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Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

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.

SUBMITTER: Kim DU

PROVIDER: S-EPMC3962850 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature

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Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

Kim Dong-Uk DU Hayles Jacqueline J Kim Dongsup D Wood Valerie V Park Han-Oh HO Won Misun M Yoo Hyang-Sook HS Duhig Trevor T Nam Miyoung M Palmer Georgia G Han Sangjo S Jeffery Linda L Baek Seung-Tae ST Lee Hyemi H Shim Young Sam YS Lee Minho M Kim Lila L Heo Kyung-Sun KS Noh Eun Joo EJ Lee Ah-Reum AR Jang Young-Joo YJ Chung Kyung-Sook KS Choi Shin-Jung SJ Park Jo-Young JY Park Youngwoo Y Kim Hwan Mook HM Park Song-Kyu SK Park Hae-Joon HJ Kang Eun-Jung EJ Kim Hyong Bai HB Kang Hyun-Sam HS Park Hee-Moon HM Kim Kyunghoon K Song Kiwon K Song Kyung Bin KB Nurse Paul P Hoe Kwang-Lae KL

Nature biotechnology 20100516 6

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 mit ...[more]

PMID: 20473289

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Project description:BackgroundHIV-1 protease (PR) is an essential viral enzyme. Its primary function is to proteolyze the viral Gag-Pol polyprotein for production of viral enzymes and structural proteins and for maturation of infectious viral particles. Increasing evidence suggests that PR cleaves host cellular proteins. However, the nature of PR-host cellular protein interactions is elusive. This study aimed to develop a fission yeast (Schizosaccharomyces pombe) model system and to examine the possible interaction of HIV-1 PR with cellular proteins and its potential impact on cell proliferation and viability.ResultsA fission yeast strain RE294 was created that carried a single integrated copy of the PR gene in its chromosome. The PR gene was expressed using an inducible nmt1 promoter so that PR-specific effects could be measured. HIV-1 PR from this system cleaved the same indigenous viral p6/MA protein substrate as it does in natural HIV-1 infections. HIV-1 PR expression in fission yeast cells prevented cell proliferation and induced cellular oxidative stress and changes in mitochondrial morphology that led to cell death. Both these PR activities can be prevented by a PR-specific enzymatic inhibitor, indinavir, suggesting that PR-mediated proteolytic activities and cytotoxic effects resulted from enzymatic activities of HIV-1 PR. Through genome-wide screening, a serine/threonine kinase, Hhp2, was identified that suppresses HIV-1 PR-induced protease cleavage and cell death in fission yeast and in mammalian cells, where it prevented PR-induced apoptosis and cleavage of caspase-3 and caspase-8.ConclusionsThis is the first report to show that HIV-1 protease is functional as an enzyme in fission yeast, and that it behaves in a similar manner as it does in HIV-1 infection. HIV-1 PR-induced cell death in fission yeast could potentially be used as an endpoint for mechanistic studies, and this system could be used for developing a high-throughput system for drug screenings.

Dataset Information

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

Publications

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

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