Ribonucleotide, biosynthesis

Purine ribonucleotide biosynthesis Pyrimidine ribonucleotide biosynthesis Salvage of nucleosides and nucleotides Sugar-nucleotide biosynthesis and conversions Other... 

Most stem cells can divide via either asymmetric or symmetric modes (22). Because each asymmetric division generates one daughter with a stem-cell fate (self-renewal) and one daughter that differentiates, it was postulated that asymmetric division could be a barrier to stem cell expansion. Therefore, conversion of asymmetric division to symmetric division would promote self-renewal and long-term culture of stem cells. Indeed, this idea was confirmed by using one small molecule, the purine nucleoside xanthosine (Xs) (23). This small molecule promotes guanine ribonucleotide biosynthesis that reversibly converts cells from asymmetric division kinetics to symmetric division kinetics. It was found that Xs derived from stem cell lines exhibit Xs-dependent symmetric kinetics, and this derived stable line shows enhanced self-renewal. This study underscores the importance of balance between the two modes of division, both to stem cell expansion and to the regenerative capacity of adult stem cells. 

PP-Ribose-P is the most important ribose phosphate donor for purine metabolism (see Chapters 7, 8) and participates in several important reactions of pyrimidine metabolism (Chapters 11, 12) it also transfers this group to a number of other acceptors (Chapter 5). In the course of studies of purine ribonucleotide biosynthesis, a product of the reaction of ribose-5-P and ATP was isolated and eventually identified as 5-phosphoribosyl 1-pyrophosphate. The pyrophosphate group is in the a-configuration, is quite labile, and almost certainly reacts enzymaticaUy as the magnesium complex. It has been chemically synthesized by Tener and Khorana 33). 

The pathway of purine ribonucleotide biosynthesis de novo is summarized below. The enzymes involved are listed in Table 7-IV. 

Fig. 3. The pathway of de novo purine ribonucleotide biosynthesis. The pathway includes the synthesis of PRPP, which is also used in the synthesis of pyrimidines, pyridine nucleotides, histidine, and tryptophan in plants. The enzymes catalyzing the numbered reactions are (1) PRPP synthetase, (2) PRPP amidotransferase, (3) GAR synthetase, (4) GAR transformylase, (5) FGAR amidotransferase, (6) AIR synthetase, (7) AIR carboxylase, (8) succino-AICAR synthetase, (9) adenylosuccinase, (10) AICAR transformylase, and (11) IMP cyclohydrolase.

As discussed in the previous section, the synthesis of ribose 5-phosphate must be quite high to provide the ribose 5-phosphate required for de novo purine ribonucleotide biosynthesis. Ribose 5-phosphate required for PRPP synthesis can be synthesized de novo via the oxidative or nonoxidative arms of the pentose phosphate pathway or by recycling of ribose released by the action of nucleotidases/nucleosidases (Fig. 5). The latter pathway requires ribose phosphotransferase (ribokinase), which has been detected in soybean and pea nodule extracts (Christensen and Jochimsen, 1983). The efficient recycling of ribose could eliminate the need for the continuous production of ribose 5-phosphate. Two enzymes of the oxidative branch of the pentose phosphate... 

The discovery of nbozymes (Section 28 11) in the late 1970s and early 1980s by Sidney Altman of Yale University and Thomas Cech of the University of Colorado placed the RNA World idea on a more solid footing Altman and Cech independently discovered that RNA can catalyze the formation and cleavage of phosphodiester bonds—exactly the kinds of bonds that unite individual ribonucleotides in RNA That plus the recent discovery that ribosomal RNA cat alyzes the addition of ammo acids to the growing peptide chain in protein biosynthesis takes care of the most serious deficiencies in the RNA World model by providing precedents for the catalysis of biologi cal processes by RNA... 

One of the steps in the biosynthesis of a nucleotide called inosine monophosphate is the formation of aminoimidazole ribonucleotide from formyjglycin-amidine ribonucleotide. Propose a mechanism. 

As already mentioned, RNR is the metalloenzyme in which the first definitively characterized stable amino acid radical (1), later identified as a tyrosyl radical, was found in 1972. The RNR enzymes catalyse the reduction of ribonucleotides to their corresponding deoxyribonucleotides utilized in DNA biosynthesis. There are three unique classes of this enzyme, differing in composition and cofactor requirements all of them, however, make use of metal ions and free radical chemistry. Excellent reviews on RNRs are available (60, 61, 70, 89-97). 

The effect of 6-mercaptopurine on the incorporation of a number of C-labelled compounds into soluble purine nucleotides and into RNA and DNA has been studied in leukemia L1210, Ehrlich ascites carcinoma, and solid sarcoma 180. At a level of 6-mercaptopurine that markedly inhibited the incorporation of formate and glycine, the utilization of adenine or 2-aminoadenine was not affected. There was no inhibition of the incorporation of 5(or 4)-aminoimidazole-4(5)-carboxamide (AIC) into adenine derivatives and no marked or consistent inhibition of its incorporation into guanine derivatives. The conversion of AIC to purines in ascites cells was not inhibited at levels of 6-mercaptopurine 8-20 times those that produced 50 per cent or greater inhibition of de novo synthesis [292]. Furthermore, AIC reverses the inhibition of growth of S180 cells (AH/5) in culture by 6-mercaptopurine [293]. These results suggest that in all these systems, in vitro and in vivo, the principal site at which 6-mercaptopurine inhibits nucleic acid biosynthesis is prior to the formation of AIC, and that the interconversion of purine ribonucleotides (see below) is not the primary site of action [292]. Presumably, this early step is the conversion of PRPP to 5-phosphoribosylamine inhibited allosterically by 6-mercaptopurine ribonucleotide (feedback inhibition is not observed in cells that cannot convert 6-mercaptopurine to its ribonucleotide [244]. 

Hydroxycarbamide (hydroxyurea) is an inhibitor of the enzyme ribonucleoside reductase which catalyzes the conversion of ribonucleotides to deoxyri-bonucleotides, a crucial step in the biosynthesis of DNA. The drug is S-phase specihc. Resistance can occur by an increase of ribonucleohde reductase. 

Glycinamide ribonucleotide transformylase (GAR Tfase) is a folate-dependent enzyme essential to the de novo purine biosynthetic pathway. It utilizes the cofactor 10-formyl tetrahydrofohc acid (10-formyl-THF) to transfer a formyl group to the primary amine of its substrate a-glycinamide ribonucleotide. Potent, and potentially selective, inhibitors of GARTfase and de novo purine biosynthesis have been shown to be promising as antitumor drugs. 

RNA directs biosynthesis of various peptides and proteins essential for any living organisms. Protein biosynthesis seems to be catalysed by mRNA rather than protein-based enzymes and occur on the ribosome. On the ribosome, the mRNA acts as a template to pass on the genetic information that it has transcribed from the DNA. The specific ribonucleotide sequence in mRNA forms an instruction or codon that determines the order in which different amino acid residues are to be joined. Each instruction or codon along the mRNA chain comprises a sequence of three ribonucleotides that is specific for a given amino acid. For example, the codon U-U-C on mRNA directs incorporation of the amino acid phenylalanine into the growing protein. 

In the second control mechanism, exerted at a later stage, an excess of GMP in the cell inhibits formation of xanthylate from inosinate by IMP dehydrogenase, without affecting the formation of AMP (Fig. 22-35). Conversely, an accumulation of adenylate inhibits formation of adenylosuccinate by adenylosuccinate synthetase, without affecting the biosynthesis of GMP. In the third mechanism, GTP is required in the conversion of IMP to AMP (Fig. 22-34, step (T)), whereas ATP is required for conversion of IMP to GMP (step (4)), a reciprocal arrangement that tends to balance the synthesis of the two ribonucleotides. 

The common pyrimidine ribonucleotides are cytidine 5 -monophosphate (CMP cytidylate) and uridine 5 -monophosphate (UMP uridylate), which contain the pyrimidines cytosine and uracil. De novo pyrimidine nucleotide biosynthesis (Fig. 22-36) proceeds in a somewhat different manner from purine nucleotide synthesis the six-membered pyrimidine ring is made first and then attached to ribose 5-phosphate. Required in this process is carbamoyl phosphate, also an intermediate in the urea cycle (see Fig. 18-10). However, as we noted... 

FIGURE 22-43 Biosynthesis of thymidylate (dTMP). The pathways are shown beginning with the reaction catalyzed by ribonucleotide reductase. Figure 22-44 gives details of the thymidylate synthase reaction. 

Hydroxyurea interferes with the synthesis of both pyrimidine and purine nucleotides (see table 23.3). It interferes with the synthesis of deoxyribonucleotides by inhibiting ribonucleotide reductase of mammalian cells, an enzyme that is crucial and probably rate-limiting in the biosynthesis of DNA. It probably acts by disrupting the iron-tyrosyl radical structure at the active site of the reductase. Hydroxyurea is in clinical use as an anticancer agent. 

Chapter 23, Nucleotides, deals with the biosynthesis of ribonucleotides, deoxyribonucleotides, the roles of these biomolecules in metabolic processes, and the pathways for their degradation. Medically related topics such as nucleotide metabolism deficiencies or the use of nucleotide analogs in chemotherapy are also considered. 

Protein biosynthesis is directed by a special kind of RNA called messenger RNA, or mRNA, and takes place on knobby protuberances within a cell called ribosomes. The specific ribonucleotide sequence in mRNA acts like a long coded sentence to specify the order in which different amino acid residues are to be joined. Each of the estimated 100,000 proteins in the human body is synthesized from a different mRNA that has been transcribed from a specific gene segment on DNA. 

In the biosynthesis pathways of histidine and tryptophan, the enzymes HisA (N -[(5 -phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide isomerase) and TrpF (PRAI,phosphoribosylanthranilate isomerase) (Figure 16.13), both of which are ()3a)8-barrels, both catalyze Amadori rearrangements of a ther-molabile aminoaldose into the corresponding aminoketose (Figure 16.13). 

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