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Chapter 19 : Purine, Pyrimidine, and Pyridine Nucleotide Metabolism

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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

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Gene Expression and Regulation
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Bacteria and Archaea
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Pyrimidine Nucleotide Biosynthesis
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Purine Nucleotide Biosynthesis
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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
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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
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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
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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
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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
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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
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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
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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
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Tables

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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

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