Ancient Adaptations |
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NADP-use in the IDH phylogeny arose prior to eukaryotes on three occasions: twice in the Eubacteria (1 and 3) and once in the Archaea (2). X-ray structures reveal that events 1 and 3 involve parallel mutations. Event 3 represents an independent solution. |
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| Metabolic flux analyses show that E. coli IDH provides ~ 90% of the NADPH needed for growth on acetate. We replaced the wildtype NADP-specific IDH by an engineered one with the ancestral NAD-specific phenotype. The engineered enzyme is disfavored during competition for acetate. Selection intensifies in genetic backgrounds where other sources of NADPH have been removed. | |
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| Genome sequences reveal that isocitrate lyase (essential for growth on acetate) is always associated with an NADP-specific IDH. Genomes with only an NAD-specific IDH never have the lyase. This association confirms that the NADP-dependence of prokaryotic IDHs is adaptation to metabolic demand for NADPH during growth on acetate. | |
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| Our studies provide a general approach to reconstruct ancient adaptive events. Phylogenetics provides molecular history. Structural biology reveals key replacements responsible for functional changes. Protein engineering tests structure-function relationships. Studies of metabolism identify selectable phenotypes. Competition studies explore the adaptive basis of any claim. Genomic comparisons confirm the generality of the results. By completing each of these steps, it is possible to identify the most probable causes of truly ancient adaptive events, even ones that occurred billions of years ago. | |
| *root, NADP-use/NAD-use | Zhu, Golding & Dean. 2005. Science 307:1279-1282. |
