Prokaryote, biosynthesis

Although the interior of a prokaryotic cell is not subdivided into compartments by internal membranes, the cell still shows some segregation of metabolism. For example, certain metabolic pathways, such as phospholipid synthesis and oxidative phosphorylation, are localized in the plasma membrane. Also, protein biosynthesis is carried out on ribosomes. 

Keto add-dependent enzymes are involved in numerous reactions and are found in prokaryotes as well as eukaryotes. Apart from scopolamine and clavulanic add biosynthesis, a-keto add-dependent enzymes are also found in the biosynthetic... 

Because sugars are involved in most of the mechanisms established for the synthesis of these heterocycles, the development of carbohydrate chemistry has been most helpful in these researches—especially for the preparation of specifically labeled molecules. Conversely, the contribution of these efforts to carbohydrate chemistry and biochemistry has shown the involvement in biosynthesis of 1 -deoxy-D-f/rreo-pentulose—scarcely before recognized and considered a rare sugar—and of fully functionalized pentuloses of still unknown configuration (or their phosphates). Finally, evidence has been found in prokaryotes for a most extraordinary transformation of 5-amino-l-(P-D-ribofuranosyl)imidazole 5 -phos-phate into a pyrimidine. Surely, this transformation should be explained in terms... 

Armstrong, G.A., Alberti, M., and Hearst, J.E., Conserved enzymes mediate the early reactions of carotenoid biosynthesis in nonphotosynthetic and photosynthetic prokaryotes, Proc. Natl. Acad. Sci. USA 87, 9975, 1990. 

Harker, M. and Bramley, P.M., Expression of prokaryotic l-deoxy-D-xylulose-5-phosphatases in Escherichia coli increases carotenoid and ubiquinone biosynthesis, EBBS Lett. 448, 115, 1999. 

The dihydrofolate reductase enzyme (DHFR) is involved in one-carbon metabolism and is required for the survival of prokaryotic and eukaryotic cells. The enzyme catalyzes the reduction of dihydrofolate to tetrahydrofolate, which is required for the biosynthesis of serine, methionine, purines, and thymidylate. The mouse dihydrofolate reductase (mDHFR) is a small (21 kD), monomeric enzyme that is highly homologous to the E. coli enzyme (29% identify) (Pelletier et al., 1998). The three-dimensional structure of DHFR indicates that it is comprised of three structural fragments F[l], F[2] andF[3] (Gegg etal., 1997). 

There are two distinct pathways for biosynthesis of the IPP and DMAPP the mevalonate (MVA) pathway and the DXP pathway (Figure 12.3). The MVA pathway functions primarily in eukaryotes, while the DXP pathway is typically present in prokaryotes and the plastids of plants [90,91]. The first reaction in the DXP pathway is the condensation of pyruvate and D-glyceraldehyde-3-phosphate (G3P) to form DXP, which is catalyzed by DXP synthase encoded by the gene dxs [92]. In the second step, DXP is reduced to 2-C-methyl-D-erythritol-4-phosphate (MEP) by DXP reductoisomerase, which is encoded by the gene dxr (ispC) in E. coli. An array of other enzymes encoded by is pi), ispE, ispF, ispG, and ispH act in subsequent sequential reactions, leading to the conversion of MEP to IPP and DMAPP, which are interconverted by the enzyme encoded by idi [93-97],... 

Naturally, if such materials are going to be useful as antibiotic drugs, we require a selective action. We need to be able to inhibit protein biosynthesis in bacteria, whilst producing no untoward effects in man or animals. Although the mechanisms for protein biosynthesis are essentially the same in prokaryotes and eukaryotes, there are some subtle differences, e.g. in the nature of the ribosome and how the process is initiated. Without such differences, the agent would be toxic to man as well as to bacteria. 

Bacterial protein biosynthesis is a cascade of events which manufacture chains of amino acids before they are folded into specific structures to carry out various biological functions. Protein biosynthesis is absolutely essential for the survival of prokaryotic and eukaryotic cells. Ribosomes, macromolecular complexes made up of proteins and RNA, participate in decoding the genetic message to synthesize both essential and nonessential proteins to carry out cellular functions. 

Biosynthesis.—Ubiquinone. The identification of 3,4-dihydroxyhexaprenylben-zoate (162) in a Saccharomyces cerevisiae mutant strain that cannot synthesize ubiquinone suggests that (162) may be an intermediate in ubiquinone-6 biosynthesis in eukaryotes, in contrast to the pathway via 2-polyprenylphenol which operates in prokaryotes. In mammalian systems alternative routes have been discussed for ubiquinone biosynthesis in rats." Some properties of mitochondrial 4-hydroxybenzoate-polyprenol transferase have been described."" ... 

ImHNL is a nonglycosylated homodimer (84 kDa) which catalyzes the reversible cleavage of aliphatic (R)-cyanohydrins [34]. This HNL does not require complex protein modification after protein biosynthesis. Thus, expression in prokaryotic Escherichia coli) and eukaryotic hosts Pichia pastoris) is possible [35-37]. However, initial trials to express IwHNL in E. coli were hampered by formation of inclusion bodies [36]. 

A very different ribonuclease participates in the biosynthesis of all of the transfer RNAs of E. coli. Ribonuclease P cuts a 5 leader sequence from precursor RNAs to form the final 5 termini of the tRNAs. Sidney Altman and coworkers in 1980 showed that the enzyme consists of a 13.7-kDa protein together with a specific 377-nucleotide RNA component (designated Ml RNA) that is about five times more massive than the protein.779 Amazingly, the Ml RNA alone is able to catalyze the ribonuclease reaction with the proper substrate specificity.780 7823 The protein apparently accelerates the reaction only about twofold for some substrates but much more for certain natural substrates. The catalytic center is in the RNA, which functions well only in a high salt concentration. A major role of the small protein subunit may be to provide counterions to screen the negative charges on the RNA and permit rapid binding of substrate and release of products.783 Eukaryotes, as well as other prokaryotes, have enzymes similar to the E. coli RNase R However, the eukaryotic enzymes require the protein part as well as the RNA for activity.784... 

Figure 21-4 Biosynthesis of triacylglycerols, glycol ipids, and major phospholipids that are formed both in prokaryotes and eukaryotes. More complete schemes of phospholipid synthesis are shown in Figs. 21-3 and 21-5. Green arrow pathway occurring only in eukaryotes.

One mechanism of transcriptional control in prokaryotes, especially of several operons controlling the biosynthesis of amino acids, is attenuation. 

Until 1993, all terpenes were considered to be derived from the classical acetate/mevalonate pathway involving the condensation of three units of acetyl CoA to 3-hydroxy-3-methylglutaryl CoA, reduction of this intermediate to mevalonic acid and the conversion of the latter to the essential, biological isoprenoid unit, isopentenyl diphosphate (IPP) [17,18,15]. Recently, a totally different IPP biosynthesis was found to operate in certain eubacteria, green algae and higher plants. In this new pathway glyceradehyde-3-phosphate (GAP) and pyruvate are precursurs of isopentenyl diphosphate, but not acetyl-CoA and mevalonate [19,20]. So, an isoprene unit is derived from isopentenyl diphosphate, and can be formed via two alternative pathways, the mevalonate pathway (in eukaryotes) and the deoxyxylulose pathway in prokaryotes and plant plastids [16,19]. 

In prokaryotes, phosphatidylserine is made from CDP-diacylglycerol (see fig. 19.3). The enzyme for this reaction is absent in animal cells, which rely on a base exchange reaction in which serine and ethanolamine are interchanged (fig. 19.8). Although the reaction is reversible, it usually proceeds in the direction of phosphatidylserine synthesis. Phosphatidylserine can be converted back to phos-phatidylethanolamine by a decarboxylation reaction in the mitochondria. This may be the preferred route for phosphatidylethanolamine biosynthesis in some animal cells. Furthermore these two reactions (see fig. 19.8) establish a cycle that has the net effect of converting serine into ethanolamine. This is the main route for ethanolamine synthesis... 

A strong influence on the biosynthesis of peptide metabolites exerted by exogenously supplied amino-acid precursors has been observed earlier both in prokaryotes and eukaryotes [26]. In several cases, enhanced yields of a desired metabolite can be obtained and a replacement of certain constitutional building elements by other amino acids may occur [27, 28]. 

---