Functional Genomics and Morphological Profiling in Saccharomyces cerevisiae

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Plant, Algae and Fungi Cell Biology".

Deadline for manuscript submissions: 24 December 2025 | Viewed by 309

Special Issue Editors


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Guest Editor
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan. Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
Interests: functional genomics; morphological profiling; Saccharomyces cerevisiae; fermentation; agrichemicals

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Guest Editor
Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
Interests: yeast; overexpression; functional genomics

Special Issue Information

Dear Colleagues,

Functional genomics aims to systematically elucidate gene functions and the molecular basis of phenotypic traits and disease susceptibility. Saccharomyces cerevisiae has long served as a central model organism in this field, owing to its genetic tractability and the wealth of experimental resources available. Recent advances, including large-scale phenotypic libraries (~5,000 deletion strains across >7,500 conditions) and transcriptomic datasets for over 1,500 strains, have provided unprecedented insights into gene regulatory networks and diverse cellular features—such as morphology, protein localization, and intracellular environments.

The field is now rapidly expanding beyond traditional knockout approaches. Emerging directions include gene overexpression systems, machine learning-guided predictions of uncharacterized ORFs, and the causal inference of drug-response phenotypes. Particular attention is being paid toward rare, condition-specific phenotypes that may offer novel biological insights.

Today, the functional genomics of S. cerevisiae are increasingly being recognized as a versatile platform for integrative biology, with broad applications in drug discovery, disease modeling, and industrial biotechnology. This Special Issue highlights recent developments in functional genomics and morphological profiling in yeast, and invites contributions that address new methodologies, biological discoveries, and conceptual advances shaping the future of this field.

Prof. Dr. Yoshikazu Ohya
Prof. Dr. Hisao Moriya
Guest Editors

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Keywords

  • functional genomics
  • morphological profiling
  • Saccharomyces cerevisiae
  • overexpression

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Published Papers (1 paper)

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Research

16 pages, 4747 KB  
Article
Divergent Morphologies and Common Signaling Features of Active and Inactive Oncogenic RHOA Mutants in Yeast
by Chenwei Wang, Shinsuke Ohnuki, Anna Savchenko, Hiroyuki Aburatani, Satoshi Yoshida, Riko Hatakeyama and Yoshikazu Ohya
Cells 2025, 14(18), 1439; https://doi.org/10.3390/cells14181439 - 15 Sep 2025
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Abstract
RHOA, a member of the Rho family of small GTPases, harbors recurrent mutations in diverse cancers, but how these mutations cause their cellular effects remains poorly understood. To investigate their cellular consequences, we expressed oncogenic RHOA variants (R5Q, G17V, C16R, and A161P) [...] Read more.
RHOA, a member of the Rho family of small GTPases, harbors recurrent mutations in diverse cancers, but how these mutations cause their cellular effects remains poorly understood. To investigate their cellular consequences, we expressed oncogenic RHOA variants (R5Q, G17V, C16R, and A161P) in Saccharomyces cerevisiae, substituting for the essential yeast homologue RHO1. While the E40Q variant failed to complement RHO1 deletion, other mutants supported viability and enabled phenotypic characterization. All four variants conferred myriocin resistance, suggesting activation of the membrane stress response pathway, but induced no major changes in growth or caspofungin sensitivity. Using high-dimensional image analysis, we quantified 501 morphological parameters and applied principal component analysis and linear discriminant analysis to determine distinct phenotypic profiles. Gain-of-function (C16R and A161P) and loss-of-function (R5Q and G17V) mutants formed separate morphological clusters, indicating functional divergence. Our yeast model enabled systematic dissection of the functions of RHOA mutants and highlighted the utility of morphology-based approaches to characterize context-dependent mechanisms of oncogenesis. Full article
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