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Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pHc in Saccharomyces cerevisiae

Rick Orij1, Malene L Urbanus2, Franco J Vizeacoumar2, Guri Giaever3, Charles Boone2, Corey Nislow2, Stanley Brul1 and Gertien J Smits1*

Author Affiliations

1 Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands

2 Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada

3 Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada

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Genome Biology 2012, 13:R80  doi:10.1186/gb-2012-13-9-r80

Published: 26 September 2012

Additional files

Additional file 1:

All mutants with deviating pHc at various pHex, and during respiratory growth. Mutants with aberrant pHc under the standard condition (glucose, pH 5.0) were subjected to growth in pH 3.0, 7.5, as well as 2% ethanol/2% glycerol pH 5.0. Mutants were pre-grown overnight under standard conditions except for the 2% ethanol/2% glycerol experiment, in which case mutants were pre-grown in 2% ethanol/2% glycerol because of the long adaptation time to non-fermentable carbon source conditions. Cells were re-inoculated in described conditions and grown for 4 hours prior to measurements. Mutants were measured at least six times at pH 5.0 and at least three times at all other conditions. Mutants with significantly low pHc in any condition are indicated in orange, while mutants with significantly high pHc are indicated in blue.

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Additional file 2:

pHc analysis of 432 slow growing mutants. All strains were grown in standard conditions (2% glucose, pHex of 5.0) and fluorescence was registered in three to six biological replicates, and are presented as average and 95% confidence interval. pHc was compared to wild-type (WT) controls in the same replicate, to determine a Z-value. Significance of the pHc difference with WT was determined using a two-tailed t-test assuming equal variance with a P-value < 0.05. ND refers to mutants for which fewer than three replicates were successfully measured. Significantly low pHc values are shown in orange, significantly high pHc values in blue.

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Additional file 3:

Classification of mutants. Mutants are classified as having a growth rate-pHc relationship similar to wild type (WT; no significant deviation from the predicted growth rate based on pHc-growth rate relationship of the parent strain, low growth rate/pHc (significant positive deviation from the parent fit), or high growth rate/pHc (significant negative deviation from the parent fit), and are categorized according to functional classification.

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Additional file 4:

Figures S1 to S4. See Additional file 5 for further data pertaining to Figure S3.

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Additional file 5:

Data belonging to the hierarchical cluster plot in Figure S3 in Additional file 4. Mutants are listed in the order in which they appear in the cluster plot, for all three clusters. Mutant growth profiles were fitted to the parent strain pHc-growth rate relationship, and at each time point the Z-value of the digression from the fit was determined compared to the average and variance of 96 parent strain growth curves at the same time point. Time courses during the growth phase (t = 4 h to t = 9 h) of these Z-values were used to statistically categorize the mutants as wild type (WT; 92/173 mutants; 96 parent strain profiles also fall in this category), significantly (corrected P-value < 0.01) slow growing (62/173 mutants), or significantly fast growing (19/173 mutants) with respect to pHc.

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