Global analysis of protein phosphorylation in yeast

@article{Ptacek2005GlobalAO,
  title={Global analysis of protein phosphorylation in yeast},
  author={Jason Ptacek and Geeta Devgan and Gregory A. Michaud and Hengying Zhu and Xiaowei Zhu and Joseph Fasolo and Hong Guo and Ghil Jona and Ashton Breitkreutz and Richelle Sopko and Rhonda R. McCartney and Martin C Schmidt and Najma Rachidi and Soo-Jung Lee and Angie S. Mah and Lihao Meng and Michael J R Stark and David F. Stern and Claudio De Virgilio and Mike Tyers and Brenda J. Andrews and Mark B. Gerstein and Barry Schweitzer and Paul F. Predki and Michael Snyder},
  journal={Nature},
  year={2005},
  volume={438},
  pages={679-684}
}
Protein phosphorylation is estimated to affect 30% of the proteome and is a major regulatory mechanism that controls many basic cellular processes. Until recently, our biochemical understanding of protein phosphorylation on a global scale has been extremely limited; only one half of the yeast kinases have known in vivo substrates and the phosphorylating kinase is known for less than 160 phosphoproteins. Here we describe, with the use of proteome chip technology, the in vitro substrates… 
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References

SHOWING 1-10 OF 35 REFERENCES
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
Protein kinases are coded by more than 2,000 genes and thus constitute the largest single enzyme family in the human genome. Most cellular processes are in fact regulated by the reversible
Analysis of yeast protein kinases using protein chips
TLDR
A novel protein chip technology is developed that allows the high-throughput analysis of biochemical activities, and this approach is used to analyse nearly all of the protein kinases from Saccharomyces cerevisiae, finding many novel activities and that a large number ofprotein kinases are capable of phosphorylating tyrosine.
Evolution of protein kinase signaling from yeast to man.
TLDR
Fly and human share several kinase families involved in immunity, neurobiology, cell cycle and morphogenesis that are absent from worm, suggesting that these functions might have evolved after the divergence of nematodes from the main metazoan lineage.
Targets of the cyclin-dependent kinase Cdk1
TLDR
The identities of these substrates reveal that Cdk1 employs a global regulatory strategy involving phosphorylation of other regulatory molecules as well as phosphorylated of the molecular machines that drive cell-cycle events.
Functional organization of the yeast proteome by systematic analysis of protein complexes
TLDR
The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery.
Global Analysis of Protein Activities Using Proteome Chips
TLDR
Microarrays of an entire eukaryotic proteome can be prepared and screened for diverse biochemical activities and can be used to screen protein-drug interactions and to detect posttranslational modifications.
Global analysis of protein expression in yeast
TLDR
A Saccharomyces cerevisiae fusion library is created where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location, and it is found that about 80% of the proteome is expressed during normal growth conditions.
Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S
TLDR
Of more than 700 identified phosphopeptides, 139 were differentially regulated at least 2-fold in response to mating pheromone and among these regulated proteins were components belonging to the mitogen-activated protein kinase signaling pathway and to downstream processes including transcriptional regulation, the establishment of polarized growth, and the regulation of the cell cycle.
Cyclin specificity in the phosphorylation of cyclin-dependent kinase substrates
TLDR
Comparing the specificity of two budding yeast cyclins in the phosphorylation of 150 Cdk1 (Cdc28) substrates found that Clb2–Cdk1 possessed higher intrinsic kinase activity than Clb5–C DK1, enabling efficient phosphorylated of a broad range of mitotic Cdk 1 targets.
Cytoskeletal activation of a checkpoint kinase.
TLDR
The results suggest that binding to multiple septins activates Hsl1 kinase activity, thereby promoting cell cycle progression, and indicates that similar mechanisms may monitor cytoskeletal organization in other eukaryotes.
...
1
2
3
4
...