Multidimensional quantification of subcellular morphology of Saccharomyces cerevisiae using CalMorph, the high-throughput image-processing program.

To quantitatively and multidimensionally assess the morphology of subcellular organelles and protein complexes in budding yeast cells, we applied our recently developed image-processing program, CalMorph. In this study, mitochondria, vacuole, endoplasmic reticulum, Golgi body, endosome, spindle pole body, and septin morphology were evaluated. In addition to the originally developed 501 parameters for cell wall morphology, nuclear DNA, and actin, we proposed an additional 610 parameters for the morphology of subcellular components, resulting in a total of 1111 quantitative parameters to evaluate the morphology of budding yeast. This approach enables one to conduct more detailed phenotypic studies, which is advantageous in yeast functional genomics.

[1]  M. Iwase,et al.  Ybr267w is a new cytoplasmic protein belonging to the mitotic signaling network of Saccharomyces cerevisiae. , 2004, Cell structure and function.

[2]  A. Nakano,et al.  Live imaging of yeast Golgi cisternal maturation , 2006, Nature.

[3]  W. Neupert,et al.  Connection of the Mitochondrial Outer and Inner Membranes by Fzo1 Is Critical for Organellar Fusion , 2001, The Journal of cell biology.

[4]  Shinichi Morishita,et al.  Development of Image Processing Program for Yeast Cell Morphology , 2004, J. Bioinform. Comput. Biol..

[5]  R. Rachubinski,et al.  Orchestrating organelle inheritance in Saccharomyces cerevisiae. , 2007, Current opinion in microbiology.

[6]  A. Nakano,et al.  Rer1p, a Retrieval Receptor for Endoplasmic Reticulum Membrane Proteins, Is Dynamically Localized to the Golgi Apparatus by Coatomer , 2001, The Journal of cell biology.

[7]  Dannel McCollum,et al.  Centrosomes in cellular regulation. , 2005, Annual review of cell and developmental biology.

[8]  J. Boeke,et al.  Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications , 1998, Yeast.

[9]  S. Ishihara,et al.  Dissection of upstream regulatory components of the Rho1p effector, 1,3-beta-glucan synthase, in Saccharomyces cerevisiae. , 2002, Genetics.

[10]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[11]  J. Thorner,et al.  Some assembly required: yeast septins provide the instruction manual. , 2005, Trends in cell biology.

[12]  T. Stevens,et al.  Vacuole Biogenesis in Saccharomyces cerevisiae: Protein Transport Pathways to the Yeast Vacuole , 1998, Microbiology and Molecular Biology Reviews.

[13]  Gerald R. Fink,et al.  Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: Regulation by starvation and RAS , 1992, Cell.

[14]  Taro L. Saito,et al.  High-dimensional and large-scale phenotyping of yeast mutants. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B. Wendland,et al.  Fluorescent Labeling of Yeast , 2003, Current protocols in cell biology.

[16]  Y. Ohya,et al.  Involvement of Rho-type GTPase in control of cell size in Saccharomyces cerevisiae. , 2007, FEMS yeast research.

[17]  K. Wirtz,et al.  Peptide-based targeting of fluorophores to organelles in living cells. , 2001, Experimental cell research.

[18]  Rachel B. Brem,et al.  The landscape of genetic complexity across 5,700 gene expression traits in yeast. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Yoshikazu Ohya,et al.  Genetic Complexity and Quantitative Trait Loci Mapping of Yeast Morphological Traits , 2007, PLoS genetics.

[20]  J. Pringle,et al.  CDC42 and CDC43, two additional genes involved in budding and the establishment of cell polarity in the yeast Saccharomyces cerevisiae , 1990, The Journal of cell biology.

[21]  L. Weisman.  Organelles on the move: insights from yeast vacuole inheritance , 2006, Nature Reviews Molecular Cell Biology.

[22]  W. Neupert,et al.  Fzo1p Is a Mitochondrial Outer Membrane Protein Essential for the Biogenesis of Functional Mitochondria in Saccharomyces cerevisiae* , 1998, The Journal of Biological Chemistry.

[23]  Shinichi Morishita,et al.  G1/S cyclin-dependent kinase regulates small GTPase Rho1p through phosphorylation of RhoGEF Tus1p in Saccharomyces cerevisiae. , 2008, Molecular biology of the cell.

[24]  E. Salmon,et al.  Spindle dynamics and cell cycle regulation of dynein in the budding yeast, Saccharomyces cerevisiae , 1995, The Journal of cell biology.

[25]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[26]  S. Jaspersen,et al.  The budding yeast spindle pole body: structure, duplication, and function. , 2004, Annual review of cell and developmental biology.

[27]  Y. Ohya,et al.  Diversity of Ca2+-Induced Morphology Revealed by Morphological Phenotyping of Ca2+-Sensitive Mutants of Saccharomyces cerevisiae , 2007, Eukaryotic Cell.

[28]  J. Thatcher,et al.  Mitochondrial Fusion in Yeast Requires the Transmembrane GTPase Fzo1p , 1998, The Journal of cell biology.

[29]  Y. Ohya,et al.  Dynactin is involved in a checkpoint to monitor cell wall synthesis in Saccharomyces cerevisiae , 2004, Nature Cell Biology.

[30]  J. Shaw,et al.  Mitochondrial morphology and dynamics in yeast and multicellular eukaryotes. , 2005, Annual review of genetics.