Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast
AffiliationPresent address: Ecology & Evolutionary Biology, University of Arizona, 1041 E Lowell St, Tucson, AZ, 85721, USA
Present address: Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
KeywordsProtein-protein interaction networks
Stochastic gene expression
MetadataShow full item record
CitationBrettner and Masel BMC Systems Biology 2012, 6:128 http://www.biomedcentral.com/1752-0509/6/128
JournalBMC Systems Biology
Rights© 2012 Brettner and Masel; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection InformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at firstname.lastname@example.org.
AbstractBACKGROUND: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.
VersionFinal published version
Showing items related by title, author, creator and subject.
Methods for the Detection of Protein-Nucleic Acid and Protein-Protein InteractionsStains, Cliff (The University of Arizona., 2008)We describe the first general approach for the DNA templated reassembly of proteins, which we term SEquence-Enabled Reassembly or SEER. SEER makes use of dissected signaling domains which are each attached to separate, sequence specific DNA-binding proteins. Described herein is an embodiment of SEER in which DNA catalyzes the reassembly of the green fluorescent protein which leads to a direct fluorescence readout of the corresponding DNA sequence. This strategy has also been extended to the first direct method for the site specific detection of DNA methylation. This mCpG-SEER system is capable of discriminating between methylated versus nonmethylated DNA with a 40-fold increase in fluorescence signal.In a separate undertaking we tested the efficiency of disulfide bond formation within the context of the ribosome display in vitro selection methodology. We established conditions for the enrichment of a cyclic peptide, which is specific for Neutravidin, by 2 x 10^6-fold. Using the knowledge gained from the above experiments, we combined the rapid protein expression and folding benefits of cell-free translation systems with a sensitive split-luciferase reassembly assay to yield the most rapid method to date for the detection of protein-nucleic acid and protein-protein interactions. Furthermore, we have shown that these split-luciferase cell-free reassembly systems can be compartmentalized, allowing for future molecular evolution studies.Lastly, we have applied this rapid cell-free split-luciferase assay system to the direct detection of clinically relevant proteins. We have engineered a system for the rapid characterization of HIV-1 clades utilizing single-chain antibody specificities. We also demonstrate that this platform can be used to determine the relative amounts of HER2 expression in human breast cancer cells, using a homogeneous assay format in which cells and reagents are mixed and luminescence is monitored directly.We envision that the assay platforms described herein will find applications in the rapid detection of nucleic acid sequences, protein identities, and relative protein abundances in the laboratory and clinic.
Split-Protein Systems for the Detection and Interrogation of Protein-Nucleic Acid InteractionsBadran, Ahmed Hussein (The University of Arizona., 2010-05)Cys2-His2 zinc fingers constitute one of the largest classes of DNA-binding domains in the human genome. The modularity of these domains has been recently exploited to design artificial zinc fingers, capable of targeting virtually any sequence. However, the resultant zinc fingers have had significantly high failure rate, owing to low binding affinity and selectivity. Despite much research on the topic, a proper understanding of all the factors involved in zinc finger selectivity, be they natural or artificial, has proved elusive. Here, we present a modification of our previously reported SEquence-Enabled Reassembly (SEER) methodology, allowing us to study zinc finger selectivity with base pair resolution. Using this modified strategy, we show that the natural 3-finger zinc finger Zif268 binding to its consensus site is highly dependent on the availability of specific base pairs, or 'hot spots,' and independent of mutations at adjacent positions. Additionally, we show that positional interdependence plays a large role in the selectivity of both Zif268 and the artificial 6-finger zinc finger Aart for their respective targets. We envision that this technique can be easily applied towards the interrogation of any DNA-binding domain in a high throughput and accurate manner.
Modulation of Helix Stability to Investigate Protein-Protein Interactions in the Paramyxovirus Replication ComplexArias, Victor H. (The University of Arizona., 2013)The focus of this project is to develop a greater understanding of the protein-protein interaction between the measles Nucleocapsid Binding Domain (NBD) protein and its ligand N-protein, which are part of the paramyxovirus replication complex. This interaction is an example of a binding reaction where one partner (the N protein) is intrinsically unstructured, but undergoes a coil-to helix transition upon binding. The NBD’s biological role is to bind the N protein which coats the viral RNA genome. However, it must quickly release as the replication complex moves along the RNA during replication. To facilitate this biological function, NBD displays a weak and short-lived interaction with the N-protein that is heavily dependent on the structural stability of both proteins. We are utilizing this pair of proteins as a model system for the study of coupled folding and binding processes. In this work, we have investigated the influence of helix formation in N protein on the NBD-N interaction. Helix stabilizing and destabilizing mutations were introduced into the NBD binding site on the measles N-protein in order to analyze the effects that the structural stability of N-protein have in the binding equilibrium between NBD and N. The measles N protein was mutated by site directed mutagenesis into an unstable mutant, L496G, and a more favorably stable mutant, L496A. These were fused to a small protein, SUMO, to facilitate purification. After, induction and expression of the desired proteins, the proteins were extracted from their respective transformed E. coli BL21-D3 gold expression strain and submitted to protein purification techniques such as Co²⁺ affinity column chromatography, dialysis, and centrifuge concentration. The purity and success of the purification was evaluated by SDS-PAGE electrophoresis, and absorption spectroscopy. The binding reaction between measles NBD wild type, N protein and the mutated variants was analyzed by isothermal titration calorimetry (ITC).