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Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network.

Vaggi F, Dodgson J, Bajpai A, Chessel A, Jordán F, Sato M, Carazo-Salas RE, Csikász-Nagy A - PLoS Comput. Biol. (2012)

Bottom Line: The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms.Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation.As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.

View Article: PubMed Central - PubMed

Affiliation: The Microsoft Research-University of Trento Centre for Computational Systems Biology, Rovereto, Italy.

ABSTRACT
The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify 'linker' proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted 'linkers' also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.

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Localization in cells of Sts5 during the cell cycle.(A) Imaging of fission yeast cells co-expressing Sts5-3GFP and mCh-atb2 (labelling the different microtubule structures seen through the cell cycle, and hence acting as cell cycle stage indicators). Interphase cells (I) have diffuse Sts5 localization (with a few cytoplasmic speckles) while cells in mitosis (either in anaphase (A) or during the time of the post anaphase array (PAA)) have several Sts5 cytoplasmic dots. Scalebar: 5 µm. (B) Population based analysis of cycling cells revealed that at metaphase the number of Sts5 speckles greatly increases and sharply drops during septum formation. Average and standard deviation of number of dots were automatically detected in multiple cells (see Materials and Methods for details).
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pcbi-1002732-g005: Localization in cells of Sts5 during the cell cycle.(A) Imaging of fission yeast cells co-expressing Sts5-3GFP and mCh-atb2 (labelling the different microtubule structures seen through the cell cycle, and hence acting as cell cycle stage indicators). Interphase cells (I) have diffuse Sts5 localization (with a few cytoplasmic speckles) while cells in mitosis (either in anaphase (A) or during the time of the post anaphase array (PAA)) have several Sts5 cytoplasmic dots. Scalebar: 5 µm. (B) Population based analysis of cycling cells revealed that at metaphase the number of Sts5 speckles greatly increases and sharply drops during septum formation. Average and standard deviation of number of dots were automatically detected in multiple cells (see Materials and Methods for details).

Mentions: Among predicted linker proteins we focused on Sts5, which is known to genetically interact with Ssp2 [69], which itself is likely to be linked with the cell cycle machinery as ssp2Δ cells cannot start mitosis when nutrient-starved [77]. Sts5 is an orthologue of budding yeast SSD1 [78] and therefore a candidate translational repressor. It is reported to control actin localisation in interphase and sts5Δ was shown to be compensated by mutations in Ssp2. Furthermore, Sts5 mRNA levels were shown to oscillate [74], [79]. To examine the interplay between Sts5 and the cell cycle, we tagged the endogenous protein with a triple GFP tag and visualized its localization together with that of mCh-Atb2 (Alpha tubulin 2), which labels microtubules and hence served as a cell cycle stage marker. In interphase cells, Sts5 had a mostly diffuse cytoplasmic localization, however during mitosis it appeared to localize in dotted, cytoplasmic bodies (Figure 5A). The number of Sts5 dots increased throughout mitosis and peaked coinciding with the assembly of the Post Anaphase Array (PPA) of microtubules (Figure 5B). Time-lapse movies of mitotic cells also confirmed that the number of cytoplasmic dots increased until the formation of the PAA and sharply dropped to zero as cells entered interphase (Figure S6). Previous studies of Sts5 [69] showed that it was required for correct cell growth and actin patch localization during interphase. Taken together with our results, this suggests that the cell cycle controls Sts5 activity by gradually sequestering it in cytoplasmic bodies during mitosis.


Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network.

Vaggi F, Dodgson J, Bajpai A, Chessel A, Jordán F, Sato M, Carazo-Salas RE, Csikász-Nagy A - PLoS Comput. Biol. (2012)

Localization in cells of Sts5 during the cell cycle.(A) Imaging of fission yeast cells co-expressing Sts5-3GFP and mCh-atb2 (labelling the different microtubule structures seen through the cell cycle, and hence acting as cell cycle stage indicators). Interphase cells (I) have diffuse Sts5 localization (with a few cytoplasmic speckles) while cells in mitosis (either in anaphase (A) or during the time of the post anaphase array (PAA)) have several Sts5 cytoplasmic dots. Scalebar: 5 µm. (B) Population based analysis of cycling cells revealed that at metaphase the number of Sts5 speckles greatly increases and sharply drops during septum formation. Average and standard deviation of number of dots were automatically detected in multiple cells (see Materials and Methods for details).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3475659&req=5

pcbi-1002732-g005: Localization in cells of Sts5 during the cell cycle.(A) Imaging of fission yeast cells co-expressing Sts5-3GFP and mCh-atb2 (labelling the different microtubule structures seen through the cell cycle, and hence acting as cell cycle stage indicators). Interphase cells (I) have diffuse Sts5 localization (with a few cytoplasmic speckles) while cells in mitosis (either in anaphase (A) or during the time of the post anaphase array (PAA)) have several Sts5 cytoplasmic dots. Scalebar: 5 µm. (B) Population based analysis of cycling cells revealed that at metaphase the number of Sts5 speckles greatly increases and sharply drops during septum formation. Average and standard deviation of number of dots were automatically detected in multiple cells (see Materials and Methods for details).
Mentions: Among predicted linker proteins we focused on Sts5, which is known to genetically interact with Ssp2 [69], which itself is likely to be linked with the cell cycle machinery as ssp2Δ cells cannot start mitosis when nutrient-starved [77]. Sts5 is an orthologue of budding yeast SSD1 [78] and therefore a candidate translational repressor. It is reported to control actin localisation in interphase and sts5Δ was shown to be compensated by mutations in Ssp2. Furthermore, Sts5 mRNA levels were shown to oscillate [74], [79]. To examine the interplay between Sts5 and the cell cycle, we tagged the endogenous protein with a triple GFP tag and visualized its localization together with that of mCh-Atb2 (Alpha tubulin 2), which labels microtubules and hence served as a cell cycle stage marker. In interphase cells, Sts5 had a mostly diffuse cytoplasmic localization, however during mitosis it appeared to localize in dotted, cytoplasmic bodies (Figure 5A). The number of Sts5 dots increased throughout mitosis and peaked coinciding with the assembly of the Post Anaphase Array (PPA) of microtubules (Figure 5B). Time-lapse movies of mitotic cells also confirmed that the number of cytoplasmic dots increased until the formation of the PAA and sharply dropped to zero as cells entered interphase (Figure S6). Previous studies of Sts5 [69] showed that it was required for correct cell growth and actin patch localization during interphase. Taken together with our results, this suggests that the cell cycle controls Sts5 activity by gradually sequestering it in cytoplasmic bodies during mitosis.

Bottom Line: The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms.Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation.As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.

View Article: PubMed Central - PubMed

Affiliation: The Microsoft Research-University of Trento Centre for Computational Systems Biology, Rovereto, Italy.

ABSTRACT
The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify 'linker' proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted 'linkers' also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.

Show MeSH