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Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate
2009
PLoS Computational Biology
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Here, we use an integrated probabilistic modeling approach to study genomic correlates of protein evolutionary rate in Saccharomyces cerevisiae. ...
In addition, we assess information contribution of different subsets of these protein properties in the task of predicting slowly evolving proteins. ...
Author Contributions Conceived and designed the experiments: YX MBG. Performed the experiments: YX EAF. Analyzed the data: YX EAF. Wrote the paper: YX EAF. ...
doi:10.1371/journal.pcbi.1000413
pmid:19521505
pmcid:PMC2688033
fatcat:4gc6jnytobgyjjunwezjybzoea
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
2006
Journal of Biology
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We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 ...
The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. ...
) AND + (Yeast + OR + Saccharomyces + cerevisiae). ...
doi:10.1186/jbiol36
pmid:16762047
pmcid:PMC1561585
fatcat:uoapffbytfbc7fy7sqsh2gmrza
The Recent De Novo Origin of Protein C-Termini
2015
Genome Biology and Evolution
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Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure. ...
We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. ...
Materials and Methods
Yeast Data Sources For each annotated gene in one of the two reference genomes, ORF plus UTR data for S. cerevisiae and S. paradoxus sequences were downloaded from the Saccharomyces ...
doi:10.1093/gbe/evv098
pmid:26002864
pmcid:PMC4494051
fatcat:5icttmtjlvcxpf3klsqq4tdbbu
Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans
2015
Scientific Reports
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Acknowledgments We thank Sunmo Yang for computational support. ...
The limited progress in the development of molecular networks for non-model pathogenic fungi are due in large part to the lack of experimental data. ...
DC, domain co-occurrence; GN, gene neighborhood; GT, genetic interaction; HT, high throughput protein-protein interactions; LC, literature-curated protein-protein interactions; PG, phylogenetic profile ...
doi:10.1038/srep08767
pmid:25739925
pmcid:PMC4350084
fatcat:fp4ecznyrrcmhgzpriyb7clcey
The effects of incomplete protein interaction data on structural and evolutionary inferences
2006
BMC Biology
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Present protein interaction network data sets include only interactions among subsets of the proteins in an organism. ...
Effects are shown to be independent of the inherent noise in protein interaction data. ...
CW and MPHS are grateful to the Carlsberg Foundation and the Royal Society, UK, for their generous support. CW is supported by the Danish Cancer Society. ...
doi:10.1186/1741-7007-4-39
pmid:17081312
pmcid:PMC1665463
fatcat:nsfbaelirjgcxplajwt3fsaroi
Detection of protein–protein interactions at the septin collar in Saccharomyces cerevisiae using a tripartite split-GFP system
2016
Molecular Biology of the Cell
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However, a limitation of BiFC is that the proteins tested for interaction need to be fused to the halves of the fluorescent reporter (typically, YFP), which are rather bulky tags that may perturb the interaction ...
tripartite split-GFP methodology (Cabantous et al., 2013) for assessing protein-protein interaction because, in this system, the tags appended to the test proteins are of minimal size and can be attached ...
ACKNOWLEDGMENTS We would like to thank the other members of the Thorner Lab for useful suggestions and Geoffrey Waldo (Los Alamos National Laboratory) for providing invaluable research materials. ...
doi:10.1091/mbc.e16-05-0337
pmid:27385335
pmcid:PMC5007091
fatcat:qot2elswvrhh7hwuhy6ozf6zsu
δ-COP contains a helix C-terminal to its longin domain key to COPI dynamics and function
2016
Proceedings of the National Academy of Sciences of the United States of America
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We used such a complementation assay to characterize the molecular features of δ-COP. The RET2 gene of Saccharomyces cerevisiae encoding the δ-subunit of COPI is essential for viability. ...
This helix shows all features of an amphipathic helix that can enable interactions of a protein with the membrane. ...
We used such a complementation assay to characterize the molecular features of δ-COP. The RET2 gene of Saccharomyces cerevisiae encoding the δ-subunit of COPI is essential for viability. ...
doi:10.1073/pnas.1603544113
pmid:27298352
pmcid:PMC4922195
fatcat:chyv57oayfhnnp4g2ku5vktv3m
Functional assays provide a robust tool for the clinical annotation of genetic variants of uncertain significance
2016
npj Genomic Medicine
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of the functional data would significantly reduce the number of VUS associated with the C-terminal region of the BRCA1 protein by~87%. ...
Analysis of missense variants in MCPH1 and MDC1 shows that structural inference based on the BRCA1 data set can aid in prioritising variants for further analysis. ...
on the predisposition factors of cancer. ...
doi:10.1038/npjgenmed.2016.1
pmid:28781887
pmcid:PMC5539989
fatcat:2b4hhxc2djb55jlqra7f2xvwoy
Pex14p, more than just a docking protein
2006
BBA - Molecular Cell Research
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Here, we review data regarding this membrane peroxin with emphasis on the interactions that it establishes with Pex5p. ...
Defining the nature of the events that occur at this membrane system and which ultimately result in the translocation of the cargo proteins into the matrix of the organelle and in the recycling of Pex5p ...
Pex14p has been originally identified in Saccharomyces cerevisiae as a binding partner for both the PTS1-and PTS2receptor at the peroxisomal membrane and was therefore assigned as the "point-of-convergence ...
doi:10.1016/j.bbamcr.2006.09.002
pmid:17046076
fatcat:4s6tingtfzhghmxzr223c7y62e
Cox25 Teams Up with Mss51, Ssc1, and Cox14 to Regulate Mitochondrial CytochromecOxidase Subunit 1 Expression and Assembly inSaccharomyces cerevisiae
2010
Journal of Biological Chemistry
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Impaired COX assembly results in the trapping of Mss51 in the complex, thus limiting its availability for COX1 mRNA translation. ...
In the yeast Saccharomyces cerevisiae, mitochondrial cytochrome c oxidase (COX) biogenesis is translationally regulated. ...
COA3 is the standard name assigned in the SGD site. Both papers conclude that the protein encoded in this gene is involved in translational regulation of COX1 in mitochondria from S. cerevisiae. ...
doi:10.1074/jbc.m110.188805
pmid:21068384
pmcid:PMC3013015
fatcat:qdnu7jqqyvasbk7xx6jtph2jgq
A squalene–hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments
2021
Proceedings of the National Academy of Sciences of the United States of America
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Expression of the Sch. japonicus SHC gene (Sjshc1) in Saccharomyces cerevisiae enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids ...
The fast anaerobic growth of Sch. japonicus in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes. ...
We thank our colleagues in the Industrial Microbiology group of Delft University of Technology for stimulating discussions. ...
doi:10.1073/pnas.2105225118
pmid:34353908
pmcid:PMC8364164
fatcat:awsv436cwrf6fbj2hxyk4kfsjm
Human diseases through the lens of network biology
2013
Trends in Genetics
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Acknowledgments The author thanks the editor and reviewers for valuable criticisms on the manuscript. This work has received support from the IMI Joint ...
For example, in the yeast Saccharomyces cerevisiae, proteins with a high degree (Box 1) in a PIN are more likely to be encoded by essential genes [31, 32] . ...
In the aggregate interactome, ITGB3 interacts with 13 proteins, whereas in the PINs obtained by integration of gene expression data and protein interactions for brain, heart, kidneys, and liver, only a ...
doi:10.1016/j.tig.2012.11.004
pmid:23219555
fatcat:boxh5borhfelzmmjpsz6w2bgai
Towards a compendium of essential genes – From model organisms to synthetic lethality in cancer cells
2015
Critical reviews in biochemistry and molecular biology
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The systematic identification of essential gene sets not only allows insights into the fundamental building blocks of life, but may also provide novel therapeutic targets in oncology. ...
The discovery of essential genes has been tightly linked to the development and deployment of various screening technologies. ...
Declaration of interest Work in the lab of M.B. is in part supported by an ERC Advanced Grant. T.Z. is supported by a fellowship from the DKFZ International Postdoc program. ...
doi:10.3109/10409238.2015.1117053
pmid:26627871
pmcid:PMC4819810
fatcat:j3jrjfybnfcs7gz6lk2dmr4kaa
Interplay of a Ligand Sensor and an Enzyme in Controlling Expression of the Saccharomyces cerevisiae GAL Genes
2011
Eukaryotic Cell
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The regulation of the Saccharomyces cerevisiae GAL genes in response to galactose as a source of carbon has served as a paradigm for eukaryotic transcriptional control over the last 50 years. ...
Gal3p is subsequently replaced in this complex by Gal1p, and a Gal4p-Gal80p-Gal1p complex is responsible for the continued expression of the GAL genes. ...
We thank Ray Wightman and all members of the Reece lab for their help and assistance in the execution and interpretation of the work presented here. ...
doi:10.1128/ec.05294-11
pmid:22210830
pmcid:PMC3294446
fatcat:hvp4spvyqndqnpw2yoh7d2k35e
The Ktr1p, Ktr3p, and Kre2p/Mnt1p Mannosyltransferases Participate in the Elaboration of YeastO- andN-linked Carbohydrate Chains
1997
Journal of Biological Chemistry
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We have determined a role for Ktr1p and Ktr3p as mannosyltransferases in the synthesis of the carbohydrate chains attached to Saccharomyces cerevisiae Oand N-modified proteins. ...
in establishing some of the outer chain ␣1,2-linkages. ...
Acknowledgments-We thank the members of the Bussey laboratory and Dr. Annette Herscovics for helpful comments and suggestions and Carole Smith and Guy l'Heureux for photographic work. ...
doi:10.1074/jbc.272.24.15527
pmid:9182588
fatcat:3mqke3bil5e2bkrrh252ymwv5m
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