Research
Influence of metabolic network structure and function on enzyme evolution
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* Corresponding author: Dennis Vitkup dv2121@columbia.edu
1 Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, Russ Berrie Pavilion, St Nicholas Avenue, New York, NY 10032, USA
2 Department of Genetics, New Research Building, Ave Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA
3 Department of Biology, Castetter Hall, University of New Mexico, Albuquerque, NM 87131, USA
Genome Biology 2006, 7:R39 doi:10.1186/gb-2006-7-5-r39
Published: 9 May 2006Additional files
Additional data file 1:
(a) An example of the metabolic reaction network from sphingoglycolipid metabolism; metabolites are drawn as small circles (DHSP, sphinganine 1-phosphate; PETHM, ethanolamine phosphate; SPH, sphinganine; CDPETN, CDPethanolamine; ETHM, ethanolamine) and enzyme-encoding genes are shown in rectangles. (b) Metabolic connectivity of the dpl1 gene (solid edges), as defined by the reactions shown in (a). The dpl1 gene has a total of six metabolic connections: two established through ethanolamine phosphate (red edges); and four through sphinganine 1-phosphate (blue edges). Metabolic connections between other enzymes are show by dashed edges.
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Additional data file 2:
The relationship between enzyme connectivity and the average amino acid divergence Ka. Spearman's rank correlation r = -0.13, P = 1.6 × 10-2
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Additional data file 3:
The relationship between enzyme connectivity and the average silent divergence Ks. Spearman's rank correlation r = -0.056, P = 0.30.
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Additional data file 4:
Maximal uptake rate for glucose 15.3 mmol/g dry weight/h and for oxygen 0.2 mmol/g dry weight/h. Note the small number of fluxes - representing glycolysis - with disproportionately large magnitudes. Similar flux distributions were also obtained for other growth conditions.
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Additional data file 5:
The correlation between non-zero enzymatic flux through a reaction and the number of duplicates of the respective enzyme's coding gene.
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Additional data file 6:
Connectivity and evolutionary parameters (Ka/Ks, Ka, Ks) for yeast metabolic enzymes.
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