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Chapter 25 : De Novo Pyrimidine Nucleotide Synthesis

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Abstract:

The pathway of biosynthesis of pyrimidine nucleotides de novo from central metabolic intermediates is the same in all prokaryotic and eukaryotic organisms in which it has been examined, but as will be seen, the functional organization of the enzymes of the pathway and the means adopted for regulation of pyrimidine biosynthesis vary greatly from species to species. The primary structures of all of the enzymes of de novo UMP biosynthesis from are known because the genes encoding them have been sequenced. General properties of each of the enzymes have also been determined in studies with crude extracts, but only aspartate transcarbamylase has been purified to homogeneity and characterized in detail. General properties of the enzymes and genes encoding them are summarized. Further detail, with emphasis on the properties that distinguish the enzymes from their homologs in other species, follows. Enzymes of pyrimidine biosynthesis are inactivated in starving cells. Enzymes of purine and amino acid biosynthesis are also inactivated under the same conditions. The genes and enzymes of pyrimidine biosynthesis have not been extensively investigated in other grampositive species. A brief overview of pyrimidine biosynthesis in and , with emphasis on points of difference with is described. Regulation of plant carbamylphosphate synthetase invitro resembles regulation of the enzyme in many ways. The plant enzyme is inhibited by uridine nucleotides and activated by the purine nucleotides IMP, ITP, GMP, and GTP.

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25

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Transcription Start Site
0.47957793
Transcription Start Point
0.45348138
Pyrimidine Nucleotide Biosynthesis
0.44925016
Purine Nucleotide Biosynthesis
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0.47957793
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Figures

Image of Figure 1
Figure 1

Pathway for de novo synthesis of pyrimidine nucleotides. Gene designations and commonly used abbreviations for the individual enzymes are shown. These are denned fully in the text and in Table 2 . CPSase, carbamylphosphate synthetase; ATCase, aspartate transcarbamylaseelectron acceptor; DHOase, dihydroorotase; DHO-DHase, dihydroorotate dehydrogenase; A, ; AH, reduced acceptor; OPRTase, orotate phosphoribosyl-transferase; OMP-DCase, OMP decarboxylase.

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25
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Image of Figure 2
Figure 2

Allosteric regulation of the pyrimidine-repressible carbamylphosphate synthetase from Effects of allosteric activators and inhibitors as a function of the concentration of the substrate Mg-ATP are shown. In all cases, MgCl was maintained in 6 mM excess over the total ATP-plus-effector concentration. (A) ○, no effectors; Δ, plus 5 mM PRPP; □, plus 0.25 mM UMP. (B) •, no effectors; ▴, plus 2 mM GTP; ▪, plus 2 mM UTP. Reprinted from reference 73 with permission of copyright holder.

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25
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Image of Figure 3
Figure 3

Organization of the operon. Numbers represent the length of the DNA in kilobase pairs from the start of transcription, which is indicated by the arrow. Each thick dark line represents an ORF for each gene, with the overlap between lines depicting in exaggerated form the overlap between reading frames. Reprinted from reference with permission of the copyright holder.

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25
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Image of Figure 4
Figure 4

Sequence of the promoter region. The sequence spans nucleotides -125 to +170 relative to the site of transcription initiation (+1). The -35 and -10 regions of the promoter, the initial sequence of ORF1, and its predicted ribosome-binding site (RBS) are shown. A putative rho-independent transcriptional terminator sequence, in which arrows denote sequences that could base pair to form a stable stem-loop structure in the transcript, is shown. A consensus binding site for the Spo0A protein ( ) 100 bp 5' to the site of transcription initiation is indicated by double underlining. Reprinted with modifications from reference with permission of the copyright holder.

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25
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Figure 5

Features of the ORF1- intercistronic region of the operon. The sequence is of the nontranscribed strand of DNA from the 7 C-terminal codons of ORF1 through the 3 N-terminal codons of A putative weak promoter sequence is designated by -35? and -10? Sequence elements that are consistent with a coupled transcription translation mechanism of attenuation control of expression of and downstream genes are as follows: RBS, a possible ribosome-binding site and a short ORF for a putative leader peptide, whose coding sequence also includes a pyrimidine-rich transcription pause site (asterisks) and a potential rho-independent terminator (arrows indicate potential base-pairing sequences of the stem-loops). Reprinted from reference 85 with permission of the copyright holder.

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25
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Figure 6

Cessation of aspartate transcarbamylase (ATCase) synthesis prior to its degradation during stationary phase in 168. The bacteria were grown on rich medium and pulse-labeled with [H]leucine for 30 min at the times shown. The amount of radioactivity in immunoprecipitated aspartate transcarbamylase (Δ) and bulk trichloroacetic acid-precipitable protein (□) from samples collected at various times during growth and stationary phase are shown. Total aspartate transcarbamylase activity per milliliter of culture was also determined (▲) along with the turbidity of the culture (– – –). Details are given in reference , from which this figure was reprinted with permission of the copyright holder.

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25
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Tables

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Table 1

Properties of pyrimidine biosynthetic enzymes from

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25
Generic image for table
Table 2

genes of pyrimidine biosynthesis

Citation: Switzer R, Quinn C. 1993. De Novo Pyrimidine Nucleotide Synthesis, p 343-358. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch25

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