Chemoheterotrophs and photoautotrophs then utilize 3 different central pathways to synthesize individual amino acids (fig. Metabolic pathways involved in amino acid biosynthesis and energy production.1): the EMP pathway, the citric acid cycle, and the pentose phosphate pathway (Ogata et al. pen P, ribose 5-phosphate; PRPP, 5-phosphoribosyl pyrophosphate; ery P, erythrose 4-phosphate; 3pg, 3-phosphoglycerate; pep, phosphoenolpyruvate; pyr, pyruvate; ac Co A, acetyl-Co A; αkg, α-ketoglutarate; oaa, oxaloacetate; Ru BP, ribulose bisphosphate; TCA, tricarboxylic acid cycle.Blast searches were also performed on the complete genomes of all the six 6 study organisms to determine if they were capable of synthesizing each of the 20 common amino acids.When the protein-coding regions were at least 20% identical at the amino acid level with the enzymes known to be involved in the biosynthetic pathways (Atkinson 1977), it was concluded that a homolog to the enzyme used for a particular metabolic step was also available to the organism in question.Two prokaryotic organisms, , have been shown to preferentially utilize less costly amino acids in highly expressed genes, indicating that parsimony in amino acid selection may confer a selective advantage for prokaryotes.This study confirms those findings and extends them to 4 additional prokaryotic organisms: HB27.
pen P, ribose 5-phosphate; PRPP, 5-phosphoribosyl pyrophosphate; ery P, erythrose 4-phosphate; 3pg, 3-phosphoglycerate; pep, phosphoenolpyruvate; pyr, pyruvate; ac Co A, acetyl-Co A; αkg, α-ketoglutarate; oaa, oxaloacetate; Ru BP, ribulose bisphosphate; TCA, tricarboxylic acid cycle.
The 6 organisms considered in this study utilized 1 of 2 different pathways for amino acid synthesis (fig. The principle difference between these 2 pathways is that photoautotrophs utilize the Calvin cycle (Poolman et al.
2000) to feed precursors into the Embden–Meyerhof–Parnas (EMP) pathway.
Some regions of a protein's primary structure are under strong selective pressure (e.g., active sites), making the observation of even conservative substitutions uncommon in naturally occurring populations, whereas other regions of proteins are much more likely to display sequence variability (Axe 2000). Indeed, Akashi and Gojobori (2002) have demonstrated that genes that adhere to organismal codon-usage biases most strongly (and, by inference, are most highly expressed) tend to incorporate lower cost amino acids in .
The primary structure of a protein can also be constrained by a variety of cellular processes, including the organism's metabolic pathways (Craig and Weber 1998), the translation rate of the m RNA (Ikemura 1981a, 1981b), and the production cost of the amino acids (Craig and Weber 1998). By performing a Spearman rank correlation (Spearman 1904), they were able to demonstrate a negative correlation between the major codon usage (MCU) of a gene and the average biosynthetic cost of the amino acids incorporated into the expressed protein.Moreover, the standard textbook version of how this elaborate metabolic network evolved beginning with glycolysis is probably wrong, accordingly to the compelling essay by Lane et al. In this class, we will take an evolutionary approach that begins with concepts and processes fundamental to all living cells, that must have been present in the last universal common ancestor (LUCA).