A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression

Abstract

Understanding cells as integrated systems requires that we systematically decipher how single genes affect multiple biological processes and how processes are functionally linked. Here, we used multiprocess phenotypic profiling, combining high-resolution 3D confocal microscopy and multiparametric image analysis, to simultaneously survey the fission yeast genome with respect to three key cellular processes: cell shape, microtubule organization, and cell-cycle progression. We identify, validate, and functionally annotate 262 genes controlling specific aspects of those processes. Of these, 62% had not been linked to these processes before and 35% are implicated in multiple processes. Importantly, we identify a conserved role for DNA-damage responses in controlling microtubule stability. In addition, we investigate how the processes are functionally linked. We show unexpectedly that disruption of cell-cycle progression does not necessarily affect cell size control and that distinct aspects of cell shape regulate microtubules and vice versa, identifying important systems-level links across these processes.

Systematic Mapping of cell Wall Mechanics in the Regulation of Cell Morphogenesis

“…The fission yeast Schizosaccaromyces pombe is one of the most-established model to understand the emergence of cell morphogenesis (20)(21)(22)(23). Those are rod-shaped cells which grow by tip extension with a near-constant diameter of ~4 microns.…”

“…For this, we examined 26 mutants knocked out for a single open reading frame, which have been reported to bear defects in cell diameter from previous visual screens of the fission yeast KO library (22,23). After careful validation and diameter quantification (see material and methods), we refocused our analysis, on a specific set of 18 mutants, which solely exhibited diameter mis-regulation, discarding more complex misshaped mutants with other bent or branched features, for instance (22,23). Importantly, those mutants covered several physiological processes, including cell polarity, chromosome segregation, signaling, metabolism and wall synthesis ( Table 1, Fig.…”

Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli

“…It is also unclear how cellular activities are integrated to ensure that each division produces two viable daughter cells. Systematic genomewide screens, rendered possible by the creation of arrayed single-gene knockout collections, have been successfully used to gain a more comprehensive perspective on cell morphogenesis and the cell cycle in yeast (Jorgensen et al, 2002;Ohya et al, 2005;Graml et al, 2014). Beyond the functional information gained through the mapping of phenotypes associated with the deletion of genes, genomewide screens also provide a unique opportunity to interrogate the relationship between phenotypic features with thousands of independent genetic perturbations (Liberali et al, 2015).…”

Microtubule organization is determined by the shape of epithelial cells

“…In single cells, whether yeast or mammalian cells in culture, MT organization can be explained by a physical mechanism where MTs follow changes in cell geometry567. Cell geometry acts on MT organization largely by altering the dynamics of the MTs colliding with the cell boundary.…”