Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP.
Genome comparison permits identification of chromosome regions conserved during evolution. Bacillus subtilis and Escherichia coli are so distant that there exists very few conserved landmarks in their genome organisation. Analysis of the conserved cmk rpsA cluster pinpointed the importance of cytosine nucleotide metabolism. In these bacteria, mRNA turnover provides an efficient means to fulfil the need for CDP as a precursor of DNA synthesis. The cmk rpsA operon is responsible for CDP synthesis. This function is self-explained in the case of the cmk gene (which codes for cytidylate kinase). The case of rpsA, that codes for ribosomal protein S1, is more subtle. It is suggested here that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities. This provides an explanation for the elusive function of PNPase, which generates nucleoside diphosphates (not monophosphates) when degrading RNA. This also accounts for the discovery that the B. subtilis comR gene product is PNPase. This article briefly discusses the availability of cytosine nucleotides in eukaryotes, and suggests that they are derived from phospholipids turnover. Finally, the GC content of genomes is discussed in this new light.
Danchin
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Institut Pasteur, Département de Biochimie et Génétique Moléculaire, Paris, France. adanchin@pasteur.fr
D001412:Bacillus subtilis / Q000201:enzymology / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D003562:Cytidine / Q000378:metabolism; D003565:Cytidine Diphosphate / Q000096:biosynthesis*; D004247:DNA / Q000096:biosynthesis; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins; D016680:Genome, Bacterial; D008954:Models, Biological; D005810:Multigene Family; D009701:Nucleoside-Diphosphate Kinase / Q000235:genetics / Q000378:metabolism; D009703:Nucleoside-Phosphate Kinase / Q000235:genetics / Q000378:metabolism; D010770:Phosphotransferases; D011117:Polyribonucleotide Nucleotidyltransferase / Q000378:metabolism*; D011743:Pyrimidines / Q000096:biosynthesis; D012333:RNA, Messenger / Q000378:metabolism; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D011743:Pyrimidines; D012333:RNA, Messenger; D012269:Ribosomal Proteins; C015494:ribosomal protein S1; D003562:Cytidine; D003565:Cytidine Diphosphate; D004247:DNA; D010770:Phosphotransferases; C087282:cmk protein, E coli; C019979:cytidylate kinase; D009703:Nucleoside-Phosphate Kinase; D009701:Nucleoside-Diphosphate Kinase; D011117:Polyribonucleotide Nucleotidyltransferase; C030986:pyrimidine