Table 3

Deletion phenotypes predicted differently under raffinose conditions by iLL672 builds with and without α-galactosidase activity

Gene

Experimental phenotype of deletion under YPRaff

Predicted phenotype of deletion mutant made by iLL672 build with α-galctosidase

Predicted phenotype of deletion mutant made by iLL672 build without α-galctosidase

Reason for incorrect prediction made by iLL672 build with α-galactosidase activity

Gal1

Viable

Unviable

Viable

Galactose is produced when α-galactosidic bond in raffinose is cleaved. Therefore, in build with α-galactosidase, Gal genes are required to metabolize galactose produced during raffinose catabolism

Gal7

Viable

Unviable

Viable

See explanation for Gal1

Gal10

Viable

Unviable

Viable

See explanation for Gal1

YBR184W

Viable

Unviable

Viable

YBR184W is the putative α-galactosidase and is essential by definition of the model build

Suc2

Unviable

Viable

Unviable

The galactose produced when the α-galactosidic bond is cleaved can be used as the primary carbon source, with the remaining sucrose unit being excreted

Pgi1

Unviable

Viable

Unviable

Pgi1 catalyzes the reversible conversion of glucose-6-phosphate to fructose-6-phosphate in glycolysis and gluconeogenesis. The pentose phosphate pathway can be used to bypass the deletion of this gene to maintain glycolytic function Without the α-galactosidase only the fructose unit of raffinose is usable, making Pgi1 essential for its role in gluconeogenesis

Snitkin et al. Genome Biology 2008 9:R140   doi:10.1186/gb-2008-9-9-r140