Asymmetric relationships between proteins shape genome evolution

doi:10.1186/gb-2009-10-2-r19

Genome Biology

Volume 10
Issue 2

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Dutilh BE

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Asymmetric relationships between proteins shape genome evolution

Richard A Notebaart^* , Philip R Kensche^* , Martijn A Huynen and Bas E Dutilh

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands

author email corresponding author email* Contributed equally

Genome Biology 2009, 10:R19doi:10.1186/gb-2009-10-2-r19


Published:	12 February 2009

Subject areas: Genome studies, Model organisms

Additional files

Additional data file 1:

Asymmetrically dependent reaction pairs A→B for which the independent gene B was lost while gene A was retained ('AB = 10') and vice versa ('AB = 01'), both in at least five species. In this table, R is the smallest possible partition in the species tree (taken from STRING 7.0 [9]) that contained all 'AB = 10' species, and L is the remainder of the tree; we list only the cases where 'AB = 10' and 'AB = 01' were perfectly separable (neutral 'AB = 00' and 'AB = 11' species were not considered).

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Additional data file 2:

The relation between fructose-bisphosphate aldolase (A) and the fructose bisphosphatase (B) is asymmetric in E. coli and S. cerevisiae because the gluconeogenesis contains an alternative flux that converges into fructose bisphosphatase. This asymmetry is, however, not reflected in evolution because fructose-bisphosphate aldolase occurs, as part of glycolysis, in a number of species in which gluconeogenesis and its specific enzyme fructose bisphosphatase are not present. This exception shows that the predicted asymmetry is not trivial, and depends on the conservation of the metabolism between species.

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Additional data file 3:

The fraction (f_0/1= n_0/1/(n_0/1+ n_1/0)) where only B is essential in rich medium (essentiality) or has an effect on the growth across conditions (growth), where only B is expressed across conditions (expression), where only B is present across species (occurrence), where only B is present after gain, loss or maintenance over evolutionary lineages, and where A is contingently gained over evolutionary lineages (contingent gain A) is averaged over all reaction pairs (also see Materials and methods). Asterisk indicates p < 0.01.

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Additional data file 4:

Saccharomyces cerevisisae [24-34] and Escherichia coli [35-44] expression datasets.

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