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Investigating the effectiveness of DNA microarray analysis for identifying the genes involved in l-lactate production by Saccharomyces cerevisiae

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In order to determine whether transcriptome data obtained by DNA microarray analysis could be used to identify the genes involved in target metabolite production, we tried to identify the genes involved in l-lactate production by l-lactate-producing recombinant Saccharomyces cerevisiae strains. We obtained DNA microarray data for these strains. Plasmids carrying lactic acid bacteria, bovine, and human l-lactate dehydrogenase (LDH) genes were introduced into PDC1-disrupted S. cerevisiae strains. l-Lactate productivity of the strains harboring the human and bovine LDH genes was higher than that of the strains harboring lactic acid bacteria LDH genes. DNA microarray analysis revealed that the expression of 388 genes was significantly altered in the strains with the human and bovine LDH genes. Of these, the l-lactate productivity of human LDH-harboring deletion strains of 289 genes was compared with that of the standard and 56 randomly selected deletion strains containing the same LDH gene to validate the effectiveness of DNA microarray analysis for identifying the genes responsible for l-lactate production in the recombinant strains. Only deletion strains of the genes selected on the basis of the DNA microarray data showed significantly altered l-lactate production as compared to the standard and the randomly selected deletion strains. Our results indicated that the genes related to l-lactate production could be successfully identified by selecting the genes that exhibited significantly altered expression on DNA microarray analysis, and the effectiveness of DNA microarray analysis for identifying the genes responsible for l-lactate production was discussed.

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This work was supported by a Grant-in-Aid for Scientific Research (B) to HS (21360401) from Japan Society for Promotion of Science and Grants-in-Aid for Young Scientists (B) to TH (21780071) and CF (20700270) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. This work was also supported in part by the Global COE Program of the Ministry of Education, Culture, Sports, Science, and Technology of Japan.

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Correspondence to Hiroshi Shimizu.

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Table S1

Gene expression profiles in strain Nos. 48 and 49 in comparison with that in No. 11 (PDF 487 kb)

Table S2

l-lactate production (g/l) in the pTRS48-transformed disruptants of the genes whose expression was upregulated in both Nos. 48 and 49 strains (PDF 46 kb)

Table S3

l-lactate production in the pTRS48-transformed disruptants of the genes whose expression was downregulated in both Nos. 48 and 49 strains (PDF 44 kb)

Table S4

l-lactate production in the pTRS48-transformed disruptants of the genes selected randomly (PDF 37 kb)

Table S5

l-lactate production (g/l) in the standard strain (BY4742 HIS3::kanMX4) (PDF 36 kb)

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Hirasawa, T., Ookubo, A., Yoshikawa, K. et al. Investigating the effectiveness of DNA microarray analysis for identifying the genes involved in l-lactate production by Saccharomyces cerevisiae . Appl Microbiol Biotechnol 84, 1149–1159 (2009).

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  • Saccharomyces cerevisiae
  • l-Lactate
  • DNA microarray
  • Knockout strain library