scholarly journals Genome-Wide Protein Interaction Screens Reveal Functional Networks Involving Sm-Like Proteins

Yeast ◽  
2000 ◽  
Vol 1 (2) ◽  
pp. 95-110
Author(s):  
Micheline Fromont-Racine ◽  
Andrew E. Mayes ◽  
Adeline Brunet-Simon ◽  
Jean-Christophe Rain ◽  
Alan Colley ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
Yeast Genome ◽  
Protein Protein Interactions ◽  
Sm Proteins ◽  
Functional Studies ◽  
Genome Wide ◽  
A Genome ◽  
Two Hybrid

A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence of Saccharomyces cerevisiae has identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (L¯ike Sm¯) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein–protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale.

scholarly journals Genome-Wide Protein Interaction Screens Reveal Functional Networks Involving Sm-Like Proteins

Yeast ◽  
2000 ◽  
Vol 1 (2) ◽  
pp. 95-110 ◽  
Author(s):  
Micheline Fromont-Racine ◽  
Andrew E. Mayes ◽  
Adeline Brunet-Simon ◽  
Jean-Christophe Rain ◽  
Alan Colley ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
Yeast Genome ◽  
Protein Protein Interactions ◽  
Sm Proteins ◽  
Functional Studies ◽  
Genome Wide ◽  
A Genome ◽  
Two Hybrid

A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence ofSaccharomyces cerevisiaehas identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (L¯ike Sm¯) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein–protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale.

scholarly journals Prioritization of genes associated with the pathogenesis of leukosis in cattle

2019 ◽  
Vol 22 (8) ◽  
pp. 1063-1069 ◽  
Author(s):  
N. S. Yudin ◽  
N. L. Podkolodnyy ◽  
T. A. Agarkova ◽  
E. V. Ignatieva
Keyword(s):  
Protein Interactions ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Mammalian Species ◽  
Genome Wide Association ◽  
Farm Animals ◽  
Genome Wide Association Studies ◽  
Protein Protein Interactions ◽  
Genome Wide ◽  
A Genome

Selection by means of genetic markers is a promising approach to the eradication of infectious diseases in farm animals, especially in the absence of effective methods of treatment and prevention. Bovine leukemia virus (BLV) is spread throughout the world and represents one of the biggest problems for the livestock production and food security in Russia. However, recent genome-wide association studies have shown that sensitivity/resistance to BLV is polygenic. The aim of this study was to create a catalog of cattle genes and genes of other mammalian species involved in the pathogenesis of BLV-induced infection and to perform gene prioritization using bioinformatics methods. Based on manually collected information from a range of open sources, a total of 446 genes were included in the catalog of cattle genes and genes of other mammals involved in the pathogenesis of BLV-induced infection. The following criteria were used to prioritize 446 genes from the catalog: (1) the gene is associated with leukemia according to a genome-wide association study; (2) the gene is associated with leukemia according to a case-control study; (3) the role of the gene in leukemia development has been studied using knockout mice; (4) protein-protein interactions exist between the gene-encoded protein and either viral particles or individual viral proteins; (5) the gene is annotated with Gene Ontology terms that are overrepresented for a given list of genes; (6) the gene participates in biological pathways from the KEGG or REACTOME databases, which are over-represented for a given list of genes; (7) the protein encoded by the gene has a high number of protein-protein interactions with proteins encoded by other genes from the catalog. Based on each criterion, a rank was assigned to each gene. Then the ranks were summarized and an overall rank was determined. Prioritization of 446 candidate genes allowed us to identify 5 genes of interest (TNF,LTB,BOLA-DQA1,BOLA-DRB3,ATF2), which can affect the sensitivity/resistance of cattle to leukemia.

scholarly journals Kinetochore Protein Interactions and their Regulation by the Aurora Kinase Ipl1p

2003 ◽  
Vol 14 (8) ◽  
pp. 3342-3355 ◽  
Author(s):  
Ching Shang ◽  
Tony R. Hazbun ◽  
Iain M. Cheeseman ◽  
Jennifer Aranda ◽  
Stanley Fields ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Aurora Kinase ◽  
Open Reading Frames ◽  
Binding Assays ◽  
A Genome ◽  
Physical Interactions ◽  
Dam1 Complex ◽  
Two Hybrid ◽  
Kinetochore Function

Although there has been a recent explosion in the identification of budding yeast kinetochore components, the physical interactions that underlie kinetochore function remain obscure. To better understand how kinetochores attach to microtubules and how this attachment is regulated, we sought to characterize the interactions among kinetochore proteins, especially with respect to the microtubule-binding Dam1 complex. The Dam1 complex plays a crucial role in the chromosome-spindle attachment and is a key target for phospho-regulation of this attachment by the Aurora kinase Ipl1p. To identify protein–protein interactions involving the Dam1 complex, and the effects of Dam1p phosphorylation state on these physical interactions, we conducted both a genome-wide two-hybrid screen and a series of biochemical binding assays for Dam1p. A two-hybrid screen of a library of 6000 yeast open reading frames identified nine kinetochore proteins as Dam1p-interacting partners. From 113 in vitro binding reactions involving all nine subunits of the Dam1 complex and 32 kinetochore proteins, we found at least nine interactions within the Dam1 complex and 19 potential partners for the Dam1 complex. Strikingly, we found that the Dam1p–Ndc80p and Dam1p–Spc34p interactions were weakened by mutations mimicking phosphorylation at Ipl1p sites, allowing us to formulate a model for the effects of phosphoregulation on kinetochore function.

scholarly journals Correction: Corrigendum: Structure-based prediction of protein–protein interactions on a genome-wide scale

Nature ◽  
2013 ◽  
Vol 495 (7439) ◽  
pp. 127-127 ◽  
Author(s):  
Qiangfeng Cliff Zhang ◽  
Donald Petrey ◽  
Lei Deng ◽  
Li Qiang ◽  
Yu Shi ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

scholarly journals A protein interaction map for cell polarity development

2001 ◽  
Vol 154 (3) ◽  
pp. 549-576 ◽  
Author(s):  
Becky L. Drees ◽  
Bryan Sundin ◽  
Elizabeth Brazeau ◽  
Juliane P. Caviston ◽  
Guang-Chao Chen ◽  
...  
Keyword(s):  
Cell Polarity ◽  
Protein Interactions ◽  
Large Scale ◽  
Interaction Network ◽  
Open Reading Frames ◽  
Actin Assembly ◽  
Protein Protein Interactions ◽  
Microtubule Organization ◽  
Two Hybrid ◽  
Secretory Apparatus

Many genes required for cell polarity development in budding yeast have been identified and arranged into a functional hierarchy. Core elements of the hierarchy are widely conserved, underlying cell polarity development in diverse eukaryotes. To enumerate more fully the protein–protein interactions that mediate cell polarity development, and to uncover novel mechanisms that coordinate the numerous events involved, we carried out a large-scale two-hybrid experiment. 68 Gal4 DNA binding domain fusions of yeast proteins associated with the actin cytoskeleton, septins, the secretory apparatus, and Rho-type GTPases were used to screen an array of yeast transformants that express ∼90% of the predicted Saccharomyces cerevisiae open reading frames as Gal4 activation domain fusions. 191 protein–protein interactions were detected, of which 128 had not been described previously. 44 interactions implicated 20 previously uncharacterized proteins in cell polarity development. Further insights into possible roles of 13 of these proteins were revealed by their multiple two-hybrid interactions and by subcellular localization. Included in the interaction network were associations of Cdc42 and Rho1 pathways with proteins involved in exocytosis, septin organization, actin assembly, microtubule organization, autophagy, cytokinesis, and cell wall synthesis. Other interactions suggested direct connections between Rho1- and Cdc42-regulated pathways; the secretory apparatus and regulators of polarity establishment; actin assembly and the morphogenesis checkpoint; and the exocytic and endocytic machinery. In total, a network of interactions that provide an integrated response of signaling proteins, the cytoskeleton, and organelles to the spatial cues that direct polarity development was revealed.

scholarly journals A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals

2015 ◽  
Vol 2 (9) ◽  
pp. 150156 ◽  
Author(s):  
Georgia Tsagkogeorga ◽  
Michael R. McGowen ◽  
Kalina T. J. Davies ◽  
Simon Jarman ◽  
Andrea Polanowski ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Dna Sequences ◽  
Brain Function ◽  
Molecular Adaptation ◽  
Phylogenomic Analysis ◽  
Protein Protein Interactions ◽  
Orthologous Genes ◽  
Genome Wide ◽  
A Genome ◽  
The Common

Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein–protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.

Sign in / Sign up

Export Citation Format

Share Document