989. Interaction of a putative repressor protein with an extended control region of the Bacillus subtilis pur operon . J. Biol. Chem. 264: 3553 3561.
19. Elagöz, A.,, A. Abdi,, J.-C. Hubert,, and B. Kammerer. 1996. Structure and organisation of the pyrimidine biosynthesis pathway genes in Lactobacillus plantarum: a PCR strategy for sequencing without cloning. Gene 182: 37 43.
20. Eriksen, T.A. 1998. Ph.D.thesis. University of Copenhagen, Copenhagen, Denmark.
21. Eriksen, T. A.,, A. Kadziola,, A.-K. Bentsen,, K. W. Harlow,, and S. Larsen. 2000. Structural basis for the function of Bacillus subtilis phosphoribosylpyrophosphate synthetase. Nat. Struct. Biol. 7: 303 308.
22. Ghim, S.-Y.,, C. C. Kim,, E. R. Bonner,, J. N. D'Elia,, G. K. Grabner,, and R. L. Switzer. 1999. The Enterococcus faecalis pyr operon is regulated by autogenous transcriptional attenuation at a single site in the 5' leader. J. Bacteriol. 181: 1324 1329.
23. Ghim, S.-Y.,, and J. Neuhard. 1994. The pyrimidine biosynthesis operon of the thermophile Bacillus caldolyticus includes genes for uracil phosphoribosyltransferase and uracil permease. J. Bacteriol. 176: 3698 3707.
24. Ghim, S.-Y.,, P. Nielsen,, and J. Neuhard. 1994. Molecular characterization of pyrimidine biosynthesis genes from the thermophile Bacillus caldolyticus. J. Gen. Microbiol. 140: 479 491.
25. Ghim, S.-Y.,, and R. L. Switzer. 1996. Characterization of cis-acting mutations in the first attenuator region of the B. subtilis pyr operon that are defective in regulation of expression by pyrimidines. J. Bacteriol. 178: 2351 2355.
26. Ghim, S. Y.,, S. K. Choi,, B. S. Shin,, Y. M. Jeong,, S. Sorokin,, S. D. Ehrlich,, and S. H. Park. 1998. Sequence analysis of the Bacillus subtilis 168 chromosome region between the sspC and odhA loci (184 degrees-180 degrees). DNA Res 5: 195 201.
27. Hammer-Jespersen, K.,, and A. Munch-Petersen. 1973. Mutants of Escherichia coli unable to metabolize cytidine: isolation and characterization. Mol. Gen. Genet. 126: 177 186.
28. Hilden, I.,, B. N. Krath,, and B. Hove-Jensen. 1995. Tricistronic operon expression of the genes gcaD ( cms), which encodes N-acetylglucosamine 1-phosphate uridyltrans-ferase, prs, which encodes phosphoribosyl diphosphate synthetase, and etc in vegetative cells of Bacillus subtilis . J. Bacteriol. 177: 7280 7284.
29. Ipata, P. L.,, R. Sgarrella,, and M. G. Tozzi. 1985. Mechanism of purine nucleotide utilization in Bacillus cereus. Curr. Top. Cell. Regul. 26: 419 432.
30. Jensen, K. F. 1978. Two purine nucleoside phosphorylases in Bacillus subtilis. Biochim. Biophys. Acta 525: 346 356.
31. Jensen, K. F.,, and O. Björnberg. 1998. Evolutionary and functional families of dihyroorotate dehydrogenases. Paths to Pyrimidines 6: 20 28.
32. Kadziola, A.,, J. Neuhard,, and S. Larsen. 2000. Presented at the Enzymes of Nucleotide Metabolism Conference, Krogerup, Copenhagen, Denmark.
33. Kahler, A. E.,, F. S. Nielsen,, and R. L. Switzer. 1999. Biochemical characterization of the heteromeric Bacillus subtilis dihydroorotate dehydrogenase and its isolated subunits. Arch. Biochem. Biophys. 371: 191 201.
34. Kahler, A. E.,, and R. L. Switzer. 1996. Identification of a novel gene of pyrimidine nucleotide biosynthesis, pyrDII, that is required for dihydrooroate dehydrogenase activity in Bacillus subtilis. J. Bacteriol. 178: 5013 5016.
35. Kilstrup, M.,, S. G. Jessing,, S. B. Wichmand-Jorgensen,, M. Madsen,, and D. Nilsson. 1998. Activation control of pur gene expression in Lactococcus lactis: proposal for a consensus activator binding sequence based on deletion analysis and site-directed mutagenesis of purC and purD promoter regions. J. Bacteriol. 180: 3900 3906.
36. Kilstrup, M.,, and J. Martinussen. 1998. A transcriptional activator, homologous to the Bacillus subtilis PurR repressor, is required for expression of purine biosynthetic genes in Lactococcus lactis. J. Bacteriol. 180: 3907 3916.
37. Kloudovi, A.,, and V. Fucik. 1974. Transport of nucleosides in Bacillus subtilis: characteristics of cytidine uptake. Nucleic Acids Res. 1: 629 637.
38. Kobayashi, M.,, Y. Fujiwara,, M. Goda,, H. Komeda,, and S. Shimizu. 1997. Identification of active sites in amidase: evolutionary relationships between amide bond- and peptide bond-cleaving enzymes. Proc. Natl. Acad. Sci. USA. 94: 11986 11991.
39. Krahn, J. M. 1998. Ph.D.thesis. Purdue University, West Lafayette, Indiana.
40. Krahn, J. M.,, J. H. Kim,, M. R. Burns,, R. R. Parry,, H. Zalkin,, and J. L. Smith. 1997. Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry 36: 11061 11068.
41. Kunst, F., et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249 256.
42. Landick, R.,, and C. Yanofsky,. 1987. Transcription attenuation, p. 1276 1301. In F. C. Neidhardt,, Roy Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low, Jr.,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, 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..
43. Li, S. 1998. M. S. thesis. Purdue University, West Lafayette, Indiana.
44. Li, X.,, G. M. Weinstock,, and B. E. Murray. 1995. Generation of auxotrophic mutants of Enterococcus faecalis. J. Bacteriol. 177: 6866 6873.
45. Lu, Y.,, and R. L. Switzer. 1996. Transcriptional attenuation of the Bacilliis subtilis pyr operon by the PyrR regulatory protein and uridine nucleotides in vitro. J. Bacteriol. 178: 7206 7211.
46. Lu, Y.,, R. J. Turner,, and R. L. Switzer. 1996. Function of the RNA secondary structures in the regulation of the Bacillus subtilis pyr operon expression. Proc. Natl. Acad. Sci. USA 93: 14462 14467.
47. Lu, Y.,, R. J. Turner,, and R. L. Switzer. 1995. Roles of the three transcriptional attenuators of the Bacillus subtilis pyrimidine biosynthetic operon in the regulation of its expression. J. Bacteriol. 177: 1315 1325.
48. Makaroff, C. A.,, H. Zalkin,, R. L. Switzer,, and S. J. Vollmer. 1983. Cloning of the Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase gene in Escherichia coli: nucleotide sequence determination and properties of the plasmid-encoded enzyme. J. Biol. Chem. 258: 10586 10593.
49. Martinussen, J.,, J. Schallert,, B. Andersen,, and K. Hammer. 2001. The pyrimidine operon pyrRPB-carA from Lactococcus lactis. J. Bacteriol. 183: 2785 2794.
50. Martinussen, J.,, P. Glaser,, P. S. Andersen,, and H. H. Saxild. 1995. Two genes encoding uracil phosphoribosyltransferase are present in Bacillus subtilis. J. Bacteriol. 177: 271 274.
51. Martinussen, J.,, and K. Hammer. 1998. The carB gene encoding the large subunit of carbamoylphosphate synthetase from Lactococcus lactis is transcribed monocistronically. J. Bacteriol. 180: 4380 4386.
52. Mehl, R. A.,, C. Kinsland,, and T. P. Begley. 2000. Identification of the Escherichia coli nicotinic acid mononucleotide adenylyltransferase gene. J. Bacteriol. 182: 4372 4374.
53. Meng, Q.,, and R. L. Switzer. Unpublished data.
54. Muchmore, C. R. A.,, J. M. Krahn,, J. H. Kim,, H. Zalkin,, and J. L. Smith. 1998. Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Protein Sci. 7: 39 51.
55. Nessi, C.,, A. M. Albertini,, M. L. Speranza,, and A. Galizzi. 1995. The outB gene of Bacillus subtilis codes for NAD synthetase. J. Biol. Chem. 270: 6181 6185.
56.[See reference 2a.]
57. Neuhard, J., 1983. Utilization of preformed pyrimidine bases and nucleosides, p. 95 148. In A. Munch-Petersen (ed.), Metabolism of Nucleotides, Nucleosides and Nudeobases in Microorganisms. Academic Press, New York, N.Y..
58. Newman, J. D. 1992. Ph.D.thesis. Marquette University, Milwaukee, Wisconsin.
59. Nielsen, F. S.,, P. S. Andersen,, and K. F. Jensen. 1996. The B form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centers. J. Biol. Chem. 271: 29359 29365.
60. Nilsson, D.,, and M. Kilstrup. 1998. Cloning and expression of the Lactococcus lactis purDEK genes, required for growth in milk. Appl. Environ. Microbiol. 64: 4321 4327.
61. Nilsson, D.,, and A. A. Lauridsen. 1992. Isolation of purine auxotrophic mutants of Lactococcus lactis and characterization of the gene hpt encoding hypoxanthine guanine phosphoribosyltransferase. Mol. Gen. Genet. 235: 359 364.
62. Nygaard, P.,, S. M. Bested,, A. K. Andersen, and H. H. Saxild. 2000. Bacillus subtilis guanine deaminase is encoded by the yknA gene and is induced during growth with purines as the nitrogen source. Microbiology 146: 3061 3069.
63. Nygaard, P.,, P. Duckert,, and H. H. Saxild. 1996. Role of adenine deaminase in purine salvage and nitrogen metabolism and characterization of the ade gene in Bacillus subtilis. J. Bacteriol. 178: 846 853.
64. Peltonen, T.,, and P. Mantsala. 1999. Isolation and characterization of a purC ( orf)QLF operon from Lactococcus lactis MG1614. Mol. Gen. Genet. 261: 31 41.
65. Penfound, T.,, and J. W. Foster,. 1996. Biosynthesis and recycling of NAD, p. 721 730. In F. C. Neidhardt,, R. Curtiss,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella. Cellular and Molecular Biology, vol. 1. American Society for Microbiology, Washington, D.C..
66. Pugmire, M. J.,, and S. E. Ealick. 1998. The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation. Structure 6: 1467 1479.
67. Quinn, C. L.,, B. T. Stephenson,, and R. L. Switzer. 1991. Functional organization and nucleotide sequence of the Bacillus subtilis pyrimidine biosynthetic operon. J. Biol. Chem. 266: 9113 9127.
68. Rappu, P.,, B. S. Shin,, H. Zalkin,, and P. Mäntsälä. 1999. A role for a highly conserved protein of unknown function in regulation of Bacillus subtilis purA by the purine repressor. J. Bacteriol. 181: 3810 3815.
69. Rizzi, M.,, C. Nessi,, A. Mattevi,, A. Coda,, M. Bolognesi,, and A. Galizzi. 1996. Crystal structure of NH 3-dependent NAD + synthetase from Bacillus subtilis. EMBO J. 15: 5125 5134.
70. Rowland, P.,, F. S. Nielsen,, F. F. Jensen,, and S. Larsen. 1997. The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis. Structure 5: 239 252.
71. Savacool, H. K.,, and R. L. Switzer. Unpublished data.
72. Saxild, H. H.,, K. Brunstedt,, K. I. Nielsen,, H. Jarmer,, and P. Nygaard. Unpublished data.
73. Saxild, H. H.,, L. N. Andersen,, and K. Hammer. 1996. dra-nupC-pdp operon of Bacillus subtilis: nucleotide sequence, induction by deoxyribonucleosides, and transcriptional regulation by the deoR-encoded DeoR repressor protein. J. Bacteriol. 178: 424 434.
74. Saxild, H. H.,, J. H. Jacobsen,, and P. Nygaard. 1994. Genetic and physiological characterization of a formate-dependent 5?-phosphoribosyl-l-glycinamide transferase activity in Bacillus subtilis. Mol. Gen. Genet. 242: 415 420.
75. Saxild, H. H.,, J. H. Jacobsen, and P. Nygaard. 1995. Functional analysis of the Bacillus subtilis purT gene encoding formate-dependent glycinamide ribonucleotide transformylase. Microbiology 141: 2211 2218.
76. Saxild, H. H.,, and P. Nygaard. 1987. Genetic and physiological characterization of Bacillus subtilis mutants resistant to purine analogs. J. Bacteriol. 169: 2977 2983.
77. Saxild, H. H.,, and P. Nygaard. 1991. Regulation of levels of purine biosynthetic enzymes in Bacillus subtilis: effects of changing purine nucleotide pools. J. Gen. Microbiol. 137: 2387 2394.
78. Saxild, H. H.,, and P. Nygaard. 2000. The yexA gene product is required for phosphoribosylformylglycinamidine synthetase activity in Bacillus subtilis. Microbiology 146: 807 814.
79. Schneider, B. L.,, and L. J. Reitzer. 1998. Salmonelh typhimurium nit is nadE: defective nitrogen utilization and ammonia-dependent NAD synthetase. J. Bacteriol. 180: 4739 4741.
80. Schuch, R.,, A. Garibian,, H. H. Saxild,, P. J. Piggot,, and P. Nygaard. 1999. Nucleosides as a carbon source in Bacillus subtilis: characterization of the drm-pupG operon. Microbiology 145: 2957 2966.
81. Schultz, A. C.,, P. Nygaard,, and H. H. Saxild. 2001. Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator. J. Bacteriol. 183: 3293 3302.
82. Schultz, C. P.,, L. Ylisastigui-Pons,, L. Serina,, H. Sakamoto,, H. H. Mantsch,, J. Neuhard,, O. Barzu,, and A.-M. Gilles. 1997. Structural and catalytic properties of CMP kinase from Bacillus subtilis: a comparative analysis with the homologous enzyme from Escherichia coli. Arch. Biochem. Biophys. 340: 144 153.
83. Schumacher, M. A.,, K. Y. Choi,, H. Zalkin,, and R. G. Brennan. 1994. Crystal structure of the Lacl member, PurR, bound to DNA: minor groove binding by a-helices. Science 266: 763 770.
84. Shin, B. S.,, A. Stein,, and H. Zalkin. 1997. Interaction of the Bacillus subtilis purine repressor with DNA. J. Bacteriol. 179: 7394 7402.
85. Sinha, S.,, P. Rappu,, S. C. Lange,, P. Mantsala,, H. Zalkin,, and J. Smith. 1999. Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family. Proc. Natl. Acad. Sci. USA 96: 13074 13079.
85a.. Smith, J. L. Unpublished data.
86. Smith, J. L.,, E. J. Zaluzec,, J. P. Wary,, L. Niu,, R. L. Switzer,, H. Zalkin,, and Y. Satow. 1994. Structure of the allosteric regulatory enzyme of purine biosynthesis. Science 264: 1427 1433.
87. Sonenshein, A. L.,, J. A. Hoch,, and R. Losick (ed.). 1993. Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, D.C..
88. Sorokin, A. P.,, P. Serror,, P. Pujic,, V. Azevedo,, and S. D. Ehrlich. 1995. The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rspA gene products. Microbiology 141: 311 319.
89. Switzer, R. L.,, and R. J. Turner. 1998. PyrR: a widespread and mechanistically versatile regulator of bacterial pyr genes. Paths to Pyrimidines 6: 45 53.
90. Switzer, R. L.,, R. J. Turner,, and Y. Lu. 1999. Regulation of the Bacillus subtilis pyrimidine biosynthetic operon by transcriptional attenuation: control of gene expression by an mRNA-binding protein. Prog. Nucleic Acid Res. Mol. Biol. 62: 329 367.
91. Tomchick, D. R.,, R. J. Turner,, R. L. Switzer,, and J. L. Smith. 1998. Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a bifunctional pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Structure 6: 337 350.
92. Trach, K.,, J. W. Chapman,, P. Piggot,, D. LeCog,, and J. A. Hoch. 1988. Complete sequence and transcriptional analysis of the spoOF region of the Bacillus subtilis chromosome. J. Bacteriol. 170: 4194 4208.
93. Turner, R. J.,, E. R. Bonner,, G. K. Grabner,, and R. L. Switzer. 1998. Purification and characterization of Bacillus subtilis PyrR, a bifunctional pyr mRNA-binding attenuation protein/uracil phosphoribosyltransferase. J. Biol. Chem. 273: 5932 5938.
94. Turner, R. J.,, Y. Lu,, and R. L. Switzer. 1994. Regulation of the Bacillus subtilis pyrimidine biosynthetic ( pyr) gene cluster by an autogenous transcriptional attenuation mechanism. J. Bacteriol. 176: 3708 3722.
95. Van de Casteele, M.,, P. Chen,, M. Roovers,, C. Legrain,, and N. Glansdorff. 1997. Structure and expression of a pyrimidine gene cluster from the extreme thermophile Thermus Strain Z05. J. Bacteriol. 179: 3470 3481.
96. Waleh, N. S.,, and J. L. Ingraham. 1976. Pyrimidine ribonucleoside monophosphokinase and the mode of RNA turnover in Bacillus subtilis. Arch. Microbiol. 110: 49 54.
97. Weng, M.,, P. L. Nagy,, and H. Zalkin. 1995. Identification of the Bacillus subtilis pur operon repressor. Proc. Natl. Acad. Sci. USA 92: 7455 7459.
98. Weng, M.,, and H. Zalkin. 2000. Mutations in the Bacillus subtilis purine repressor that perturb PRPP effector function in vitro and in vivo. Curr. Microbiol. 41: 56 59.
99. Willison, J. C.,, and G. Tissot. 1994 - The Escherichia coli efg gene and the Rhodobacter capsulatus adgA gene code for the NH 3-dependent NAD synthetase. J. Bacteriol. 176: 3400 3402.
100. Yi, C. K.,, and L. S. Dietrich. 1972. Purification and properties of yeast nicotinamide adenine dinucleotide sunthetase. J. Biol. Chem. 247: 4794 4802.
100a.. Zalkin, H., 1993. De novo purine nucleotide synthesis, p. 335 341. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, D.C..
101. Zalkin, H.,, and J. E. Dixon. 1992. De novo purine nucleotide biosynthesis. Prog. Nucleic Acid Res. Mol. Biol. 42: 259 287.
102. Zalkin, H.,, and P. Nygaard,. 1996. Biosynthesis of purine nucleotides, p. 561 579. In F. C. Niedhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low, Jr.,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, vol. 1. American Society for Microbiology, Washington, D.C..
103. Zalkin, H.,, and J. L. Smith. 1998. Enzymes utilizing glutamine as an amide donor. Adv. Enzymol. Relat. Areas Mo. Biol. 72: 87 144.

Tables

Generic image for table
TABLE 1

Gene-enzyme relationships of the purine uptake, salvage, and interconversion pathway of and regulatory components involved in control of gene expression

Gene names in parentheses indicate previous or systematic designations.

PurR, purine repressor ( ); PucR, purine catabolism activator ( ). Repression by hypoxanthine and guanine is mediated by a putative transcription attenuation mechanism ( ). Repression by glucose is most likely mediated by the binding of CcpA to a CRE element in the control region ( ).

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19
Generic image for table
TABLE 2

Purine transport, salvage, and interconversion genes in the genomes of six low-G+C gram-positive bacteria, as identified by percent sequence identity to their homologs

The genome sequences of , , , , and (http://www.tigr.org) were analyzed for open reading frames with amino acid sequence similarity to the Ade, GuaC, DeoD, PupG, Hpt, Xpt, Apt, Gde, PbuG, or PbuX reading frame. The dreived amino acid sequence of the gene, which encodes adenosine deaminase, was taken from .

The metabolic steps are indicated by their gene symbols (see Fig. 3 ).

NF, not found.

A percentage figure indicates that, when using the tBLASTn algorithm, a reading frame with amino acid sequence similarity to the entire or open reading frame was found in the genome sequence in question. The numerical value indicates the degree of amino acid sequence identity.

The 75% amino acid sequence similarity between the . reading frame and the Apt reading frame was restricted to amino acid positions 125 to 170 of the sequence. A possible sequencing error in the sequence may have caused this lack of an overall similarity to the Apt sequence.

The plus sign refers to the presence of a similar gene designation in the published annotation list for the genome sequence ( ).

NA, no annotation.

The 25% amino acid sequence similarity between the candidate DeoD reading frame and the DeoD reading frame was restricted to a 45-animo-acid segment out of the total of 177 amino acids of the reading frame.

Citation: Switzer R, Zalkin H, Saxild H. 2002. Purine, Pyrimidine, and Pyridine Nucleotide Metabolism, p 255-269. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch19

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error