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Wirtz L, Casanova F, Schaffrath U, Wegner A. Development of a telomere vector-based approach to overcome limitations caused by lethal phenotypes in the study of essential genes in Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2024; 25:e13460. [PMID: 38695626 PMCID: PMC11064798 DOI: 10.1111/mpp.13460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Reverse genetic approaches are common tools in genomics for elucidating gene functions, involving techniques such as gene deletion followed by screening for aberrant phenotypes. If the generation of gene deletion mutants fails, the question arises whether the failure stems from technical issues or because the gene of interest (GOI) is essential, meaning that the deletion causes lethality. In this report, we introduce a novel method for assessing gene essentiality using the phytopathogenic ascomycete Magnaporthe oryzae. The method is based on the observation that telomere vectors are lost in transformants during cultivation without selection pressure. We tested the hypothesis that essential genes can be identified in deletion mutants co-transformed with a telomere vector. The M. oryzae gene MoPKC, described in literature as essential, was chosen as GOI. Using CRISPR/Cas9 technology transformants with deleted GOI were generated and backed up by a telomere vector carrying a copy of the GOI and conferring fenhexamid resistance. Transformants in which the GOI deletion in the genome was not successful lost the telomere vector on media without fenhexamid. In contrast, transformants with confirmed GOI deletion retained the telomere vector even in absence of fenhexamid selection. In the latter case, the maintenance of the telomere indicates that the GOI is essential for the surveillance of the fungi, as it would have been lost otherwise. The method presented here allows to test for essentiality of genes when no mutants can be obtained from gene deletion approaches, thereby expanding the toolbox for studying gene function in ascomycetes.
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Affiliation(s)
- Louisa Wirtz
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | - Florencia Casanova
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | - Ulrich Schaffrath
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | - Alex Wegner
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
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2
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Shraim R, Nieuwenhuis BPS. The search for Schizosaccharomyces fission yeasts in environmental meta-transcriptomes. Yeast 2021; 39:83-94. [PMID: 34967063 DOI: 10.1002/yea.3689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/09/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022] Open
Abstract
Fission yeast is an important model organism in evolutionary genetics and cell biology research. Nevertheless, most research is limited to a single laboratory strain and knowledge of its natural occurrence is limited, which reduces our understanding of its life history and hinders isolation of new strains from nature. Understanding the natural diversity of fission yeast can provide insight into its genetic and phenotypic diversity and the evolutionary processes that shaped these. Here we aimed to identify candidate natural habitats of fission yeasts by searching through a large collection of publicly available environmental metatranscriptomic datasets. Using a custom pipeline, we processed over 13,000 NCBI SRA accessions, from a wide range of 34 different environmental categories. Overall, we found a very low abundance of putative yeast transcripts, with most fission yeast signatures coming from the categories of 'food' and 'terrestrial arthropods'. Additionally, a signal could be found in a variety of marine and fresh aquatic habitats. Our results do not provide a conclusive answer on the natural habitat of fission yeasts, but our analysis further narrows the range of locations where fission yeasts naturally occur.
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Affiliation(s)
- Rasha Shraim
- The SFI Centre for Research Training in Genomics Data Sciences, National University of Ireland Galway and Department of Public Health and Primary Care, School of Medicine, Trinity College Dublin, Republic of Ireland.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Germany
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Germany
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3
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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4
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de Souza ID, Reis CF, Morais DAA, Fernandes VGS, Cavalcante JVF, Dalmolin RJS. Ancestry analysis indicates two different sets of essential genes in eukaryotic model species. Funct Integr Genomics 2021; 21:523-531. [PMID: 34279742 DOI: 10.1007/s10142-021-00794-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 11/28/2022]
Abstract
Essential genes are so-called because they are crucial for organism perpetuation. Those genes are usually related to essential functions to cellular metabolism or multicellular homeostasis. Deleterious alterations on essential genes produce a spectrum of phenotypes in multicellular organisms. The effects range from the impairment of the fertilization process, disruption of fetal development, to loss of reproductive capacity. Essential genes are described as more evolutionarily conserved than non-essential genes. However, there is no consensus about the relationship between gene essentiality and gene age. Here, we identified essential genes in five model eukaryotic species (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus) and estimate their evolutionary ancestry and their network properties. We observed that essential genes, on average, are older than other genes in all species investigated. The relationship of network properties and gene essentiality convey with previous findings, showing essential genes as important nodes in biological networks. As expected, we also observed that essential orthologs shared by the five species evaluated here are old. However, all the species evaluated here have a specific set of young essential genes not shared among them. Additionally, these two groups of essential genes are involved with distinct biological functions, suggesting two sets of essential genes: (i) a set of old essential genes common to all the evaluated species, regulating basic cellular functions, and (ii) a set of young essential genes exclusive to each species, which perform specific essential functions in each species.
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Affiliation(s)
- Iara D de Souza
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Clovis F Reis
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Diego A A Morais
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Vítor G S Fernandes
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - João Vitor F Cavalcante
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil. .,Department of Biochemistry - CB, Federal University of Rio Grande Do Norte, Campus Universitário UFRN, Lagoa Nova, Natal, RN, 59078-970, Brazil.
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CSNK1G2 differently sensitizes tamoxifen-induced decrease in PI3K/AKT/mTOR/S6K and ERK signaling according to the estrogen receptor existence in breast cancer cells. PLoS One 2021; 16:e0246264. [PMID: 33861751 PMCID: PMC8051802 DOI: 10.1371/journal.pone.0246264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/17/2021] [Indexed: 11/19/2022] Open
Abstract
Tamoxifen (TAM) is a selective estrogen receptor modulator used for breast cancer patients. Prolonged use of tamoxifen is not recommended for some patients. In this study, we aimed to identify molecular targets sensitive to TAM using a genome-wide gene deletion library screening of fission yeast heterozygous mutants. From the screening, casein kinase 1 gamma 2 (CSNK1G2), a serine-/threonine protein kinase, was the most sensitive target to TAM with a significant cytotoxicity in estrogen receptor-positive (ER+) breast cancer cells but with only a slight toxicity in the case of ER- cells. In addition, tumor sphere formation and expression of breast stem cell marker genes such as CD44/CD2 were greatly inhibited by CSNK1G2 knockdown in ER+ breast cancer cells. Consistently, CSNK1G2 altered ERα activity via phosphorylation, specifically at serine (Ser)167, as well as the regulation of estrogen-responsive element (ERE) of estrogen-responsive genes such as CTSD and GREB1. However, ERα silencing almost completely blocked CSNK1G2-induced TAM sensitivity. In ER+ breast cancer cells, combined treatment with TAM and CSNK1G2 knockdown further enhanced the TAM-mediated decrease in phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR)/ribosomal protein S6 kinase (S6K) signaling but not extracellular signal-regulated kinase (ERK) signaling. Inversely, in ER- cells treated with TAM, only ERK and PI3K signaling was altered by CSNK1G2 knockdown. The CK1 inhibitor, D4476, partly mimicked the CSNK1G2 knockdown effect in ER+ breast cancer cells, but with a broader repression ranging from PI3K/AKT/mTOR/S6K to ERK signaling. Collectively, these results suggest that CSNK1G2 plays a key role in sensitizing TAM toxicity in ER+ and ER- breast cancer cells via differently regulating PI3K/AKT/mTOR/S6K and ERK signaling.
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Wiley DJ, D’Urso G, Zhang F. Posttranslational Arginylation Enzyme Arginyltransferase1 Shows Genetic Interactions With Specific Cellular Pathways in vivo. Front Physiol 2020; 11:427. [PMID: 32435206 PMCID: PMC7218141 DOI: 10.3389/fphys.2020.00427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/07/2020] [Indexed: 12/20/2022] Open
Abstract
Arginyltransferase1 (ATE1) is a conserved enzyme in eukaryotes mediating posttranslational arginylation, the addition of an extra arginine to an existing protein. In mammals, the dysregulations of the ATE1 gene (ate1) is shown to be involved in cardiovascular abnormalities, cancer, and aging-related diseases. Although biochemical evidence suggested that arginylation may be involved in stress response and/or protein degradation, the physiological role of ATE1 in vivo has never been systematically determined. This gap of knowledge leads to difficulties for interpreting the involvements of ATE1 in diseases pathogenesis. Since ate1 is highly conserved between human and the unicellular organism Schizosaccharomyces pombe (S. pombe), we take advantage of the gene-knockout library of S. pombe, to investigate the genetic interactions between ate1 and other genes in a systematic and unbiased manner. By this approach, we found that ate1 has a surprisingly small and focused impact size. Among the 3659 tested genes, which covers nearly 75% of the genome of S. pombe, less than 5% of them displayed significant genetic interactions with ate1. Furthermore, these ate1-interacting partners can be grouped into a few discrete clustered categories based on their functions or their physical interactions. These categories include translation/transcription regulation, biosynthesis/metabolism of biomolecules (including histidine), cell morphology and cellular dynamics, response to oxidative or metabolic stress, ribosomal structure and function, and mitochondrial function. Unexpectedly, inconsistent to popular belief, very few genes in the global ubiquitination or degradation pathways showed interactions with ate1. Our results suggested that ATE1 specifically regulates a handful of cellular processes in vivo, which will provide critical mechanistic leads for studying the involvements of ATE1 in normal physiologies as well as in diseased conditions.
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Affiliation(s)
- David J. Wiley
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
| | - Gennaro D’Urso
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
| | - Fangliang Zhang
- Department of Molecular and Cellular Pharmacology, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Leonard M. Miller School of Medicine, Miami, FL, United States
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7
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Martínez-Cano DJ, Bor G, Moya A, Delaye L. Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions. Life (Basel) 2018; 8:life8020017. [PMID: 29843462 PMCID: PMC6027505 DOI: 10.3390/life8020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola. We provide statistical evidence indicating pairs of genes in B. aphidicola showing correlated gene loss tend to have orthologs in Escherichia coli known to have alleviating epistasis. In contrast, pairs of genes in B. aphidicola not showing correlated gene loss tend to have orthologs in E. coli known to have aggravating epistasis. These results suggest that during the process of genome reduction in B. aphidicola by gene loss, positive or alleviating epistasis facilitates correlated gene losses while negative or aggravating epistasis impairs correlated gene losses. We interpret this as evidence that the reduced proteome of B. aphidicola contains less pathway redundancy and more compensatory interactions, mimicking the situation of E. coli when grown under environmental constrains.
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Affiliation(s)
- David J Martínez-Cano
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
| | - Gil Bor
- CIMAT, A.P. 402, Guanajuato 36000, Gto., Mexico.
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, Avenida de Catalunya 21, 46020 València, Spain.
- Institute for Integrative Systems Biology, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain.
| | - Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
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8
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Kim J, Kim DU, Hoe KL. Gene Deletion by Synthesis in Yeast. Methods Mol Biol 2018; 1472:169-85. [PMID: 27671940 DOI: 10.1007/978-1-4939-6343-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Targeted gene deletion is a useful tool for understanding the function of a gene and its protein product. We have developed an efficient and robust gene deletion approach in yeast that employs oligonucleotide-based gene synthesis. This approach requires a deletion cassette composed of three modules: a central 1397-bp KanMX4 selection marker module and two 366-bp gene-specific flanking modules. The invariable KanMX4 module can be used in combination with different pairs of flanking modules targeting different genes. The two flanking modules consist of both sequences unique to each cassette (chromosomal homologous regions and barcodes) and those common to all deletion constructs (artificial linkers and restriction enzyme sites). Oligonucleotides for each module and junction regions are designed using the BatchBlock2Oligo program and are synthesized on a 96-well basis. The oligonucleotides are ligated into a single deletion cassette by ligase chain reaction, which is then amplified through two rounds of nested PCR to obtain sufficient quantities for yeast transformation. After removal of the artificial linkers, the deletion cassettes are transformed into wild-type diploid fission yeast SP286 cells. Verification of correct clone and gene deletion is achieved by performing check PCR and tetrad analysis. This method with proven effectiveness, as evidenced by a high success rate of gene deletion, can be potentially applicable to create systematic gene deletion libraries in a variety of yeast species.
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Affiliation(s)
- Jinsil Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Dong-Uk Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.
| | - Kwang-Lae Hoe
- Department of New Drug Discovery and Development, Chungnam National University, 125 Gwahak-ro, Daejeon, 34141, South Korea.
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9
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Mülleder M, Campbell K, Matsarskaia O, Eckerstorfer F, Ralser M. Saccharomyces cerevisiae single-copy plasmids for auxotrophy compensation, multiple marker selection, and for designing metabolically cooperating communities. F1000Res 2016; 5:2351. [PMID: 27830062 PMCID: PMC5081161 DOI: 10.12688/f1000research.9606.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2016] [Indexed: 01/23/2023] Open
Abstract
Auxotrophic markers are useful tools in cloning and genome editing, enable a large spectrum of genetic techniques, as well as facilitate the study of metabolite exchange interactions in microbial communities. If unused background auxotrophies are left uncomplemented however, yeast cells need to be grown in nutrient supplemented or rich growth media compositions, which precludes the analysis of biosynthetic metabolism, and which leads to a profound impact on physiology and gene expression. Here we present a series of 23 centromeric plasmids designed to restore prototrophy in typical Saccharomyces cerevisiae laboratory strains. The 23 single-copy plasmids complement for deficiencies in HIS3, LEU2, URA3, MET17 or LYS2 genes and in their combinations, to match the auxotrophic background of the popular functional-genomic yeast libraries that are based on the S288c strain. The plasmids are further suitable for designing self-establishing metabolically cooperating (SeMeCo) communities, and possess a uniform multiple cloning site to exploit multiple parallel selection markers in protein expression experiments.
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Affiliation(s)
- Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Mill Hill Laboratory, The Francis Crick Institute, London, UK
| | - Kate Campbell
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Chalmers University of Technology, Gothenburg, Sweden
| | - Olga Matsarskaia
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Florian Eckerstorfer
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Mill Hill Laboratory, The Francis Crick Institute, London, UK
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10
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Systematic targeted gene deletion using the gene-synthesis method in fission yeast. J Microbiol Methods 2014; 106:72-77. [DOI: 10.1016/j.mimet.2014.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/04/2014] [Accepted: 08/11/2014] [Indexed: 11/24/2022]
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van der Burgt A, Karimi Jashni M, Bahkali AH, de Wit PJGM. Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past. MOLECULAR PLANT PATHOLOGY 2014; 15:133-44. [PMID: 24393451 PMCID: PMC6638865 DOI: 10.1111/mpp.12072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non- or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment-based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi-gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).
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Affiliation(s)
- Ate van der Burgt
- Laboratory of Phytopathology, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, the Netherlands; Applied Bioinformatics, Plant Research International, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, the Netherlands
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12
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Song Y, Kenworthy AK, Sanders CR. Cholesterol as a co-solvent and a ligand for membrane proteins. Protein Sci 2013; 23:1-22. [PMID: 24155031 DOI: 10.1002/pro.2385] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 01/23/2023]
Abstract
As of mid 2013 a Medline search on "cholesterol" yielded over 200,000 hits, reflecting the prominence of this lipid in numerous aspects of animal cell biology and physiology under conditions of health and disease. Aberrations in cholesterol homeostasis underlie both a number of rare genetic disorders and contribute to common sporadic and complex disorders including heart disease, stroke, type II diabetes, and Alzheimer's disease. The corresponding author of this review and his lab stumbled only recently into the sprawling area of cholesterol research when they discovered that the amyloid precursor protein (APP) binds cholesterol, a topic covered by the Hans Neurath Award lecture at the 2013 Protein Society Meeting. Here, we first provide a brief overview of cholesterol-protein interactions and then offer our perspective on how and why binding of cholesterol to APP and its C99 domain (β-CTF) promotes the amyloidogenic pathway, which is closely related to the etiology of Alzheimer's disease.
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Affiliation(s)
- Yuanli Song
- Department of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
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13
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Sasaki M, Kumagai H, Takegawa K, Tohda H. Characterization of genome-reduced fission yeast strains. Nucleic Acids Res 2013; 41:5382-99. [PMID: 23563150 PMCID: PMC3664816 DOI: 10.1093/nar/gkt233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Schizosaccharomyces pombe genome is one of the smallest among the free-living eukaryotes. We further reduced the S. pombe gene number by large-scale gene deletion to identify a minimal gene set required for growth under laboratory conditions. The genome-reduced strain has four deletion regions: 168.4 kb in the left arm of chromosome I, 155.4 kb in the right arm of chromosome I, 211.7 kb in the left arm of chromosome II and 121.6 kb in the right arm of chromosome II. The deletions corresponded to a loss of 223 genes of the original ~5100. The quadruple-deletion strain, with a total deletion size of 657.3 kb, showed a decreased ability to uptake glucose and some amino acids in comparison with the parental strain. The strain also showed increased gene expression of the mating pheromone M-factor precursor and the nicotinamide adenine dinucleotide phosphate -specific glutamate dehydrogenase. There was also a 2.7-fold increase in the concentration of cellular adenosine triphosphate, and levels of the heterologous proteins, enhanced green fluorescent protein and secreted human growth hormone were increased by 1.7- and 1.8-fold, respectively. The transcriptome data from this study have been submitted to the Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE38620 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=vjkxjewuywgcovc&acc=GSE38620).
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Affiliation(s)
- Mayumi Sasaki
- ASPEX Division, Research Center, Asahi Glass Co, Ltd, Yokohama, Kanagawa 221-8755, Japan
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14
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Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network. PLoS Comput Biol 2012; 8:e1002732. [PMID: 23093924 PMCID: PMC3475659 DOI: 10.1371/journal.pcbi.1002732] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/21/2012] [Indexed: 11/19/2022] Open
Abstract
The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify ‘linker’ proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted ‘linkers’ also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes. Analysis of protein interaction networks has been of use as a means to grapple with the complexity of the interactome of biological organisms. So far, network based approaches have only been used in a limited number of organisms due to the lack of high-throughput experiments. In this study, we investigate by graph theoretical network analysis approaches the protein-protein interaction network of fission yeast, and present a new network measure, linkerity, that predicts the ability of certain proteins to function as bridges between diverse cellular processes. We apply this linkerity measure to a highly conserved and coupled subset of the fission yeast network, consisting of the proteins that regulate cell cycle, polarized cell growth, and cell division. In depth literature analysis confirms that several proteins identified as linkers of cell polarity regulation are indeed also associated with cell cycle and/or cell division control. Similarly, experimental testing confirms that a mostly uncharacterized polarity regulator identified by the method as an important linker is regulated by the cell cycle, as predicted.
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15
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Fashe T, Saarikettu J, Isomäki P, Yang J, Silvennoinen O. Expression analysis of Tudor-SN protein in mouse tissues. Tissue Cell 2012; 45:21-31. [PMID: 23068188 DOI: 10.1016/j.tice.2012.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 12/26/2022]
Abstract
Tudor-SN (SND1, p100) has been shown to function as a transcriptional coactivator as well as a modulator of RNA metabolism and biogenesis and a component in the RNA-induced silencing complex (RISC). Tudor-SN consists of five repeats of staphylococcus nuclease-like domains (SN1-SN5) and, a Tudor domain implicated in binding to methylated ligands. The protein is highly conserved through evolution from fission yeast to mammals and it exists as a single gene without any close homologs. Tudor-SN is found to be overexpressed in several cancers such as colon adenocarcinomas and prostate cancer. The conservation of Tudor-SN along evolution suggests it may have important functions; however, the physiological function of Tudor-SN has not yet been characterized. In this study we analyzed the expression and localization of Tudor-SN in mouse tissues and organs by immunohistochemistry, fluorescent immunostaining, Western blotting and RT-qPCR. Expression analysis indicated that Tudor-SN is widely expressed in most organs with the exception of muscle cells. Up-regulated expression was observed in rapidly dividing cells and progenitor cells such as in spermatogonial cells in testis, in the follicular cells of ovary, in the cells of crypts of Lieberkühn of ileum and basal keratinocytes of skin and hair follicle when compared to more differentiated or terminally differentiated cells in the respective organs. Moreover, Tudor-SN was robustly expressed in T-cells and Tudor-SN was co-expressed with CD3 in T-cells in the Peyer's patch, spleen and lymph node. The wide expression pattern of Tudor-SN and high expression in proliferating and self-differentiating cells suggests that the protein serves functions related to activated state of cells.
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Affiliation(s)
- Tekele Fashe
- Laboratory of Molecular Immunology, Institute of Biomedical Technology, Biomeditech, 33014 University of Tampere, Tampere, Finland
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16
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Tamm T, Grallert A, Grossman EPS, Alvarez-Tabares I, Stevens FE, Hagan IM. Brr6 drives the Schizosaccharomyces pombe spindle pole body nuclear envelope insertion/extrusion cycle. ACTA ACUST UNITED AC 2012; 195:467-84. [PMID: 22042620 PMCID: PMC3206342 DOI: 10.1083/jcb.201106076] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Insertion into and release of the cytoplasmic domain of the Schizosaccharomyces pombe spindle pole body from a nuclear envelope fenestra during mitosis requires Brr6. The fission yeast interphase spindle pole body (SPB) is a bipartite structure in which a bulky cytoplasmic domain is separated from a nuclear component by the nuclear envelope. During mitosis, the SPB is incorporated into a fenestra that forms within the envelope during mitotic commitment. Closure of this fenestra during anaphase B/mitotic exit returns the cytoplasmic component to the cytoplasmic face of an intact interphase nuclear envelope. Here we show that Brr6 is transiently recruited to SPBs at both SPB insertion and extrusion. Brr6 is required for both SPB insertion and nuclear envelope integrity during anaphase B/mitotic exit. Genetic interactions with apq12 and defective sterol assimilation suggest that Brr6 may alter envelope composition at SPBs to promote SPB insertion and extrusion. The restriction of the Brr6 domain to eukaryotes that use a polar fenestra in an otherwise closed mitosis suggests a conserved role in fenestration to enable a single microtubule organizing center to nucleate both cytoplasmic and nuclear microtubules on opposing sides of the nuclear envelope.
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Affiliation(s)
- Tiina Tamm
- Cancer Research UK Cell Division Group, Paterson Institute for Cancer Research, Manchester M20 4BX, England, UK
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17
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Dixon SJ, Andrews BJ, Boone C. Exploring the conservation of synthetic lethal genetic interaction networks. Commun Integr Biol 2011; 2:78-81. [PMID: 19704894 DOI: 10.4161/cib.7501] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Accepted: 11/25/2008] [Indexed: 11/19/2022] Open
Abstract
High-throughput studies have enabled the large-scale mapping of synthetic lethal genetic interaction networks in the budding yeast Saccharomyces cerevisiae (S. cerevisiae). Recently, complementary high-throughput methods have been developed to map genetic interactions in the fission yeast Schizosaccharomyces pombe (S. pombe), enabling comparative analyses of genetic interaction networks between S. pombe and S. cerevisiae, two species separated by hundreds of millions of years of evolution. The resultant data has providing our first view of a possible core genetic interaction network shared between two distantly related eukaryotes, and identified numerous species-specific interactions that may contribute to the unique biology of these two different organisms. These and other results suggest that comparative interactomic studies will provide novel insights into the structure of genetic interaction networks.
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Affiliation(s)
- Scott J Dixon
- Banting and Best Department of Medical Research; Terrence Donnelly Center for Cellular and Biomolecular Research; University of Toronto; Toronto, ON CA
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18
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Rockel B, Kopec KO, Lupas AN, Baumeister W. Structure and function of tripeptidyl peptidase II, a giant cytosolic protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:237-45. [PMID: 21771670 DOI: 10.1016/j.bbapap.2011.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 01/25/2023]
Abstract
Tripeptidyl peptidase II is the largest known eukaryotic peptidase. It has been described as a multi-purpose peptidase, which, in addition to its house-keeping function in intracellular protein degradation, plays a role in several vital cellular processes such as antigen processing, apoptosis, or cell division, and is involved in diseases like muscle wasting, obesity, and in cancer. Biochemical studies and bioinformatics have identified TPPII as a subtilase, but its structure is very unusual: it forms a large homooligomeric complex (6 MDa) with a spindle-like shape. Recently, the high-resolution structure of TPPII homodimers (300 kDa) was solved and a hybrid structure of the holocomplex built of 20 dimers was obtained by docking it into the EM-density. Here, we summarize our current knowledge about TPPII with a focus on structural aspects. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Beate Rockel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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19
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Stewart FJ, Sharma AK, Bryant JA, Eppley JM, DeLong EF. Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol 2011; 12:R26. [PMID: 21426537 PMCID: PMC3129676 DOI: 10.1186/gb-2011-12-3-r26] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/28/2011] [Accepted: 03/22/2011] [Indexed: 12/02/2022] Open
Abstract
Background Combined metagenomic and metatranscriptomic datasets make it possible to study the molecular evolution of diverse microbial species recovered from their native habitats. The link between gene expression level and sequence conservation was examined using shotgun pyrosequencing of microbial community DNA and RNA from diverse marine environments, and from forest soil. Results Across all samples, expressed genes with transcripts in the RNA sample were significantly more conserved than non-expressed gene sets relative to best matches in reference databases. This discrepancy, observed for many diverse individual genomes and across entire communities, coincided with a shift in amino acid usage between these gene fractions. Expressed genes trended toward GC-enriched amino acids, consistent with a hypothesis of higher levels of functional constraint in this gene pool. Highly expressed genes were significantly more likely to fall within an orthologous gene set shared between closely related taxa (core genes). However, non-core genes, when expressed above the level of detection, were, on average, significantly more highly expressed than core genes based on transcript abundance normalized to gene abundance. Finally, expressed genes showed broad similarities in function across samples, being relatively enriched in genes of energy metabolism and underrepresented by genes of cell growth. Conclusions These patterns support the hypothesis, predicated on studies of model organisms, that gene expression level is a primary correlate of evolutionary rate across diverse microbial taxa from natural environments. Despite their complexity, meta-omic datasets can reveal broad evolutionary patterns across taxonomically, functionally, and environmentally diverse communities.
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Affiliation(s)
- Frank J Stewart
- School of Biology, Georgia Institute of Technology, Ford ES&T Building, Rm 1242, 311 Ferst Drive, Atlanta, GA 30332, USA
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20
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Spirek M, Benko Z, Carnecka M, Rumpf C, Cipak L, Batova M, Marova I, Nam M, Kim DU, Park HO, Hayles J, Hoe KL, Nurse P, Gregan J. S. pombe genome deletion project: an update. Cell Cycle 2010; 9:2399-402. [PMID: 20519959 DOI: 10.4161/cc.9.12.11914] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe is a model organism used widely to study various aspects of eukaryotic biology. A collection of heterozygous diploid strains containing individual deletions in nearly all S. pombe genes has been created using a PCR based strategy. However, deletion of some genes has not been possible using this methodology. Here we use an efficient knockout strategy based on plasmids that contain large regions homologous to the target gene to delete an additional 29 genes. The collection of deletion mutants now covers 99% of the fission yeast open reading frames.
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Affiliation(s)
- Mario Spirek
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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21
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Kim DU, Hayles J, Kim D, Wood V, Park HO, Won M, Yoo HS, Duhig T, Nam M, Palmer G, Han S, Jeffery L, Baek ST, Lee H, Shim YS, Lee M, Kim L, Heo KS, Noh EJ, Lee AR, Jang YJ, Chung KS, Choi SJ, Park JY, Park Y, Kim HM, Park SK, Park HJ, Kang EJ, Kim HB, Kang HS, Park HM, Kim K, Song K, Song KB, Nurse P, Hoe KL. Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol 2010; 28:617-623. [PMID: 20473289 PMCID: PMC3962850 DOI: 10.1038/nbt.1628] [Citation(s) in RCA: 534] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 03/30/2010] [Indexed: 01/28/2023]
Abstract
We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome providing a tool for studying eukaryotic biology. Comprehensive gene dispensability comparisons with budding yeast--the only other eukaryote for which a comprehensive knockout library exists--revealed that 83% of single-copy orthologs in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than nonessential genes to be present in a single copy, to be broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.
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Affiliation(s)
- Dong-Uk Kim
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Jacqueline Hayles
- Cancer Research UK, The London Research Institute, 44, Lincoln's Inn Fields, LondonWC2A 3PX, UK
| | - Dongsup Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science & Technology (KAIST), Yuseong, Daejeon, Korea
| | - Valerie Wood
- Cancer Research UK, The London Research Institute, 44, Lincoln's Inn Fields, LondonWC2A 3PX, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Han-Oh Park
- Bioneer Corporation, Daedeok, Daejeon, Korea
| | - Misun Won
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Hyang-Sook Yoo
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Trevor Duhig
- Cancer Research UK, The London Research Institute, 44, Lincoln's Inn Fields, LondonWC2A 3PX, UK
| | - Miyoung Nam
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Georgia Palmer
- Cancer Research UK, The London Research Institute, 44, Lincoln's Inn Fields, LondonWC2A 3PX, UK
| | - Sangjo Han
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science & Technology (KAIST), Yuseong, Daejeon, Korea
| | - Linda Jeffery
- Cancer Research UK, The London Research Institute, 44, Lincoln's Inn Fields, LondonWC2A 3PX, UK
| | - Seung-Tae Baek
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Hyemi Lee
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Young Sam Shim
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Minho Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science & Technology (KAIST), Yuseong, Daejeon, Korea
| | - Lila Kim
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Kyung-Sun Heo
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Eun Joo Noh
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Ah-Reum Lee
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Young-Joo Jang
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Kyung-Sook Chung
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Shin-Jung Choi
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Jo-Young Park
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Youngwoo Park
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
| | - Hwan Mook Kim
- Bioevaluation Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Chungcheongbuk-do, Korea
| | - Song-Kyu Park
- Bioevaluation Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Chungcheongbuk-do, Korea
| | | | | | - Hyong Bai Kim
- Department of Bioinformatics & Biotechnology, Korea University, Jochiwon, Chungnam, Korea
| | - Hyun-Sam Kang
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hee-Moon Park
- Department of Microbiology, Chungnam National University, Yuseong, Daejeon, Korea
| | - Kyunghoon Kim
- Division of Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Korea
| | - Kiwon Song
- Department of Biochemistry, Yonsei University, Seoul, Korea
| | - Kyung Bin Song
- Department of Food and Nutrition, Chungnam National University, Yuseong, Daejeon, Korea
| | - Paul Nurse
- Cancer Research UK, The London Research Institute, 44, Lincoln's Inn Fields, LondonWC2A 3PX, UK
- The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399, USA
| | - Kwang-Lae Hoe
- Integrative Omics Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong, Daejeon, Korea
- Bioevaluation Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Chungcheongbuk-do, Korea
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22
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dit Frey NF, Muller P, Jammes F, Kizis D, Leung J, Perrot-Rechenmann C, Bianchi MW. The RNA binding protein Tudor-SN is essential for stress tolerance and stabilizes levels of stress-responsive mRNAs encoding secreted proteins in Arabidopsis. THE PLANT CELL 2010; 22:1575-91. [PMID: 20484005 PMCID: PMC2899877 DOI: 10.1105/tpc.109.070680] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 05/20/2023]
Abstract
Tudor-SN (TSN) copurifies with the RNA-induced silencing complex in animal cells where, among other functions, it is thought to act on mRNA stability via the degradation of specific dsRNA templates. In plants, TSN has been identified biochemically as a cytoskeleton-associated RNA binding activity. In eukaryotes, it has recently been identified as a conserved primary target of programmed cell death-associated proteolysis. We have investigated the physiological role of TSN by isolating null mutations for two homologous genes in Arabidopsis thaliana. The double mutant tsn1 tsn2 displays only mild growth phenotypes under nonstress conditions, but germination, growth, and survival are severely affected under high salinity stress. Either TSN1 or TSN2 alone can complement the double mutant, indicating their functional redundancy. TSN accumulates heterogeneously in the cytosol and relocates transiently to a diffuse pattern in response to salt stress. Unexpectedly, stress-regulated mRNAs encoding secreted proteins are significantly enriched among the transcripts that are underrepresented in tsn1 tsn2. Our data also reveal that TSN is important for RNA stability of its targets. These findings show that TSN is essential for stress tolerance in plants and implicate TSN in new, potentially conserved mechanisms acting on mRNAs entering the secretory pathway.
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Affiliation(s)
- Nicolas Frei dit Frey
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique 2355, 91198 Gif sur Yvette cedex, France
| | - Philippe Muller
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique 2355, 91198 Gif sur Yvette cedex, France
| | - Fabien Jammes
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique 2355, 91198 Gif sur Yvette cedex, France
- Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche, Institut National de la Recherche Agronomique 1165, Centre National de la Recherche Scientifique 8114, Université d'Evry Val d'Essonne, 91057 Evry cedex, France
| | - Dimosthenis Kizis
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique 2355, 91198 Gif sur Yvette cedex, France
| | - Jeffrey Leung
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique 2355, 91198 Gif sur Yvette cedex, France
| | - Catherine Perrot-Rechenmann
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique 2355, 91198 Gif sur Yvette cedex, France
| | - Michele Wolfe Bianchi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique 2355, 91198 Gif sur Yvette cedex, France
- Faculté des Sciences et Technologie, Université Paris Est-Créteil, 94010 Créteil cedex, France
- Address correspondence to
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23
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Cipak L, Spirek M, Novatchkova M, Chen Z, Rumpf C, Lugmayr W, Mechtler K, Ammerer G, Csaszar E, Gregan J. An improved strategy for tandem affinity purification-tagging of Schizosaccharomyces pombe genes. Proteomics 2010; 9:4825-8. [PMID: 19750511 DOI: 10.1002/pmic.200800948] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tandem affinity purification (TAP) is a method that allows rapid purification of native protein complexes. We developed an improved technique to fuse the fission yeast genes with a TAP tag. Our technique is based on tagging constructs that contain regions homologous to the target gene cloned into vectors carrying a TAP tag. We used this technique to design strategies for TAP-tagging of predicted Schizosaccharomyces pombe genes (http://mendel.imp.ac.at/Pombe_tagging/). To validate the approach, we purified the proteins, which associated with two evolutionarily conserved proteins Swi5 and Sfr1 as well as three protein kinases Ksg1, Orb6 and Sid1.
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Affiliation(s)
- Lubos Cipak
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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24
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Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C. Systematic Mapping of Genetic Interaction Networks. Annu Rev Genet 2009; 43:601-25. [DOI: 10.1146/annurev.genet.39.073003.114751] [Citation(s) in RCA: 216] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Scott J. Dixon
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Michael Costanzo
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
| | - Anastasia Baryshnikova
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
| | - Brenda Andrews
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
| | - Charles Boone
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada;
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25
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Production of heterologous proteins using the fission-yeast (Schizosaccharomyces pombe) expression system. Biotechnol Appl Biochem 2009; 53:227-35. [PMID: 19531030 DOI: 10.1042/ba20090048] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The fission yeast Schizosaccharomyces pombe is a particularly useful model for studying the function and regulation of genes from higher eukaryotes. The genome of Sc. pombe has been sequenced, and DNA microarray, proteome and transcriptome analyses have been carried out. Among the well-characterized yeast species, Sc. pombe is considered an attractive host for the production of heterologous proteins. Expression vectors for high-level expression in Sc. pombe have been developed and many foreign proteins have been successfully expressed. However, further improvements in the protein-expressing host systems are still required for the production of heterologous proteins involved in post-translational modification, metabolism and intracellular trafficking. This minireview focuses on recent advances in heterologous protein production by use of engineered fission-yeast strains.
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26
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Functional genomics of adhesion, invasion, and mycelial formation in Schizosaccharomyces pombe. EUKARYOTIC CELL 2009; 8:1298-306. [PMID: 19542312 DOI: 10.1128/ec.00078-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Investigation into the switch between single-celled and filamentous forms of fungi may provide insights into cell polarity, differentiation, and fungal pathogenicity. At the molecular level, much of this investigation has fallen on two closely related budding yeasts, Candida albicans and Saccharomyces cerevisiae. Recently, the much more distant fission yeast Schizosaccharomyces pombe was shown to form invasive filaments after nitrogen limitation (E. Amoah-Buahin, N. Bone, and J. Armstrong, Eukaryot. Cell 4:1287-1297, 2005) and this genetically tractable organism provides an alternative system for the study of dimorphic growth. Here we describe a second mode of mycelial formation of S. pombe, on rich media. Screening of an S. pombe haploid deletion library identified 12 genes required for mycelial development which encode potential transcription factors, orthologues of S. cerevisiae Sec14p and Tlg2p, and the formin For3, among others. These were further grouped into two phenotypic classes representing different stages of the process. We show that galactose-dependent cell adhesion and actin assembly are both required for mycelial formation and mutants lacking a range of genes controlling cell polarity all produce mycelia but with radically altered morphology.
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27
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Deshpande GP, Hayles J, Hoe KL, Kim DU, Park HO, Hartsuiker E. Screening a genome-wide S. pombe deletion library identifies novel genes and pathways involved in genome stability maintenance. DNA Repair (Amst) 2009; 8:672-9. [PMID: 19264558 DOI: 10.1016/j.dnarep.2009.01.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 11/27/2022]
Abstract
The maintenance of genome stability is essential for an organism to avoid cell death and cancer. Based on screens for mutant sensitivity against DNA damaging agents a large number of DNA repair and DNA damage checkpoint genes have previously been identified in genetically amenable model organisms. These screens have however not been exhaustive and various genes have been, and remain to be, identified by other means. We therefore screened a genome-wide Schizosaccharomyces pombe deletion library for mutants sensitive against various DNA damaging agents. Screening the library on different concentrations of these genotoxins allowed us to assign a semi-quantitative score to each mutant expressing the degree of sensitivity. We isolated a total of 229 mutants which show sensitivity to one or more of the DNA damaging agents used. This set of mutants was significantly enriched for processes involved in DNA replication, DNA repair, DNA damage checkpoint, response to UV, mating type switching, telomere length maintenance and meiosis, and also for processes involved in the establishment and maintenance of chromatin architecture (notably members of the SAGA complex), transcription (members of the CCR4-Not complex) and microtubule related processes (members of the DASH complex). We also identified 23 sensitive mutants which had previously been classified as "sequence orphan" or as "conserved hypothetical". Among these, we identified genes showing extensive homology to CtIP, Stra13, Ybp1/Ybp2, Human Fragile X mental retardation interacting protein NUFIP1, and Aprataxin. The identification of these homologues will provide a basis for the further characterisation of the role of these conserved proteins in the genetically amenable model organism S. pombe.
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Affiliation(s)
- Gaurang P Deshpande
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
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Prevorovský M, Stanurová J, Půta F, Folk P. High environmental iron concentrations stimulate adhesion and invasive growth of Schizosaccharomyces pombe. FEMS Microbiol Lett 2009; 293:130-4. [PMID: 19222572 DOI: 10.1111/j.1574-6968.2009.01515.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We have found that a high iron concentration in solid complete cultivation medium potentiates cell-cell and cell-surface adhesion of the fission yeast Schizosaccharomyces pombe. Spotted giant colonies grown on iron-rich media were found to be more compact and more resistant to washing than those grown on plates with a standard iron content. Furthermore, we have documented that excess environmental iron stimulates the invasive growth of S. pombe (and Saccharomyces cerevisiae). Three-dimensional, branched, washing-resistant structures composed mostly of elongated, but separate fission yeast cells, were formed within the solid agar medium. The degree of both adhesion and invasion displayed a specific, iron concentration-dependent response. Our results suggest a novel link between iron availability and the intensively studied and important fungal virulence factors, adhesion and invasion.
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Affiliation(s)
- Martin Prevorovský
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Eriksson S, Gutiérrez OA, Bjerling P, Tomkinson B. Development, evaluation and application of tripeptidyl-peptidase II sequence signatures. Arch Biochem Biophys 2009; 484:39-45. [PMID: 19467630 DOI: 10.1016/j.abb.2009.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 01/07/2009] [Indexed: 11/24/2022]
Abstract
Tripeptidyl-peptidase II (TPP II) is a cytosolic peptidase that has been implicated in fat formation and cancer, apparently independent of the enzymatic activity. In search for alternative functional regions, conserved motifs were identified and eleven signatures were constructed. Seven of the signatures covered previously investigated residues, whereas the functional importance of the other motifs is unknown. This provides directions for future investigations of alternative activities of TPP II. The obtained signatures provide an efficient bioinformatic tool for the identification of TPP II homologues. Hence, a TPP II sequence homologue from fission yeast, Schizosaccharomyces pombe, was identified and demonstrated to encode the TPP II-like protein previously reported as multicorn. Furthermore, an homologous protein was found in the prokaryote Blastopirellula marina, albeit the TPP II function was apparently not conserved. This gene is probably the result of a rare gene transfer from eukaryote to prokaryote.
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Affiliation(s)
- Sandra Eriksson
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
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Prevorovský M, Grousl T, Stanurová J, Rynes J, Nellen W, Půta F, Folk P. Cbf11 and Cbf12, the fission yeast CSL proteins, play opposing roles in cell adhesion and coordination of cell and nuclear division. Exp Cell Res 2008; 315:1533-47. [PMID: 19101542 DOI: 10.1016/j.yexcr.2008.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 12/02/2008] [Accepted: 12/03/2008] [Indexed: 11/30/2022]
Abstract
The CSL (CBF1/RBP-Jkappa/Suppressor of Hairless/LAG-1) family is comprised of transcription factors essential for metazoan development, mostly due to their involvement in the Notch receptor signaling pathway. Recently, we identified two novel classes of CSL genes in the genomes of several fungal species, organisms lacking the Notch pathway. In this study, we characterized experimentally cbf11+ and cbf12+, the two CSL genes of Schizosaccharomyces pombe, in order to elucidate the CSL function in fungi. We provide evidence supporting their identity as genuine CSL genes. Both cbf11+ and cbf12+ are non-essential; they have distinct expression profiles and code for nuclear proteins with transcription activation potential. Significantly, we demonstrated that Cbf11 recognizes specifically the canonical CSL response element GTGA/GGAA in vitro. The deletion of cbf11+ is associated with growth phenotypes and altered colony morphology. Furthermore, we found that Cbf11 and Cbf12 play opposite roles in cell adhesion, nuclear and cell division and their coordination. Disturbed balance of the two CSL proteins leads to cell separation defects (sep phenotype), cut phenotype, and high-frequency diploidization in heterothallic strains. Our data show that CSL proteins operate in an organism predating the Notch pathway, which should be of relevance to the understanding of (Notch-independent) CSL functions in metazoans.
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Affiliation(s)
- Martin Prevorovský
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicná 7, 128 43, Prague 2, Czech Republic
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31
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Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A 2008; 105:16653-8. [PMID: 18931302 DOI: 10.1073/pnas.0806261105] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synthetic lethal genetic interaction networks define genes that work together to control essential functions and have been studied extensively in Saccharomyces cerevisiae using the synthetic genetic array (SGA) analysis technique (ScSGA). The extent to which synthetic lethal or other genetic interaction networks are conserved between species remains uncertain. To address this question, we compared literature-curated and experimentally derived genetic interaction networks for two distantly related yeasts, Schizosaccharomyces pombe and S. cerevisiae. We find that 23% of interactions in a novel, high-quality S. pombe literature-curated network are conserved in the existing S. cerevisiae network. Next, we developed a method, called S. pombe SGA analysis (SpSGA), enabling rapid, high-throughput isolation of genetic interactions in this species. Direct comparison by SpSGA and ScSGA of approximately 220 genes involved in DNA replication, the DNA damage response, chromatin remodeling, intracellular transport, and other processes revealed that approximately 29% of genetic interactions are common to both species, with the remainder exhibiting unique, species-specific patterns of genetic connectivity. We define a conserved yeast network (CYN) composed of 106 genes and 144 interactions and suggest that this network may help understand the shared biology of diverse eukaryotic species.
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Foulks JM, Weyrich AS, Zimmerman GA, McIntyre TM. A yeast PAF acetylhydrolase ortholog suppresses oxidative death. Free Radic Biol Med 2008; 45:434-42. [PMID: 18489912 PMCID: PMC2603548 DOI: 10.1016/j.freeradbiomed.2008.04.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 04/17/2008] [Accepted: 04/18/2008] [Indexed: 11/26/2022]
Abstract
Phospholipids containing sn-2 polyunsaturated fatty acyl residues are primary targets of oxidizing radicals, producing proapoptotic and membrane perturbing fragmented phospholipids. The only known phospholipases that specifically select these oxidized and/or short-chained phospholipids as substrates are mammalian group VII phospholipases A2s that were purified and cloned as PAF acetylhydrolases. Platelet-activating factor (PAF) is a short-chained phospholipid, and whether these enzymes actually are PAF hydrolases or evolved as oxidized phospholipid phospholipases is unknown. The fission yeast Schizosaccharomyces pombe, which does not form or use PAF as a signaling molecule, contains an open-reading frame potentially homologous to mammalian group VII phospholipase A2s. We cloned this SPBC106.11c locus and expressed it in distantly related Saccharomyces cerevisiae that lack homologous sequences. The S. pombe locus encoded a functional phospholipase A2, now renamed plg7+, that hydrolyzed PAF and a synthetic oxidized phospholipid. Expression of human type II PAF acetylhydrolase or S. pombe Plg7p enhanced the viability of S. cerevisiae subjected to oxidative stress. We conclude that a single-celled organism with an exceedingly spare genome still expresses an unusually discriminating phospholipase A2, and that selective hydrolysis of phospholipid oxidation products is an early, and critical, way to overcome oxidative membrane damage and oxidant-induced cell death.
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Affiliation(s)
- Jason M. Foulks
- Department of Experimental Pathology, University of Utah School of Medicine, Salt Lake City, UT, 84112
- Department of Internal Medicine and Human Molecular Biology and Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112
| | - Andrew S. Weyrich
- Department of Internal Medicine and Human Molecular Biology and Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112
| | - Guy A. Zimmerman
- Department of Internal Medicine and Human Molecular Biology and Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112
| | - Thomas M. McIntyre
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine of CWRU, 9500 Euclid Ave, Cleveland, OH 44195
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Bernard P, Schmidt CK, Vaur S, Dheur S, Drogat J, Genier S, Ekwall K, Uhlmann F, Javerzat JP. Cell-cycle regulation of cohesin stability along fission yeast chromosomes. EMBO J 2008; 27:111-21. [PMID: 18079700 PMCID: PMC2206136 DOI: 10.1038/sj.emboj.7601955] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 11/16/2007] [Indexed: 02/08/2023] Open
Abstract
Sister chromatid cohesion is mediated by cohesin, but the process of cohesion establishment during S-phase is still enigmatic. In mammalian cells, cohesin binding to chromatin is dynamic in G1, but becomes stabilized during S-phase. Whether the regulation of cohesin stability is integral to the process of cohesion establishment is unknown. Here, we provide evidence that fission yeast cohesin also displays dynamic behavior. Cohesin association with G1 chromosomes requires continued activity of the cohesin loader Mis4/Ssl3, suggesting that repeated loading cycles maintain cohesin binding. Cohesin instability in G1 depends on wpl1, the fission yeast ortholog of mammalian Wapl, suggestive of a conserved mechanism that controls cohesin stability on chromosomes. wpl1 is nonessential, indicating that a change in wpl1-dependent cohesin dynamics is dispensable for cohesion establishment. Instead, we find that cohesin stability increases at the time of S-phase in a reaction that can be uncoupled from DNA replication. Hence, cohesin stabilization might be a pre-requisite for cohesion establishment rather than its consequence.
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Affiliation(s)
- Pascal Bernard
- Université Bordeaux 2, CNRS Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | | | - Sabine Vaur
- Université Bordeaux 2, CNRS Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Sonia Dheur
- Université Bordeaux 2, CNRS Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Julie Drogat
- Université Bordeaux 2, CNRS Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Sylvie Genier
- Université Bordeaux 2, CNRS Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Karl Ekwall
- Department of Biosciences and Medical Nutrition, School of Life Sciences, Karolinska Institutet, University College Sodertorn, Huddinge, Sweden
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK, London Research Institute, London, UK
| | - Jean-Paul Javerzat
- Université Bordeaux 2, CNRS Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
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Gregan J, Rabitsch PK, Rumpf C, Novatchkova M, Schleiffer A, Nasmyth K. High-throughput knockout screen in fission yeast. Nat Protoc 2007; 1:2457-64. [PMID: 17406492 PMCID: PMC2957175 DOI: 10.1038/nprot.2006.385] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have designed the most efficient strategy to knock out genes in fission yeast Schizosaccharomyces pombe on a large scale. Our technique is based on knockout constructs that contain regions homologous to the target gene cloned into vectors carrying dominant drug-resistance markers. Most of the steps are carried out in a 96-well format, allowing simultaneous deletion of 96 genes in one batch. Based on our knockout technique, we designed a strategy for cloning knockout constructs for all predicted fission yeast genes, which is available in a form of a searchable database http://mendel.imp.ac.at/Pombe_deletion/. We validated this technique in a screen where we identified novel genes required for chromosome segregation during meiosis. Here, we present our protocol with detailed instructions. Using this protocol, one person can knock out 96 S. pombe genes in 8 days.
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Affiliation(s)
- Juraj Gregan
- Research Institute of Molecular Pathology, Dr Bohr-Gasse 7, 1030 Vienna, Austria.
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Abstract
Background The CSL (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1) transcription factor family members are well-known components of the transmembrane receptor Notch signaling pathway, which plays a critical role in metazoan development. They function as context-dependent activators or repressors of transcription of their responsive genes, the promoters of which harbor the GTG(G/A)GAA consensus elements. Recently, several studies described Notch-independent activities of the CSL proteins. Conclusion Our findings support the evolutionary origin of the CSL transcription factor family in the last common ancestor of fungi and metazoans. We hypothesize that the ancestral CSL function involved DNA binding and Notch-independent regulation of transcription and that this function may still be shared, to a certain degree, by the present CSL family members from both fungi and metazoans.
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36
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Balaña-Fouce R, Reguera RM. RNA interference in Trypanosoma brucei: a high-throughput engine for functional genomics in trypanosomatids? Trends Parasitol 2007; 23:348-51. [PMID: 17604223 DOI: 10.1016/j.pt.2007.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 04/26/2007] [Accepted: 06/15/2007] [Indexed: 11/26/2022]
Abstract
RNA interference (RNAi) is the technique of choice for down-regulating the gene function of suitable genes in African trypanosomes. A recent report by Subramanian and co-workers describes a high-throughput method for gene function discovery using RNAi in Trypanosoma brucei. The phenotype of most of the Open Reading Frames from chromosome 1 of T. brucei was analysed using a battery test of standard protocols. The authors propose that this technique could be used to mine the full genome of T. brucei and to reveal the core proteomic map of the other two major trypanosomatids, Trypanosoma cruzi and Leishmania major, despite the lack of a homologous mechanism of genetic silencing.
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Affiliation(s)
- Rafael Balaña-Fouce
- Department of Pharmacology and Toxicology (INTOXCAL), University of León, Campus de Vegazaza s/n, 24071 León, Spain.
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Relationship between insertion/deletion (indel) frequency of proteins and essentiality. BMC Bioinformatics 2007; 8:227. [PMID: 17598914 PMCID: PMC1925122 DOI: 10.1186/1471-2105-8-227] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 06/28/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such indels may provide sufficient spatial differences between the pathogenic protein and human proteins to allow for selective targeting. In one example, an indel difference was targeted via large scale in-silico screening. This resulted in selective antibodies and small compounds which were capable of binding to the deletion-bearing essential pathogen protein without any cross-reactivity to the highly similar human protein. The objective of the current study was to investigate whether indels were found more frequently in essential than non-essential proteins. RESULTS We have investigated three species, Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae, for which high-quality protein essentiality data is available. Using these data, we demonstrated with t-test calculations that the mean indel frequencies in essential proteins were greater than that of non-essential proteins in the three proteomes. The abundance of indels in both types of proteins was also shown to be accurately modeled by the Weibull distribution. However, Receiver Operator Characteristic (ROC) curves showed that indel frequencies alone could not be used as a marker to accurately discriminate between essential and non-essential proteins in the three proteomes. Finally, we analyzed the protein interaction data available for S. cerevisiae and observed that indel-bearing proteins were involved in more interactions and had greater betweenness values within Protein Interaction Networks (PINs). CONCLUSION Overall, our findings demonstrated that indels were not randomly distributed across the studied proteomes and were likely to occur more often in essential proteins and those that were highly connected, indicating a possible role of sequence insertions and deletions in the regulation and modification of protein-protein interactions. Such observations will provide new insights into indel-based drug design using bioinformatics and cheminformatics tools.
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Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. BMC Genomics 2007; 8:9. [PMID: 17212814 PMCID: PMC1779777 DOI: 10.1186/1471-2164-8-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 01/09/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Ashbya Genome Database (AGD) 3.0 is an innovative cross-species genome and transcriptome browser based on release 40 of the Ensembl developer environment. DESCRIPTION AGD 3.0 provides information on 4726 protein-encoding loci and 293 non-coding RNA genes present in the genome of the filamentous fungus Ashbya gossypii. A synteny viewer depicts the chromosomal location and orientation of orthologous genes in the budding yeast Saccharomyces cerevisiae. Genome-wide expression profiling data obtained with high-density oligonucleotide microarrays (GeneChips) are available for nearly all currently annotated protein-coding loci in A. gossypii and S. cerevisiae. CONCLUSION AGD 3.0 hence provides yeast- and genome biologists with comprehensive report pages including reliable DNA annotation, Gene Ontology terms associated with S. cerevisiae orthologues and RNA expression data as well as numerous links to external sources of information. The database is accessible at http://agd.vital-it.ch/.
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Subramaniam C, Veazey P, Redmond S, Hayes-Sinclair J, Chambers E, Carrington M, Gull K, Matthews K, Horn D, Field MC. Chromosome-wide analysis of gene function by RNA interference in the african trypanosome. EUKARYOTIC CELL 2006; 5:1539-49. [PMID: 16963636 PMCID: PMC1563588 DOI: 10.1128/ec.00141-06] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trypanosomatids of the order Kinetoplastida are major contributors to global disease and morbidity, and understanding their basic biology coupled with the development of new drug targets represents a critical need. Additionally, trypanosomes are among the more accessible divergent eukaryote experimental systems. The genome of Trypanosoma brucei contains 8,131 predicted open reading frames (ORFs), of which over half have no known homologues beyond the Kinetoplastida and a substantial number of others are poorly defined by in silico analysis. Thus, a major challenge following completion of the T. brucei genome sequence is to obtain functional data for all trypanosome ORFs. As T. brucei is more experimentally tractable than the related Trypanosoma cruzi and Leishmania spp. and shares >75% of their genes, functional analysis of T. brucei has the potential to inform a range of parasite biology. Here, we report methods for systematic mRNA ablation by RNA interference (RNAi) and for phenotypic analysis, together with online data dissemination. This represents the first systematic analysis of gene function in a parasitic organism. In total, 210 genes have been targeted in the bloodstream form parasite, representing an essentially complete phenotypic catalogue of chromosome I together with a validation set. Over 30% of the chromosome I genes generated a phenotype when targeted by RNAi; most commonly, this affected cell growth, viability, and/or cell cycle progression. RNAi against approximately 12% of ORFs was lethal, and an additional 11% had growth defects but retained short-term viability in culture. Although we found no evidence for clustering or a bias towards widely evolutionarily conserved genes within the essential ORF cohort, the putative chromosome I centromere is adjacent to a domain containing genes with no associated phenotype. Involvement of such a large proportion of genes in robust growth in vitro indicates that a high proportion of the expressed trypanosome genome is required for efficient propagation; many of these gene products represent potential drug targets.
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Affiliation(s)
- Chandra Subramaniam
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester, United Kingdom
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40
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Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Predicting essential genes in fungal genomes. Genome Res 2006; 16:1126-35. [PMID: 16899653 PMCID: PMC1557763 DOI: 10.1101/gr.5144106] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Essential genes are required for an organism's viability, and the ability to identify these genes in pathogens is crucial to directed drug development. Predicting essential genes through computational methods is appealing because it circumvents expensive and difficult experimental screens. Most such prediction is based on homology mapping to experimentally verified essential genes in model organisms. We present here a different approach, one that relies exclusively on sequence features of a gene to estimate essentiality and offers a promising way to identify essential genes in unstudied or uncultured organisms. We identified 14 characteristic sequence features potentially associated with essentiality, such as localization signals, codon adaptation, GC content, and overall hydrophobicity. Using the well-characterized baker's yeast Saccharomyces cerevisiae, we employed a simple Bayesian framework to measure the correlation of each of these features with essentiality. We then employed the 14 features to learn the parameters of a machine learning classifier capable of predicting essential genes. We trained our classifier on known essential genes in S. cerevisiae and applied it to the closely related and relatively unstudied yeast Saccharomyces mikatae. We assessed predictive success in two ways: First, we compared all of our predictions with those generated by homology mapping between these two species. Second, we verified a subset of our predictions with eight in vivo knockouts in S. mikatae, and we present here the first experimentally confirmed essential genes in this species.
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Affiliation(s)
- Michael Seringhaus
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Alberto Paccanaro
- Department of Computer Science, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
- Corresponding author.E-mail ; fax (360) 838-7861
| | - Anthony Borneman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Michael Snyder
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
- Corresponding author.E-mail ; fax (360) 838-7861
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Goddard A, Ladds G, Forfar R, Davey J. Identification of Gnr1p, a negative regulator of G alpha signalling in Schizosaccharomyces pombe, and its complementation by human G beta subunits. Fungal Genet Biol 2006; 43:840-51. [PMID: 16884933 DOI: 10.1016/j.fgb.2006.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 06/02/2006] [Accepted: 06/05/2006] [Indexed: 10/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are involved in the response of eukaryotic cells to a wide variety of stimuli, traditionally mediating their effects through heterotrimeric G proteins comprised of G alpha, G beta and G gamma subunits. The fission yeast Schizosaccharomyces pombe is an established tool for GPCR research, possessing two G alpha-dependent signalling cascades. A complete G alpha beta gamma complex has been characterised for the glucose-sensing pathway, but only the G alpha subunit, Gpa1p, has been identified in the pheromone-response pathway. Here, we report the use of the yeast two-hybrid system to identify a novel protein, Gnr1p, which interacts with Gpa1p. Gnr1p is predicted to contain seven WD repeats and to adopt a structure similar to typical G beta subunits. Disruption and overexpression studies reveal that Gnr1p negatively regulates the pheromone-response pathway but is not required for signalling. Human G beta subunits complement the loss of Gnr1p, functioning as negative regulators of G alpha signalling in fission yeast.
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Affiliation(s)
- Alan Goddard
- Department of Biological Sciences, University of Warwick, Coventry, UK.
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42
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Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 2006; 5:11. [PMID: 16762047 PMCID: PMC1561585 DOI: 10.1186/jbiol36] [Citation(s) in RCA: 222] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 03/17/2006] [Accepted: 03/30/2006] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND 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. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. RESULTS 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 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases. CONCLUSION Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks.
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Affiliation(s)
- Teresa Reguly
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Ashton Breitkreutz
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Lorrie Boucher
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
| | - Bobby-Joe Breitkreutz
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Gary C Hon
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Chad L Myers
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, NJ 08544, USA
| | - Ainslie Parsons
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Helena Friesen
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Rose Oughtred
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Amy Tong
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Chris Stark
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Yuen Ho
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Brenda Andrews
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Charles Boone
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Olga G Troyanskya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, NJ 08544, USA
| | - Trey Ideker
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Kara Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Nizar N Batada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
| | - Mike Tyers
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5S 1A8, Canada
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Walling LL. Recycling or regulation? The role of amino-terminal modifying enzymes. CURRENT OPINION IN PLANT BIOLOGY 2006; 9:227-33. [PMID: 16597508 DOI: 10.1016/j.pbi.2006.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 03/22/2006] [Indexed: 05/08/2023]
Abstract
Post-translational modifications are essential for a variety of functions, such as the translocation, activation, regulation, and, ultimately, degradation of proteins. The amino-terminal (N-terminal) region is a particularly active area for such alterations. Three types of reactions predominate: limited proteolysis to remove one or more amino acids; modification of the alpha-amino group; and side-chain-specific changes. The N-terminal peptidases expose penultimate residues, providing new substrates for peptidase or transferase action. These enzymes can act sequentially or competitively to influence a protein's longevity, location or activity. N-terminal modifying enzymes (NTMEs) might target a protein for ubiquitination and degradation or protect a protein from rapid turnover. The N-terminal peptidases might also have important roles in processing the peptides that are released from the proteasome. Plant NTMEs have roles in senescence, meiosis and defense, and proposed roles in polar auxin transport.
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Affiliation(s)
- Linda L Walling
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA.
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Lebel K, MacPherson S, Turcotte B. New tools for phenotypic analysis in Candida albicans: the WAR1 gene confers resistance to sorbate. Yeast 2006; 23:249-59. [PMID: 16544288 DOI: 10.1002/yea.1346] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Availability of the complete sequence of the Candida albicans genome allows for global gene analysis. We designed a gene deletion method to facilitate such studies. First, we constructed C. albicans strains that are both Deltaura3 and Deltatrp1. Second, we designed a system that relies on in vitro recombination, using the Gateway((R)) technology, for efficient generation of deletion cassettes. They are generated in two steps: (a) upstream and downstream DNA fragments of the chromosomal region to be deleted are amplified by PCR and introduced into two separate entry vectors; (b) the second step involves a quadruple recombination event including the two entry vectors, a plasmid bearing a marker of interest and a destination vector, in order to generate a plasmid containing the deletion cassette. The deletion plasmid contains very rare restriction sites for convenient excision of the knockout cassette. Selection in C. albicans can be performed with one of the following markers: the C. albicans URA3 gene, a modified S. cerevisiae TRP1 gene or the mycophenolic acid resistance (MPA(R)) gene. Upon integration into the genome, these markers can be removed by the use of 5-fluoroorotic acid (URA3), 5-fluoroanthranilic acid (TRP1) or the FLP recombinase (MPA(R)). Using this approach, we show that removal of the C. albicans orf19.1035 gene results in sensitivity to the weak acid sorbate, while its overexpression increases resistance to this compound. We named it WAR1, in analogy to its S. cerevisiae orthologue.
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Affiliation(s)
- Karine Lebel
- Department of Medicine, Royal Victoria Hospital, McGill University, 687 Pine Avenue West, Montréal, Québec, Canada H3A 1A1
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45
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Gregan J, Rabitsch PK, Sakem B, Csutak O, Latypov V, Lehmann E, Kohli J, Nasmyth K. Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast. Curr Biol 2006; 15:1663-9. [PMID: 16169489 DOI: 10.1016/j.cub.2005.07.059] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 07/16/2005] [Accepted: 07/19/2005] [Indexed: 11/20/2022]
Abstract
Two rounds of chromosome segregation after only a single round of DNA replication enable the production of haploid gametes from diploid precursors during meiosis. To identify genes involved in meiotic chromosome segregation, we developed an efficient strategy to knock out genes in the fission yeast on a large scale. We used this technique to delete 180 functionally uncharacterized genes whose expression is upregulated during meiosis. Deletion of two genes, sgo1 and mde2, caused massive chromosome missegregation. sgo1 is required for retention of centromeric sister-chromatid cohesion after anaphase I. We show here that mde2 is required for formation of the double-strand breaks necessary for meiotic recombination.
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Affiliation(s)
- Juraj Gregan
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
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46
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Feder ME, Walser JC. The biological limitations of transcriptomics in elucidating stress and stress responses. J Evol Biol 2005; 18:901-10. [PMID: 16033562 DOI: 10.1111/j.1420-9101.2005.00921.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Global analysis of mRNA abundance via genomic arrays (i.e. transcriptomics or transcriptional profiling) is one approach to finding the genes that matter to organisms undergoing environmental stress. In evolutionary analyses of stress, mRNA abundance is often invoked as a proxy for the protein activity that may underlie variation in fitness. To provoke discussion of the utility and sensible application of this valuable approach, this manuscript examines the adequacy of mRNA abundance as a proxy for protein activity, fitness and stress. Published work to date suggests that mRNA abundance typically provides little information on protein activity and fitness and cannot substitute for detailed functional and ecological analyses of candidate genes. While the transcriptional profile can be an exquisitely sensitive indicator of stress, simpler indicators will often suffice. In view of this outcome, transcriptomics should undergo careful cost-benefit analysis before investigators deploy it in studies of stress responses and their evolution.
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Affiliation(s)
- M E Feder
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA.
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Laufman O, Yosef RB, Adir N, Manor H. Cloning and characterization of the Schizosaccharomyces pombe homologs of the human protein Translin and the Translin-associated protein TRAX. Nucleic Acids Res 2005; 33:4128-39. [PMID: 16043634 PMCID: PMC1180670 DOI: 10.1093/nar/gki727] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Translin is a human octameric protein that specifically binds the single-stranded microsatellite repeats d(GT)n and the corresponding transcripts (GU)n. It also binds, with lesser affinities, other single-stranded G-rich DNA and RNA sequences. TRAX is a human protein that bears a homology to Translin and interacts with it. Translin and TRAX have been proposed to be involved in DNA recombination, chromosomal translocation and mRNA transport and translation. Both proteins are highly conserved in eukaryotes, including the fission yeast Schizosaccharomyces pombe, which is amenable to genetic analysis. Here, we report the first study of the S.pombe Translin and TRAX homologs. We have deleted the genes encoding Translin and TRAX in S.pombe and found that the proliferation of the mutant cells was slightly stimulated, suggesting that these genes are not essential for the fission yeast. We have also shown that the S.pombe Translin and TRAX interact. Biochemical analysis of the S.pombe Translin, which was cloned and expressed in Escherichia coli, revealed that it is octameric and that it selectively binds d(GT)n and d(GTT)n microsatellite repeats. However, unlike the human protein, it has much higher affinities for the homologous RNA sequences (GU)n and (GUU)n. These data suggest that the S.pombe Translin is primarily involved in functions related to RNA metabolism.
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Affiliation(s)
| | | | - Noam Adir
- Department of Chemistry, Technion-Israel Institute of TechnologyHaifa 32,000, Israel
| | - Haim Manor
- To whom correspondence should be addressed. Tel: +972 4 8293456; Fax: +972 4 8225153;
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48
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Book AJ, Yang P, Scalf M, Smith LM, Vierstra RD. Tripeptidyl peptidase II. An oligomeric protease complex from Arabidopsis. PLANT PHYSIOLOGY 2005; 138:1046-57. [PMID: 15908606 PMCID: PMC1150419 DOI: 10.1104/pp.104.057406] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The breakdown of most nuclear and cytoplasmic proteins involves their partial cleavage by the 26S proteasome followed by further disassembly to free amino acids by the combined action of endo- and exopeptidases. In animals, one important intermediate exopeptidase is tripeptidyl peptidase (TPP)II, which digests peptide products of the 26S proteasome and other endopeptidases into tripeptides. Here, we describe the purification and characterization of TPPII from Arabidopsis (Arabidopsis thaliana). Like its animal counterparts, Arabidopsis TPPII exists as a soluble, approximately 5- to 9-MD complex. Two related species of 153 and 142 kD are present in the purified preparations that are derived from a single TPP2 gene. Sequencing by Edman degradation of the intact polypeptides and mass spectrometry of proteolytic fragments demonstrated that the 142-kD form mainly differs from the 153-kD form by a truncation at the C-terminal end. This serine protease is a member of the subtilisin superfamily and is sensitive to the inhibitors alanine-alanine-phenylalanine-chloromethylketone and butabindide, which are diagnostic for the TPPII subfamily. The Arabidopsis TPP2 gene is widely expressed in many tissue types with related genes evident in other plant genomes. Whereas the 26S proteasome is essential, TPPII appears not as important for plant physiology. An Arabidopsis T-DNA mutant defective in TPP2 expression displays no phenotypic abnormalities and is not hypersensitive to either amino acid analogs or the 26S proteasome inhibitor MG132. As a consequence, plants likely contain other intermediate exopeptidases that assist in amino acid recycling.
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Affiliation(s)
- Adam J Book
- Department of Genetics , University of Wisconsin, Madison, Wisconsin 53706, USA
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49
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Hsiang T, Baillie DL. Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes. J Mol Evol 2005; 60:475-83. [PMID: 15883882 DOI: 10.1007/s00239-004-0218-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 10/04/2004] [Indexed: 11/26/2022]
Abstract
The purpose of this research was to search for evolutionarily conserved fungal sequences to test the hypothesis that fungi have a set of core genes that are not found in other organisms, as these genes may indicate what makes fungi different from other organisms. By comparing 6355 predicted or known yeast (Saccharomyces cerevisiae) genes to the genomes of 13 other fungi using Standalone TBLASTN at an e-value <1E-5, a list of 3340 yeast genes was obtained with homologs present in at least 12 of 14 fungal genomes. By comparing these common fungal genes to complete genomes of animals (Fugu rubripes, Caenorhabditis elegans), plants (Arabidopsis thaliana, Oryza sativa), and bacteria (Agrobacterium tumefaciens, Xylella fastidiosa), a list of common fungal genes with homologs in these plants, animals, and bacteria was produced (938 genes), as well as a list of exclusively fungal genes without homologs in these other genomes (60 genes). To ensure that the 60 genes were exclusively fungal, these were compared using TBLASTN to the major sequence databases at GenBank: NR (nonredundant), EST (expressed sequence tags), GSS (genome survey sequences), and HTGS (unfinished high-throughput genome sequences). This resulted in 17 yeast genes with homologs in other fungal genomes, but without known homologs in other organisms. These 17 core, fungal genes were not found to differ from other yeast genes in GC content or codon usage patterns. More intensive study is required of these 17 genes and other common fungal genes to discover unique features of fungi compared to other organisms.
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Affiliation(s)
- Tom Hsiang
- Department of Environmental Biology, University of Guelph, Guelph, Ontario, NIG 2W1, Canada.
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50
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Kabir MA, Rustchenko E. Determination of gaps by contig alignment with telomere-mediated chromosomal fragmentation in Candida albicans. Gene 2005; 345:279-87. [PMID: 15716104 DOI: 10.1016/j.gene.2004.11.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 10/29/2004] [Accepted: 11/24/2004] [Indexed: 10/26/2022]
Abstract
We have adopted a method of telomere-mediated chromosome fragmentation in order to demonstrate the alignment of contigs and determination of gaps. We established the order and orientation of four contigs of Candida albicans chromosome 5 and determined the sizes of three gaps between these contigs. We confirmed this proposed alignment of contigs, as well as gap sizes, by sequencing one gap and analyzing three mega deletions of approximately 41 kbp, 58 kbp, and 77 kbp, which covered two other gaps. These gaps could be also conveniently sequenced, which is an important step in establishing a complete sequence. The combined length of contigs and gaps covered approximately 422 kbp, which is one third of chromosome 5. Telomere-mediated chromosome fragmentation, used here for the first time to align the contigs of C. albicans and determine the gaps, proved to be a reliable method. The method could be helpful in sequencing projects of other diploid organisms, in particular those in which centromeres have not been identified. In addition, our approach can be used to assign any contig to a chromosome, or to induce the loss of a specific chromosome.
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Affiliation(s)
- M Anaul Kabir
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical School, Rochester, NY 14642, USA
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