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BMC Syst Biol. 2012 Sep 27;6:128. doi: 10.1186/1752-0509-6-128.

Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast.

Author information

1
Ecology & Evolutionary Biology, University of Arizona, 1041 E Lowell St, Tucson, AZ 85721, USA.

Abstract

BACKGROUND:

A hub protein is one that interacts with many functional partners. The annotation of hub proteins, or more generally the protein-protein interaction "degree" of each gene, requires quality genome-wide data. Data obtained using yeast two-hybrid methods contain many false positive interactions between proteins that rarely encounter each other in living cells, and such data have fallen out of favor.

RESULTS:

We find that protein "stickiness", measured as network degree in ostensibly low quality yeast two-hybrid data, is a more predictive genomic metric than the number of functional protein-protein interactions, as assessed by supposedly higher quality high throughput affinity capture mass spectrometry data. In the yeast Saccharomyces cerevisiae, a protein's high stickiness, but not its high number of functional interactions, predicts low stochastic noise in gene expression, low plasticity of gene expression across different environments, and high probability of forming a homo-oligomer. Our results are robust to a multiple regression analysis correcting for other known predictors including protein abundance, presence of a TATA box and whether a gene is essential. Once the higher stickiness of homo-oligomers is controlled for, we find that homo-oligomers have noisier and more plastic gene expression than other proteins, consistent with a role for homo-oligomerization in mediating robustness.

CONCLUSIONS:

Our work validates use of the number of yeast two-hybrid interactions as a metric for protein stickiness. Sticky proteins exhibit low stochastic noise in gene expression, and low plasticity in expression across different environments.

PMID:
23017156
PMCID:
PMC3527306
DOI:
10.1186/1752-0509-6-128
[Indexed for MEDLINE]
Free PMC Article

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