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Extracting the hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA microarray data using the self-organizing map: biosynthesis of amino acids.
Appl Microbiol Biotechnol. 2007 May; 75(2):415-26.AM

Abstract

During saline stress, Saccharomyces cerevisiae changes its metabolic fluxes through the direct accumulation of metabolites such as glycerol and trehalose, which in turn provide tolerance to the cell against stress. Previous research shows that the various controls at both transcriptional and translational levels decide the phenomenon of stress, but details about such transition is still not very clear. This paper attempts to extract some hidden features through the information extraction approach from DNA microarray data during transition to osmotic tolerance, which are expected to be important in directing to the tolerance stage upon encountering osmotic stress in yeast. Time course of DNA microarray data during osmotic tolerance was analyzed by computational approach 'self-organizing map (SOM) extended with hierarchical clustering'. Since eukaryotic gene expression is governed by short regulatory sequences found upstream in promoter regions, therefore clusters containing the similar profiles obtained by SOM were further analyzed for overrepresentation of known regulatory binding sites in promoter region. It was found that apart from known and expected 'STRE' during osmotic stress, the 'GCN4' binding site is also found to be significant. Hence, it was suggested that the process of osmotic tolerance proceeds through a stage of amino acid starvation. The intracellular amino acids pool also found to be depleted during transition and restoration is faster in brewing strain than laboratory strain. Experiments involving supplementation of amino acids helps in reducing the lag time for recovery, which was found to be similar to that of brewing strain.

Authors+Show Affiliations

Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17262206

Citation

Pandey, Gaurav, et al. "Extracting the Hidden Features in Saline Osmotic Tolerance in Saccharomyces Cerevisiae From DNA Microarray Data Using the Self-organizing Map: Biosynthesis of Amino Acids." Applied Microbiology and Biotechnology, vol. 75, no. 2, 2007, pp. 415-26.
Pandey G, Yoshikawa K, Hirasawa T, et al. Extracting the hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA microarray data using the self-organizing map: biosynthesis of amino acids. Appl Microbiol Biotechnol. 2007;75(2):415-26.
Pandey, G., Yoshikawa, K., Hirasawa, T., Nagahisa, K., Katakura, Y., Furusawa, C., Shimizu, H., & Shioya, S. (2007). Extracting the hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA microarray data using the self-organizing map: biosynthesis of amino acids. Applied Microbiology and Biotechnology, 75(2), 415-26.
Pandey G, et al. Extracting the Hidden Features in Saline Osmotic Tolerance in Saccharomyces Cerevisiae From DNA Microarray Data Using the Self-organizing Map: Biosynthesis of Amino Acids. Appl Microbiol Biotechnol. 2007;75(2):415-26. PubMed PMID: 17262206.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Extracting the hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA microarray data using the self-organizing map: biosynthesis of amino acids. AU - Pandey,Gaurav, AU - Yoshikawa,Katsunori, AU - Hirasawa,Takashi, AU - Nagahisa,Keisuke, AU - Katakura,Yoshio, AU - Furusawa,Chikara, AU - Shimizu,Hiroshi, AU - Shioya,Suteaki, Y1 - 2007/01/30/ PY - 2006/08/22/received PY - 2007/01/02/accepted PY - 2006/12/30/revised PY - 2007/1/31/pubmed PY - 2007/7/20/medline PY - 2007/1/31/entrez SP - 415 EP - 26 JF - Applied microbiology and biotechnology JO - Appl Microbiol Biotechnol VL - 75 IS - 2 N2 - During saline stress, Saccharomyces cerevisiae changes its metabolic fluxes through the direct accumulation of metabolites such as glycerol and trehalose, which in turn provide tolerance to the cell against stress. Previous research shows that the various controls at both transcriptional and translational levels decide the phenomenon of stress, but details about such transition is still not very clear. This paper attempts to extract some hidden features through the information extraction approach from DNA microarray data during transition to osmotic tolerance, which are expected to be important in directing to the tolerance stage upon encountering osmotic stress in yeast. Time course of DNA microarray data during osmotic tolerance was analyzed by computational approach 'self-organizing map (SOM) extended with hierarchical clustering'. Since eukaryotic gene expression is governed by short regulatory sequences found upstream in promoter regions, therefore clusters containing the similar profiles obtained by SOM were further analyzed for overrepresentation of known regulatory binding sites in promoter region. It was found that apart from known and expected 'STRE' during osmotic stress, the 'GCN4' binding site is also found to be significant. Hence, it was suggested that the process of osmotic tolerance proceeds through a stage of amino acid starvation. The intracellular amino acids pool also found to be depleted during transition and restoration is faster in brewing strain than laboratory strain. Experiments involving supplementation of amino acids helps in reducing the lag time for recovery, which was found to be similar to that of brewing strain. SN - 0175-7598 UR - https://www.unboundmedicine.com/medline/citation/17262206/Extracting_the_hidden_features_in_saline_osmotic_tolerance_in_Saccharomyces_cerevisiae_from_DNA_microarray_data_using_the_self_organizing_map:_biosynthesis_of_amino_acids_ L2 - https://dx.doi.org/10.1007/s00253-007-0837-8 DB - PRIME DP - Unbound Medicine ER -