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Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate

Yu Xia, Eric A. Franzosa, Mark B. Gerstein, Michael Levitt
2009 PLoS Computational Biology  
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

Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho (+8 others)
2006 Journal of Biology  
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

Matthew E. Andreatta, Joshua A. Levine, Scott G. Foy, Lynette D. Guzman, Luke J. Kosinski, Matthew H.J. Cordes, Joanna Masel
2015 Genome Biology and Evolution  
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

Hanhae Kim, Kwang-Woo Jung, Shinae Maeng, Ying-Lien Chen, Junha Shin, Jung Eun Shim, Sohyun Hwang, Guilhem Janbon, Taeyup Kim, Joseph Heitman, Yong-Sun Bahn, Insuk Lee
2015 Scientific Reports  
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

Eric de Silva, Thomas Thorne, Piers Ingram, Ino Agrafioti, Jonathan Swire, Carsten Wiuf, Michael P H Stumpf
2006 BMC Biology  
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

Gregory C. Finnigan, Angela Duvalyan, Elizabeth N. Liao, Aspram Sargsyan, Jeremy Thorner, Thomas D. Pollard
2016 Molecular Biology of the Cell  
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

Eric C. Arakel, Kora P. Richter, Anne Clancy, Blanche Schwappach
2016 Proceedings of the National Academy of Sciences of the United States of America  
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

Nicholas T Woods, Rebekah Baskin, Volha Golubeva, Ankita Jhuraney, Giuliana De-Gregoriis, Tereza Vaclova, David E Goldgar, Fergus J Couch, Marcelo Alex Carvalho, Edwin S Iversen, Alvaro NA Monteiro
2016 npj Genomic Medicine  
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

Jorge E. Azevedo, Wolfgang Schliebs
2006 BBA - Molecular Cell Research  
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

Flavia Fontanesi, Paula Clemente, Antoni Barrientos
2010 Journal of Biological Chemistry  
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

Jonna Bouwknegt, Sanne J. Wiersma, Raúl A. Ortiz-Merino, Eline S. R. Doornenbal, Petrik Buitenhuis, Martin Giera, Christoph Müller, Jack T. Pronk
2021 Proceedings of the National Academy of Sciences of the United States of America  
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

Laura I. Furlong
2013 Trends in Genetics  
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

Tianzuo Zhan, Michael Boutros
2015 Critical reviews in biochemistry and molecular biology  
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

Dariusz Abramczyk, Stacey Holden, Christopher J. Page, Richard J. Reece
2011 Eukaryotic Cell  
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

Marc Lussier, Anne-Marie Sdicu, Françoise Bussereau, Michel Jacquet, Howard Bussey
1997 Journal of Biological Chemistry  
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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