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Mukhopadhyay J, Hausner G. Interconnected roles of fungal nuclear- and intron-encoded maturases: at the crossroads of mitochondrial intron splicing. Biochem Cell Biol 2024. [PMID: 38833723 DOI: 10.1139/bcb-2024-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
Group I and II introns are large catalytic RNAs (ribozymes) that are frequently encountered in fungal mitochondrial genomes. The discovery of respiratory mutants linked to intron splicing defects demonstrated that for the efficient removal of organellar introns there appears to be a requirement of protein splicing factors. These splicing factors can be intron-encoded proteins with maturase activities that usually promote the splicing of the introns that encode them (cis-acting) and/or nuclear-encoded factors that can promote the splicing of a range of different introns (trans-acting). Compared to plants organellar introns, fungal mitochondrial intron splicing is still poorly explored, especially in terms of the synergy of nuclear factors with intron-encoded maturases that has direct impact on splicing through their association with intron RNA. In addition, nuclear-encoded accessory factors might drive the splicing impetus through translational activation, mitoribosome assembly, and phosphorylation-mediated RNA turnover. This review explores protein-assisted splicing of introns by nuclear and mitochondrial-encoded maturases as a means of mitonuclear interplay that could respond to environmental and developmental factors promoting phenotypic adaptation and potentially speciation. It also highlights key evolutionary events that have led to changes in structure and ATP-dependence to accommodate the dual functionality of nuclear and organellar splicing factors.
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Affiliation(s)
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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2
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Putnam CD. Loss of mitochondrial DNA is associated with reduced DNA content variability in Saccharomyces cerevisiae. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001117. [PMID: 38533353 PMCID: PMC10964099 DOI: 10.17912/micropub.biology.001117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/20/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
DNA content measurement by fluorescence-assisted cell sorting (FACS) provides information on cell cycle progression and DNA content variability. Saccharomyces cerevisiae mutants with DNA content variability that was reduced relative to wild-type strains had defects in mitochondrial DNA (mtDNA) maintenance and mitochondrial gene expression and were correlated with strains found to lack mtDNA ([ rho 0 ] cells) by genome sequencing and fluorescence microscopy. In contrast, mutants with increased variability had defects in cell cycle progression, which may indicate a loss of coordination between mtDNA and nuclear DNA replication. Thus, FACS measurement of DNA content variability can provide insight into cell-to-cell heterogeneity in mtDNA copy number.
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Affiliation(s)
- Christopher D. Putnam
- Department of Medicine, University of California, San Diego, San Diego, California, United States
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3
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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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4
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Sandell L, König SG, Otto SP. Schrödinger's yeast: the challenge of using transformation to compare fitness among Saccharomyces cerevisiae that differ in ploidy or zygosity. PeerJ 2023; 11:e16547. [PMID: 38077443 PMCID: PMC10704993 DOI: 10.7717/peerj.16547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
How the number of genome copies modifies the effect of random mutations remains poorly known. In yeast, researchers have investigated these effects for knock-out or other large-effect mutations, but have not accounted for differences at the mating-type locus. We set out to compare fitness differences among strains that differ in ploidy and/or zygosity using a panel of spontaneously arising mutations acquired in haploid yeast from a previous study. To ensure no genetic differences, even at the mating-type locus, we embarked on a series of transformations, which first sterilized and then temporarily introduced plasmid-borne mating types. Despite these attempts to equalize the haplotypes, fitness variation introduced during transformation swamped the differences among the original mutation-accumulation lines. While colony size looked normal, we observed a bi-modality in the maximum growth rate of our transformed yeast and determined that many of the slow growing lines were respiratory deficient ("petite"). Not previously reported, we found that yeast that were TID1/RDH54 knockouts were less likely to become petite. Even for lines with the same petite status, however, we found no correlation in fitness between the two replicate transformations performed. These results pose a challenge for any study using transformation to measure the fitness effect of genetic differences among strains. By attempting to hold haplotypes constant, we introduced more mutations that overwhelmed our ability to measure fitness differences between the genetic states. In this study, we transformed over one hundred different lines of yeast, using two independent transformations, and found that this common laboratory procedure can cause large changes to the microbe studied. Our study provides a cautionary tale of the need to use multiple transformants in fitness assays.
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Affiliation(s)
- Linnea Sandell
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
| | - Stephan G. König
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah P. Otto
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
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5
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Turco G, Chang C, Wang RY, Kim G, Stoops EH, Richardson B, Sochat V, Rust J, Oughtred R, Thayer N, Kang F, Livstone MS, Heinicke S, Schroeder M, Dolinski KJ, Botstein D, Baryshnikova A. Global analysis of the yeast knockout phenome. SCIENCE ADVANCES 2023; 9:eadg5702. [PMID: 37235661 PMCID: PMC11326039 DOI: 10.1126/sciadv.adg5702] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae, enabled by its knockout collection, have produced the largest, richest, and most systematic phenotypic description of any organism. However, integrative analyses of this rich data source have been virtually impossible because of the lack of a central data repository and consistent metadata annotations. Here, we describe the aggregation, harmonization, and analysis of ~14,500 yeast knockout screens, which we call Yeast Phenome. Using this unique dataset, we characterized two unknown genes (YHR045W and YGL117W) and showed that tryptophan starvation is a by-product of many chemical treatments. Furthermore, we uncovered an exponential relationship between phenotypic similarity and intergenic distance, which suggests that gene positions in both yeast and human genomes are optimized for function.
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Affiliation(s)
- Gina Turco
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Christie Chang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Griffin Kim
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Brianna Richardson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Vanessa Sochat
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Rust
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Rose Oughtred
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Fan Kang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael S Livstone
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sven Heinicke
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mark Schroeder
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kara J Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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6
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Nguyen THM, Tinz-Burdick A, Lenhardt M, Geertz M, Ramirez F, Schwartz M, Toledano M, Bonney B, Gaebler B, Liu W, Wolters JF, Chiu K, Fiumera AC, Fiumera HL. Mapping mitonuclear epistasis using a novel recombinant yeast population. PLoS Genet 2023; 19:e1010401. [PMID: 36989278 PMCID: PMC10085025 DOI: 10.1371/journal.pgen.1010401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 04/10/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic variation in mitochondrial and nuclear genomes can perturb mitonuclear interactions and lead to phenotypic differences between individuals and populations. Despite their importance to most complex traits, it has been difficult to identify the interacting mitonuclear loci. Here, we present a novel advanced intercrossed population of Saccharomyces cerevisiae yeasts, called the Mitonuclear Recombinant Collection (MNRC), designed explicitly for detecting mitonuclear loci contributing to complex traits. For validation, we focused on mapping genes that contribute to the spontaneous loss of mitochondrial DNA (mtDNA) that leads to the petite phenotype in yeast. We found that rates of petite formation in natural populations are variable and influenced by genetic variation in nuclear DNA, mtDNA and mitonuclear interactions. We mapped nuclear and mitonuclear alleles contributing to mtDNA stability using the MNRC by integrating a term for mitonuclear epistasis into a genome-wide association model. We found that the associated mitonuclear loci play roles in mitotic growth most likely responding to retrograde signals from mitochondria, while the associated nuclear loci with main effects are involved in genome replication. We observed a positive correlation between growth rates and petite frequencies, suggesting a fitness tradeoff between mitotic growth and mtDNA stability. We also found that mtDNA stability was correlated with a mobile mitochondrial GC-cluster that is present in certain populations of yeast and that selection for nuclear alleles that stabilize mtDNA may be rapidly occurring. The MNRC provides a powerful tool for identifying mitonuclear interacting loci that will help us to better understand genotype-phenotype relationships and coevolutionary trajectories.
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Affiliation(s)
- Tuc H M Nguyen
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
- Department of Biological Sciences, New York University, New York, New York, United States of America
| | - Austen Tinz-Burdick
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Meghan Lenhardt
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Margaret Geertz
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Franchesca Ramirez
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Mark Schwartz
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Michael Toledano
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Brooke Bonney
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Benjamin Gaebler
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Weiwei Liu
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - John F Wolters
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Kenneth Chiu
- Department of Computer Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Anthony C Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
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7
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Chen L, Li Z, Zeng T, Zhang YH, Li H, Huang T, Cai YD. Predicting gene phenotype by multi-label multi-class model based on essential functional features. Mol Genet Genomics 2021; 296:905-918. [PMID: 33914130 DOI: 10.1007/s00438-021-01789-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/13/2021] [Indexed: 12/19/2022]
Abstract
Phenotype is one of the most significant concepts in genetics, which is used to describe all the characteristics of a research object that can be observed. Considering that phenotype reflects the integrated features of genotype and environment factors, it is hard to define phenotype characteristics, even difficult to predict unknown phenotypes. Restricted by current biological techniques, it is still quite expensive and time-consuming to obtain sufficient structural information of large-scale phenotype-associated genes/proteins. Various bioinformatics methods have been presented to solve such problem, and researchers have confirmed the efficacy and prediction accuracy of functional network-based prediction. But general functional descriptions have highly complicated inner structures for phenotype prediction. To further address this issue and improve the efficacy of phenotype prediction on more than ten kinds of phenotypes, we first extract functional enrichment features from GO and KEGG, and then use node2vec to learn functional embedding features of genes from a gene-gene network. All these features are analyzed by some feature selection methods (Boruta, minimum redundancy maximum relevance) to generate a feature list. Such list is fed into the incremental feature selection, incorporating some multi-label classifiers built by RAkEL and some classic base classifiers, to build an optimum multi-label multi-class classification model for phenotype prediction. According to recent researches, our method has indeed identified many literature-supported genes/proteins and their associated phenotypes, and even some candidate genes with re-assigned new phenotypes, which provide a new computational tool for the accurate and effective phenotypic prediction.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China.,College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People's Republic of China
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, 130052, People's Republic of China
| | - Tao Zeng
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, 130052, People's Republic of China
| | - Tao Huang
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China.
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8
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Stenger M, Le DT, Klecker T, Westermann B. Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae. MICROBIAL CELL 2020; 7:234-249. [PMID: 32904421 PMCID: PMC7453639 DOI: 10.15698/mic2020.09.729] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The production of metabolic energy in form of ATP by oxidative phosphorylation depends on the coordinated action of hundreds of nuclear-encoded mitochondrial proteins and a handful of proteins encoded by the mitochondrial genome (mtDNA). We used the yeast Saccharomyces cerevisiae as a model system to systematically identify the genes contributing to this process. Integration of genome-wide high-throughput growth assays with previously published large data sets allowed us to define with high confidence a set of 254 nuclear genes that are indispensable for respiratory growth. Next, we induced loss of mtDNA in the yeast deletion collection by growth on ethidium bromide-containing medium and identified twelve genes that are essential for viability in the absence of mtDNA (i.e. petite-negative). Replenishment of mtDNA by cytoduction showed that respiratory-deficient phenotypes are highly variable in many yeast mutants. Using a mitochondrial genome carrying a selectable marker, ARG8m, we screened for mutants that are specifically defective in maintenance of mtDNA and mitochondrial protein synthesis. We found that up to 176 nuclear genes are required for expression of mitochondria-encoded proteins during fermentative growth. Taken together, our data provide a comprehensive picture of the molecular processes that are required for respiratory metabolism in a simple eukaryotic cell.
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Affiliation(s)
- Maria Stenger
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Duc Tung Le
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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9
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Clowers KJ, Will JL, Gasch AP. A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Mol Ecol 2015; 24:5886-98. [PMID: 26518477 PMCID: PMC4824287 DOI: 10.1111/mec.13439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 12/24/2022]
Abstract
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of S. cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak × vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases, the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche.
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Affiliation(s)
- Katie J Clowers
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Jessica L Will
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, 53706, USA
- Great Lakes Bioenergy Research Center, 1552 University Ave., Madison, WI, 53704, USA
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10
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Cary GA, Vinh DBN, May P, Kuestner R, Dudley AM. Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly. G3 (BETHESDA, MD.) 2015; 5:2497-511. [PMID: 26392412 PMCID: PMC4632068 DOI: 10.1534/g3.115.021444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/16/2015] [Indexed: 12/18/2022]
Abstract
P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci when cells are exposed to stress. Although the conserved mRNA decay and translational repression machineries are known components of PB, how and why cells assemble RNP complexes into large foci remain unclear. Using mass spectrometry to analyze proteins immunoisolated with the core PB protein Dhh1, we show that a considerable number of proteins contain low-complexity sequences, similar to proteins highly represented in mammalian RNP granules. We also show that the Hsp40 chaperone Ydj1, which contains an low-complexity domain and controls prion protein aggregation, is required for the formation of Dhh1-GFP foci on glucose depletion. New classes of proteins that reproducibly coenrich with Dhh1-GFP during PB induction include proteins involved in nucleotide or amino acid metabolism, glycolysis, transfer RNA aminoacylation, and protein folding. Many of these proteins have been shown to form foci in response to other stresses. Finally, analysis of RNA associated with Dhh1-GFP shows enrichment of mRNA encoding the PB protein Pat1 and catalytic RNAs along with their associated mitochondrial RNA-binding proteins. Thus, global characterization of PB composition has uncovered proteins important for PB assembly and evidence suggesting an active role for RNA in PB function.
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Affiliation(s)
- Gregory A Cary
- Institute for Systems Biology, Seattle, Washington 98109 Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Dani B N Vinh
- Institute for Systems Biology, Seattle, Washington 98109
| | - Patrick May
- Institute for Systems Biology, Seattle, Washington 98109 Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Esch-sur-Alzette, Luxembourg L-4362
| | - Rolf Kuestner
- Institute for Systems Biology, Seattle, Washington 98109
| | - Aimée M Dudley
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195 Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
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11
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Tigano M, Ruotolo R, Dallabona C, Fontanesi F, Barrientos A, Donnini C, Ottonello S. Elongator-dependent modification of cytoplasmic tRNALysUUU is required for mitochondrial function under stress conditions. Nucleic Acids Res 2015; 43:8368-80. [PMID: 26240381 PMCID: PMC4787798 DOI: 10.1093/nar/gkv765] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 07/15/2015] [Indexed: 11/12/2022] Open
Abstract
To gain a wider view of the pathways that regulate mitochondrial function, we combined the effect of heat stress on respiratory capacity with the discovery potential of a genome-wide screen in Saccharomyces cerevisiae. We identified 105 new genes whose deletion impairs respiratory growth at 37°C by interfering with processes such as transcriptional regulation, ubiquitination and cytosolic tRNA wobble uridine modification via 5-methoxycarbonylmethyl-2-thiouridine formation. The latter process, specifically required for efficient decoding of AA-ending codons under stress conditions, was covered by multiple genes belonging to the Elongator (e.g. ELP3) and urmylation (e.g., NCS6) pathways. ELP3 or NCS6 deletants had impaired mitochondrial protein synthesis. Their respiratory deficiency was selectively rescued by overexpression of tRNA(Lys) UUU as well by overexpression of genes (BCK1 and HFM1) with a strong bias for the AAA codon read by this tRNA. These data extend the mitochondrial regulome, demonstrate that heat stress can impair respiration by disturbing cytoplasmic translation of proteins critically involved in mitochondrial function and document, for the first time, the involvement in such process of the Elongator and urmylation pathways. Given the conservation of these pathways, the present findings may pave the way to a better understanding of the human mitochondrial regulome in health and disease.
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Affiliation(s)
- Marco Tigano
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Roberta Ruotolo
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | | | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Claudia Donnini
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Simone Ottonello
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
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12
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Abstract
The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MATa and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general.
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13
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Callegari S, McKinnon RA, Andrews S, de Barros Lopes MA. The MEF2
gene is essential for yeast longevity, with a dual role in cell respiration and maintenance of mitochondrial membrane potential. FEBS Lett 2011; 585:1140-6. [DOI: 10.1016/j.febslet.2011.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/25/2011] [Accepted: 03/10/2011] [Indexed: 10/18/2022]
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14
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Watts T, Khalimonchuk O, Wolf RZ, Turk EM, Mohr G, Winge DR. Mne1 is a novel component of the mitochondrial splicing apparatus responsible for processing of a COX1 group I intron in yeast. J Biol Chem 2011; 286:10137-46. [PMID: 21257754 DOI: 10.1074/jbc.m110.205625] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Saccharomyces cerevisiae cells lacking Mne1 are deficient in intron splicing in the gene encoding the Cox1 subunit of cytochrome oxidase but contain wild-type levels of the bc(1) complex. Thus, Mne1 has no role in splicing of COB introns or expression of the COB gene. Northern experiments suggest that splicing of the COX1 aI5β intron is dependent on Mne1 in addition to the previously known Mrs1, Mss116, Pet54, and Suv3 factors. Processing of the aI5β intron is similarly impaired in mne1Δ and mrs1Δ cells and overexpression of Mrs1 partially restores the respiratory function of mne1Δ cells. Mrs1 is known to function in the initial transesterification reaction of splicing. Mne1 is a mitochondrial matrix protein loosely associated with the inner membrane and is found in a high mass ribonucleoprotein complex specifically associated with the COX1 mRNA even within an intronless strain. Mne1 does not appear to have a secondary function in COX1 processing or translation, because disruption of MNE1 in cells containing intronless mtDNA does not lead to a respiratory growth defect. Thus, the primary defect in mne1Δ cells is splicing of the aI5β intron in COX1.
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Affiliation(s)
- Talina Watts
- Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA
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15
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Barnes VL, Strunk BS, Lee I, Hüttemann M, Pile LA. Loss of the SIN3 transcriptional corepressor results in aberrant mitochondrial function. BMC BIOCHEMISTRY 2010; 11:26. [PMID: 20618965 PMCID: PMC2909972 DOI: 10.1186/1471-2091-11-26] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 07/09/2010] [Indexed: 11/17/2022]
Abstract
BACKGROUND SIN3 is a transcriptional repressor protein known to regulate many genes, including a number of those that encode mitochondrial components. RESULTS By monitoring RNA levels, we find that loss of SIN3 in Drosophila cultured cells results in up-regulation of not only nuclear encoded mitochondrial genes, but also those encoded by the mitochondrial genome. The up-regulation of gene expression is accompanied by a perturbation in ATP levels in SIN3-deficient cells, suggesting that the changes in mitochondrial gene expression result in altered mitochondrial activity. In support of the hypothesis that SIN3 is necessary for normal mitochondrial function, yeast sin3 null mutants exhibit very poor growth on non-fermentable carbon sources and show lower levels of ATP and reduced respiration rates. CONCLUSIONS The findings that both yeast and Drosophila SIN3 affect mitochondrial activity suggest an evolutionarily conserved role for SIN3 in the control of cellular energy production.
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Affiliation(s)
- Valerie L Barnes
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, Michigan 48202, USA
| | - Bethany S Strunk
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, Michigan 48202, USA
- Chemical Biology, University of Michigan, 930 N. University Ave. Rm. 4250, Ann Arbor, Michigan 48109, USA
| | - Icksoo Lee
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield, Detroit, Michigan 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield, Detroit, Michigan 48201, USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, Michigan 48202, USA
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16
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Merz S, Westermann B. Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae. Genome Biol 2009; 10:R95. [PMID: 19751518 PMCID: PMC2768984 DOI: 10.1186/gb-2009-10-9-r95] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 09/14/2009] [Indexed: 12/13/2022] Open
Abstract
A genome-wide deletion mutant analysis in budding yeast reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis. Background The mitochondrial respiratory chain produces metabolic energy by oxidative phosphorylation. Biogenesis of the respiratory chain requires the coordinated expression of two genomes: the nuclear genome encoding the vast majority of mitochondrial proteins, and the mitochondrial genome encoding a handful of mitochondrial proteins. The understanding of the molecular processes contributing to respiratory chain assembly and maintenance requires the systematic identification and functional analysis of the genes involved. Results We pursued a systematic, genome-wide approach to define the sets of genes required for respiratory activity and maintenance and expression of the mitochondrial genome in yeast. By comparative gene deletion analysis we found an unexpected phenotypic plasticity among respiratory-deficient mutants, and we identified ten previously uncharacterized genes essential for respiratory growth (RRG1 through RRG10). Systematic functional analysis of 319 respiratory-deficient mutants revealed 16 genes essential for maintenance of the mitochondrial genome, 88 genes required for mitochondrial protein translation, and 10 genes required for expression of specific mitochondrial gene products. A group of mutants acquiring irreversible damage compromising respiratory capacity includes strains defective in assembly of the cytochrome c oxidase that were found to be particularly sensitive to aging. Conclusions These data advance the understanding of the molecular processes contributing to maintenance of the mitochondrial genome, mitochondrial protein translation, and assembly of the respiratory chain. They revealed a number of previously uncharacterized components, and provide a comprehensive picture of the molecular processes required for respiratory activity in a simple eukaryotic cell.
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Affiliation(s)
- Sandra Merz
- Institut für Zellbiologie, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany.
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17
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Ccm1p/Ygr150cp, a pentatricopeptide repeat protein, is essential to remove the fourth intron of both COB and COX1 pre-mRNAs in Saccharomyces cerevisiae. Curr Genet 2009; 55:475-84. [PMID: 19562342 DOI: 10.1007/s00294-009-0260-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/11/2009] [Accepted: 06/13/2009] [Indexed: 10/20/2022]
Abstract
YGR150C gene product (Ygr150cp) is one of the three mitochondrially located Saccharomyces cerevisiae proteins with pentatricopeptide repeat (PPR) motifs. Ygr150cp is essential for mitochondrial functionality but its molecular targets are still unknown. This study was undertaken to define the role of Ygr150cp in mitochondria biogenesis. Repression of Ygr150cp expression in complemented mutants prevented their use of glycerol or lactate, but allowed limited growth on ethanol-containing medium. RNA hybridization studies showed that Deltaygr150c meiotic segregants produced COB and COX1 transcripts but failed to process them into the mature forms. Detailed RT-PCR assays revealed that Deltaygr150c specifically failed to remove the fourth intron of both COB and COX1 pre-mRNAs while all other group I introns were excised. Expression of Ygr150cp mutants without any of the PPR motifs did not complement the growth phenotype. Accordingly, we designate YGR150C as CCM1 (COB and COX1 mRNA maturation). This report provides the first evidence of PPR protein involvement in the specific removal of group I introns in mitochondria of S. cerevisiae.
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18
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Zhao J, Lambowitz AM. A bacterial group II intron-encoded reverse transcriptase localizes to cellular poles. Proc Natl Acad Sci U S A 2005; 102:16133-40. [PMID: 16186487 PMCID: PMC1283441 DOI: 10.1073/pnas.0507057102] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Lactococcus lactis Ll.LtrB group II intron encodes a reverse transcriptase (LtrA protein) that binds the intron RNA to promote RNA splicing and intron mobility. Here, we used LtrA-GFP fusions and immunofluorescence microscopy to show that LtrA localizes to cellular poles in Escherichia coli and Lactococcus lactis. This polar localization occurs with or without coexpression of Ll.LtrB intron RNA, is observed over a wide range of cellular growth rates and expression levels, and is independent of replication origin function. The same localization pattern was found for three nonoverlapping LtrA subsegments, possibly reflecting dependence on common redundant signals and/or protein physical properties. When coexpressed in E. coli, LtrA interferes with the polar localization of the Shigella IcsA protein, which mediates polarized actin tail assembly, suggesting competition for a common localization determinant. The polar localization of LtrA could account for the preferential insertion of the Ll.LtrB intron in the origin and terminus regions of the E. coli chromosome, may facilitate access to exposed DNA in these regions, and could potentially link group II intron mobility to the host DNA replication and/or cell division machinery.
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Affiliation(s)
- Junhua Zhao
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
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