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Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains.

Yang M, Ohnuki S, Ohya Y - BMC Genomics (2014)

Bottom Line: However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model.Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg, FSB-101, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Chiba Prefecture, Japan. ohya@k.u-tokyo.ac.jp.

ABSTRACT

Background: Phenotypes are variable within species, with high phenotypic variation in the fitness and cell morphology of natural yeast strains due to genetic variation. A gene deletion collection of yeast laboratory strains also contains phenotypic variations, demonstrating the involvement of each gene and its specific function. However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.

Results: The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model. The gene deletion strains had higher morphological variance than the natural strains. Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

Conclusion: Based on the morphological analysis, we discovered gene deletion mutants whose morphologies were not seen in nature. Our multivariate approach to the morphological diversity provided a new insight into the evolution and species conservation of yeast.

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Summary of the phenotypes annotated to the 36 heteroclite genes. Annotations of the phenotypes in Additional file 10: Table S3 are summarized. Asterisks indicate the genes annotated to the GOs as detected by MANOVA (Figure 7A and Additional file 12: Table S4).
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Fig5: Summary of the phenotypes annotated to the 36 heteroclite genes. Annotations of the phenotypes in Additional file 10: Table S3 are summarized. Asterisks indicate the genes annotated to the GOs as detected by MANOVA (Figure 7A and Additional file 12: Table S4).

Mentions: Of the 36 heteroclite strains, 22 were identified as slow-growth mutants in normal medium [15] (Additional file 10: Table S3 and Figure 5). We found that all of the remaining 14 heteroclite strains were assigned to at least one phenotype relating to a decrease in the stress response, such as “decrease of resistance to environmental stress,” “decrease of resistance to chemical stress,” and “decrease of resistance to ethanol stress” (Additional file 10: Table S3 and Figure 5). This suggested that the loss-of-function mutation of these 14 genes was negatively selected for under these special environmental conditions.Figure 5


Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains.

Yang M, Ohnuki S, Ohya Y - BMC Genomics (2014)

Summary of the phenotypes annotated to the 36 heteroclite genes. Annotations of the phenotypes in Additional file 10: Table S3 are summarized. Asterisks indicate the genes annotated to the GOs as detected by MANOVA (Figure 7A and Additional file 12: Table S4).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4221665&req=5

Fig5: Summary of the phenotypes annotated to the 36 heteroclite genes. Annotations of the phenotypes in Additional file 10: Table S3 are summarized. Asterisks indicate the genes annotated to the GOs as detected by MANOVA (Figure 7A and Additional file 12: Table S4).
Mentions: Of the 36 heteroclite strains, 22 were identified as slow-growth mutants in normal medium [15] (Additional file 10: Table S3 and Figure 5). We found that all of the remaining 14 heteroclite strains were assigned to at least one phenotype relating to a decrease in the stress response, such as “decrease of resistance to environmental stress,” “decrease of resistance to chemical stress,” and “decrease of resistance to ethanol stress” (Additional file 10: Table S3 and Figure 5). This suggested that the loss-of-function mutation of these 14 genes was negatively selected for under these special environmental conditions.Figure 5

Bottom Line: However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model.Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg, FSB-101, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Chiba Prefecture, Japan. ohya@k.u-tokyo.ac.jp.

ABSTRACT

Background: Phenotypes are variable within species, with high phenotypic variation in the fitness and cell morphology of natural yeast strains due to genetic variation. A gene deletion collection of yeast laboratory strains also contains phenotypic variations, demonstrating the involvement of each gene and its specific function. However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast.

Results: The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model. The gene deletion strains had higher morphological variance than the natural strains. Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation.

Conclusion: Based on the morphological analysis, we discovered gene deletion mutants whose morphologies were not seen in nature. Our multivariate approach to the morphological diversity provided a new insight into the evolution and species conservation of yeast.

Show MeSH