scholarly journals A genome-wide almanac of co-essential modules assigns function to uncharacterized genes

2019 ◽  
Author(s):  
Michael Wainberg ◽  
Roarke A. Kamber ◽  
Akshay Balsubramani ◽  
Robin M. Meyers ◽  
Nasa Sinnott-Armstrong ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Functional Modules ◽  
Web Tool ◽  
Coated Pits ◽  
Robust Identification ◽  
Genome Wide ◽  
A Genome ◽  
Gene Functions ◽  
Key Enzyme ◽  
Transferrin Uptake

SUMMARYA central remaining question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into ‘co-essential’ pathways, but this approach has been limited by ubiquitous false positives. Here, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. This almanac recapitulates diverse pathways and protein complexes and predicts the functions of 102 uncharacterized genes. Validating top predictions, we show that TMEM189 encodes plasmanylethanolamine desaturase, the long-sought key enzyme for plasmalogen synthesis. We also show that C15orf57 binds the AP2 complex, localizes to clathrin-coated pits, and enables efficient transferrin uptake. Finally, we provide an interactive web tool for the community to explore the results (coessentiality.net). Our results establish co-essentiality profiling as a powerful resource for biological pathway identification and discovery of novel gene functions.

Regulation of clathrin-dependent endocytosis by diacylglycerol kinase δ: importance of kinase activity and binding to AP2α

2007 ◽  
Vol 409 (2) ◽  
pp. 471-479 ◽  
Author(s):  
Takumi Kawasaki ◽  
Takeshi Kobayashi ◽  
Takehiko Ueyama ◽  
Yasuhito Shirai ◽  
Naoaki Saito
Keyword(s):  
Catalytic Domain ◽  
Intracellular Localization ◽  
Adaptor Protein ◽  
Diacylglycerol Kinase ◽  
Wild Type ◽  
Coated Pits ◽  
Genome Wide ◽  
A Subunit ◽  
Transferrin Uptake ◽  
Interfering Rna

DGKδ (diacylglycerol kinase δ), which phosphorylates DAG (diacylglycerol) and converts it into PA (phosphatidic acid), has an important role in signal transduction. In the present study, we have demonstrated the molecular mechanism of DGKδ-mediated regulation of clathrin-dependent endocytosis that controls the internalization, recycling and degradation of receptors. Involvement of DGKδ in the regulation of clathrin-dependent endocytosis was previously proposed following genome-wide RNAi (RNA interference) screening. Clathrin-coated pits are mainly formed by clathrin and AP-2 (adaptor protein 2) complex. These proteins assemble a polyhedral lattice at the membrane and gather several endocytic accessory proteins. As the intracellular localization of DGKδ2 overlapped with clathrin-coated pits, we predicted the possible regulation of clathrin-dependent endocytosis by DGKδ2 and its interaction with some endocytosis-regulatory proteins. DGKδ2 contained the DXF-type binding motifs, and DGKδ2 bound to AP2α, a subunit of the AP-2 complex. DGKδ2 interacted with the platform subdomain in the AP2α ear domain via F369DTFRIL and D746PF sequences in the catalytic domain of DGKδ2. For further insight into the role for DGKδ2 in clathrin-dependent endocytosis, we measured the transferrin and EGF (epidermal growth factor) uptake-expressing wild-type or mutant DGKδ2 under knockdown of endogenous DGKδ. Mutants lacking binding ability to AP2α as well as kinase-negative mutants could not compensate for the uptake of transferrin inhibited by siRNA (small interfering RNA) treatment, whereas overexpression of wild-type DGKδ2 completely recovered the transferrin uptake. These results demonstrate that binding between DGKδ2 and AP2α is involved in the transferrin internalization and that DGK activity is also necessary for the regulation of the endocytic process.

scholarly journals A genome-wide screen for genes affecting eisosomes reveals Nce102 function in sphingolipid signaling

2009 ◽  
Vol 185 (7) ◽  
pp. 1227-1242 ◽  
Author(s):  
Florian Fröhlich ◽  
Karen Moreira ◽  
Pablo S. Aguilar ◽  
Nina C. Hubner ◽  
Matthias Mann ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Plasma Membranes ◽  
Protein Complexes ◽  
Membrane Domains ◽  
Kinase Signaling ◽  
Cortical Actin ◽  
Membrane Function ◽  
Genome Wide ◽  
A Genome ◽  
Actin Patch

The protein and lipid composition of eukaryotic plasma membranes is highly dynamic and regulated according to need. The sphingolipid-responsive Pkh kinases are candidates for mediating parts of this regulation, as they affect a diverse set of plasma membrane functions, such as cortical actin patch organization, efficient endocytosis, and eisosome assembly. Eisosomes are large protein complexes underlying the plasma membrane and help to sort a group of membrane proteins into distinct domains. In this study, we identify Nce102 in a genome-wide screen for genes involved in eisosome organization and Pkh kinase signaling. Nce102 accumulates in membrane domains at eisosomes where Pkh kinases also localize. The relative abundance of Nce102 in these domains compared with the rest of the plasma membrane is dynamically regulated by sphingolipids. Furthermore, Nce102 inhibits Pkh kinase signaling and is required for plasma membrane organization. Therefore, Nce102 might act as a sensor of sphingolipids that regulates plasma membrane function.

scholarly journals Catabolite Degradation of Fructose-1,6-bisphosphatase in the YeastSaccharomyces cerevisiae: A Genome-wide Screen Identifies Eight NovelGIDGenes and Indicates the Existence of Two Degradation Pathways

2003 ◽  
Vol 14 (4) ◽  
pp. 1652-1663 ◽  
Author(s):  
Jochen Regelmann ◽  
Thomas Schüle ◽  
Frank S. Josupeit ◽  
Jaroslav Horak ◽  
Matthias Rose ◽  
...  
Keyword(s):  
Degradation Pathway ◽  
Metabolic Adaptation ◽  
Degradation Pathways ◽  
Genome Wide ◽  
A Genome ◽  
Fructose 1,6 Bisphosphatase ◽  
Domain Of Unknown Function ◽  
Nonfermentable Carbon Source ◽  
Key Enzyme ◽  
Ubiquitin Proteasome

Metabolic adaptation of Saccharomyces cerevisiaecells from a nonfermentable carbon source to glucose induces selective, rapid breakdown of the gluconeogenetic key enzyme fructose-1,6-bisphosphatase (FBPase), a process called catabolite degradation. Herein, we identify eight novel GID genes required for proteasome-dependent catabolite degradation of FBPase. Four yeast proteins contain the CTLH domain of unknown function. All of them are Gid proteins. The site of catabolite degradation has been controversial until now. Two FBPase degradation pathways have been described, one dependent on the cytosolic ubiquitin-proteasome machinery, and the other dependent on vacuolar proteolysis. Interestingly, three of the novel Gid proteins involved in ubiquitin-proteasome–dependent degradation have also been reported by others to affect the vacuolar degradation pathway. As shown herein, additional genes suggested to be essential for vacuolar degradation are unnecessary for proteasome-dependent degradation. These data raise the question as to whether two FBPase degradation pathways exist that share components. Detailed characterization of Gid2p demonstrates that it is part of a soluble, cytosolic protein complex of at least 600 kDa. Gid2p is necessary for FBPase ubiquitination. Our studies have not revealed any involvement of vesicular intermediates in proteasome-dependent FBPase degradation. The influence of Ubp14p, a deubiquitinating enzyme, on proteasome-dependent catabolite degradation was further uncovered.

Experimental and Computational Procedures for the Assessment of Protein Complexes on a Genome-wide Scale

2007 ◽  
Vol 107 (8) ◽  
pp. 3585-3600 ◽  
Author(s):  
Gabriel A. Musso ◽  
Zhaolei Zhang ◽  
Andrew Emili
Keyword(s):  
Protein Complexes ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Computational Procedures

scholarly journals A genome-wide algal mutant library reveals a global view of genes required for eukaryotic photosynthesis

2018 ◽  
Author(s):  
Xiaobo Li ◽  
Weronika Patena ◽  
Friedrich Fauser ◽  
Robert E. Jinkerson ◽  
Shai Saroussi ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Protein Coding ◽  
Photosynthetic Organisms ◽  
Protein Coding Genes ◽  
Genome Wide ◽  
A Genome ◽  
Photosynthetic Organism ◽  
Unicellular Organisms ◽  
Life On Earth

Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms that complement the use of multicellular plants by enabling higher-throughput studies. Here, we generated a genome-wide, indexed library of mapped insertion mutants for the flagship unicellular alga Chlamydomonas reinhardtii (Chlamydomonas hereafter). The 62,389 mutants in the library, covering 83% of nuclear, protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We leveraged this feature to perform a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase CPL3, showed it is important for accumulation of multiple photosynthetic protein complexes. Strikingly, 21 of the 43 highest-confidence genes are novel, opening new opportunities for advances in our understanding of this biogeochemically fundamental process. This library is the first genome-wide mapped mutant resource in any unicellular photosynthetic organism, and will accelerate the characterization of thousands of genes in algae, plants and animals.

scholarly journals Natural Selection on Functional Modules, a Genome-Wide Analysis

2011 ◽  
Vol 7 (3) ◽  
pp. e1001093 ◽  
Author(s):  
François Serra ◽  
Leonardo Arbiza ◽  
Joaquín Dopazo ◽  
Hernán Dopazo
Keyword(s):  
Natural Selection ◽  
Functional Modules ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Establishment of a genome-wide RNAi screen; Identification of novel genes involved in clonal maintenance of ALL

2014 ◽  
Vol 226 (03) ◽  
Author(s):  
F Ponthan ◽  
D Pal ◽  
J Vormoor ◽  
O Heidenreich
Keyword(s):  
Rnai Screen ◽  
Novel Genes ◽  
Genome Wide ◽  
A Genome

A genome-wide linkage scan for familial partial lipodystrophy susceptibility genes in a German kindreds

2007 ◽  
Vol 30 (4) ◽  
pp. 86
Author(s):  
M. Lanktree ◽  
J. Robinson ◽  
J. Creider ◽  
H. Cao ◽  
D. Carter ◽  
...  
Keyword(s):  
Subcutaneous Fat ◽  
Visceral Obesity ◽  
Fat Distribution ◽  
Dominant Negative ◽  
Molecular Forms ◽  
Partial Lipodystrophy ◽  
Genome Wide ◽  
A Genome ◽  
Familial Partial Lipodystrophy ◽  
Promoter Mutations

Background: In Dunnigan-type familial partial lipodystrophy (FPLD) patients are born with normal fat distribution, but subcutaneous fat from extremities and gluteal regions are lost during puberty. The abnormal fat distribution leads to the development of metabolic syndrome (MetS), a cluster of phenotypes including hyperglycemia, dyslipidemia, hypertension, and visceral obesity. The study of FPLD as a monogenic model of MetS may uncover genetic risk factors of the common MetS which affects ~30% of adult North Americans. Two molecular forms of FPLD have been identified including FPLD2, resulting from heterozygous mutations in the LMNA gene, and FPLD3, resulting from both heterozygous dominant negative and haploinsufficiency mutations in the PPARG gene. However, many patients with clinically diagnosed FPLD have no mutation in either LMNA or PPARG, suggesting the involvement of additional genes in FPLD etiology. Methods: Here, we report the results of an Affymetrix 10K GeneChip microarray genome-wide linkage analysis study of a German kindred displaying the FPLD phenotype and no known lipodystrophy-causing mutations. Results: The investigation identified three chromosomal loci, namely 1q, 3p, and 9q, with non-parametric logarithm of odds (NPL) scores >2.7. While not meeting the criteria for genome-wide significance, it is interesting to note that the 1q and 3p peaks contain the LMNA and PPARG genes respectively. Conclusions: Three possible conclusions can be drawn from these results: 1) the peaks identified are spurious findings, 2) additional genes physically close to LMNA, PPARG, or within 9q, are involved in FPLD etiology, or 3) alternative disease causing mechanisms not identified by standard exon sequencing approaches, such as promoter mutations, alternative splicing, or epigenetics, are also responsible for FPLD.

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