Evolution of pathways

The first section of the chapter quantifies the rates at which the various aspects of genomes and the genomic context of any gene evolve. The second section shows how the conservation of genomic context can be used to predict genes, their function, and their functional relations with other genes. The last section shows how the variation of genomic context can indicate a different role of proteins in the cell and the evolution of pathways. 

Williams, P.A. and Sayers, J.R., The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas, Biodegradation, 5, 195-217, 1994. 

Livingstone DR (1991) Origins and evolution of pathways of anaerobic metabolism in the animal kingdom. Am Zool 31 522-534 Lloyd D (1996) Obligate anaerobe or not. Nature 381 121... 

Fothergill-Gilmore, L., 1986. The evolution of die glycolytic pathway. Trends in Biochemical Sciences 11 47—51. 

Wachtershanser has also suggested that early metabolic processes first occurred on the surface of pyrite and other related mineral materials. The iron-sulfur chemistry that prevailed on these mineral surfaces may have influenced the evolution of the iron-sulfur proteins that control and catalyze many reactions in modern pathways (including the succinate dehydrogenase and aconitase reactions of the TCA cycle). 

Careful observations of the course of iodo-de-diazoniation demonstrate that the detailed pathway of such reactions is still relatively complex. For instance, after adding a solution of KI to a solution of an arenediazonium salt, normally molecular iodine appears to be formed first, followed by a precipitate and evolution of N2. Carey and Millar (1960) isolated the salt ArNJIj- on adding iodide to the diazo-nium salt. Ion pairs (ArNjHlg-), suggested as primary products by Meyer et al. (1979), were identified for diazonium halides (Cl- and Br-) by Israel et al. (1983) as 1 1 complexes on the basis of JOB analyses of visible spectra (Benesi-Hildebrand method). Iodides were, however, not included in that investigation. 

Still more confusion plagued early researches, when it was not realized that the biosynthetic routes to thiamine in prokaryotes and eukaryotes are quite different, a fact not expected at the outset. Thus, evidence collected from the study of yeast could not be transposed to bacteria, and vice-versa. For instance, formate is a most efficient precursor of one of the carbon atoms of the pyrimidine part of thiamine (pyramine), both in yeasts and enterobacteria, but incorporates at C-2 in bacteria and at C-4 in yeast. However, as is briefly covered in Section VIII, this dichotomy of pathways might have a deep significance in the perspective of biochemical evolution during primitive life on Earth. 

Fothergill-Gilmore LA The evolution of the glycolytic pathway. Trends Biochem Sci 1986 11 47. 

Algal blooms in fresh water ponds occasionally poison livestock and waterfowl. Axenic cultures of Anabaena flos-aquae NRC 44-1 were shown to produce the toxic principle (5) which can be present in the algae and in the water of mature cultures (6). The discovery of the toxin was fortuitous in the sense that AChR agonists do not have a (known) constructive function in the algae evolution of the synthetic pathway was likely a by-product of metabolic pathways in the algae. The compound became evident only through its toxic effects on other organisms. 

Stafford, H.A., Anthocyanins and betalains evolution of the mutually exclusive pathways. Plant ScL, 101, 91, 1994. 

Koes, R., Verweij, W., and Quattrocchio, R, Flavonoids a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci. 10, 236, 2005. Chandler, S., Commercialization of genetically modified ornamental plants, J. Plant Biotechnol. 5, 69, 2003. 

Gallagher, C.E. et al.. Gene duplication in the carotenoid biosynthetic pathway preceded evolution of the grasses (Poaceae). Plant Physiol. 135, 1776, 2004. 

Van der Meer JR, C Werlen, SF Nishino, JC Spain (1998) Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater. Appl Environ Microbiol 64 4185-4193. 

Although the possibly incompatible pathways for the degradation of chlorobenzene and toluene has been noted, a strain of Ralstonia sp. from a site contaminated with chlorobenzene contained the genes for both chlorocatechol degradation and the dioxygenase system for the degradation of benzene/toluene (van der Meer et al. 1998). The evolution of this strain resulted in a natural lowering... 

Figure 8 shows the COj (MW=45) response curve for the standard pump-probe experimental conditions. COj would be generated from either the combustion of 1,2 C2H4 or the product 1,2 C-vinyl acetate. Since the curve has a maximum at 4.5 seconds which is before the evolution of vinyl acetate at 5.5-7.5 seconds, ethylene combustion seems to be the pathway that can be attributed to the formation of this peak. Moreover, on interpretation of Figure 7, it is apparent that both the Pd-Au w/KOAc and the Pd w/KOAc catalysts proceed less CO2 than their Pd-Au and Pd counterparts. Therefore, it can be concluded that KOAc impeded the combustion of ethylene. 

Various silver salts can be reduced to silver metal readily at temperatures well below 200 °C through different pathways [32]. We therefore used silver salt as nucleation inducing agent. Ag(acac) was used because of its good solubility in diphenyl ether. The morphology evolution of Pt multipods and nanoparticles was followed by TEM. 

Francis, J.C. and Hansche, PE. (1972) Directed evolution of metabohc pathways in microbial populations. I. Modification of the acid phosphatase pH optimum in S. cerevisiae. Genetics, 70, 59—73. 

Zhao, H.M., Chockalingam, K. and Chen, Z.L. (2002) Directed evolution of enzymes and pathways for industrial biocatalysis. Current Opinion in Biotechnology, 13, 104—110. 

Lange, B.M., Rujan, T., Martin, W. and Croteau, R. (2000) Isoprenoid biosynthesis the evolution of two ancient and distinct pathways across genomes. Proceedings of the National Academy of Sciences of the United States of America, 97, 13172-13177. 

This pleiotropic action of developmental genes is easily explained by the fact that the proteins encoded by these genes are components of pathways and networks, which have been repeatedly used during evolution for the construction of organisms. 

---