Application of genome-wide expression analysis to identify molecular markers useful in monitoring industrial fermentations

Abstract

Genome-wide expression analysis of an industrial strain of Saccharomyces cerevisiae identified the YOR387c and YGL258w homologues as highly inducible in zinc-depleted conditions. Induction was specific for zinc deficiency and was dependent on Zap1p. The results indicate that these sequences may be valuable molecular markers for detecting zinc deficiency in industrial fermentations.

FIG. 1.

YOR387c and YGL258w differential gene expression is the most rapid and responsive to zinc depletion. Northern blot kinetic analysis of YOR387c and YGL258w, ZPS1, ZRT1, and ACT1 gene expression was performed with total RNA isolated from Lager 1 cells grown in LZMM with (□; Zn⁺) and without (▵; Zn⁻) 40 μM ZnSO₄ added. Each Northern blot is a representative of a duplicate experiment, and the growth curves are the means of triplicate readings of duplicate experiments with lower than 12% standard errors. OD600nm, optical density at 600 nm.

FIG. 2.

Induction of YOR387c and YGL258w in zinc-depleted conditions is dependent on Zap1p. YOR387c and YGL258w and ACT1 expression in wild-type (BY4743) and zap1Δ mutant cells grown in Chelex-treated synthetic defined (CSD) medium (14) with (Zn⁺) and without (Zn⁻) 10 μM ZnSO₄ added was measured.

FIG. 3.

YOR387c and YGL258w expression is not induced by oxidative stress or carbon starvation. YOR387c and YGL258w, ZRT1, HSP12, and ACT1 expression was measured in Lager 1 cells grown in modified LZMM with (Zn⁺) or without (Zn⁻) 40 μM ZnSO₄ added, LZMM (Zn⁺) with 2 mM H₂O₂ added (H₂O₂), and LZMM (Zn⁺) with no added maltose (C⁻).

FIG. 4.

YOR387c and YGL258w expression is not induced by iron depletion. Shown are YOR387c and YGL258w, ZRT1, ARN2, and ACT1 expression patterns from GeneFilters microarray analysis of Lager 1 cells grown for 4 h in low-iron medium with (Fe⁺) and without (Fe⁻) 25 μM FeCl₃ added.