1
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Polo Rivera C, Deegan TD, Labib KPM. CMG helicase disassembly is essential and driven by two pathways in budding yeast. EMBO J 2024:10.1038/s44318-024-00161-x. [PMID: 39039287 DOI: 10.1038/s44318-024-00161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/24/2024] Open
Abstract
The CMG helicase is the stable core of the eukaryotic replisome and is ubiquitylated and disassembled during DNA replication termination. Fungi and animals use different enzymes to ubiquitylate the Mcm7 subunit of CMG, suggesting that CMG ubiquitylation arose repeatedly during eukaryotic evolution. Until now, it was unclear whether cells also have ubiquitin-independent pathways for helicase disassembly and whether CMG disassembly is essential for cell viability. Using reconstituted assays with budding yeast CMG, we generated the mcm7-10R allele that compromises ubiquitylation by SCFDia2. mcm7-10R delays helicase disassembly in vivo, driving genome instability in the next cell cycle. These data indicate that defective CMG ubiquitylation explains the major phenotypes of cells lacking Dia2. Notably, the viability of mcm7-10R and dia2∆ is dependent upon the related Rrm3 and Pif1 DNA helicases that have orthologues in all eukaryotes. We show that Rrm3 acts during S-phase to disassemble old CMG complexes from the previous cell cycle. These findings indicate that CMG disassembly is essential in yeast cells and suggest that Pif1-family helicases might have mediated CMG disassembly in ancestral eukaryotes.
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Affiliation(s)
- Cristian Polo Rivera
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom D Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Karim P M Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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2
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Shao M, Wang P, Gou H, Ma Z, Chen B, Mao J. Identification and Expression Analysis of the SKP1-Like Gene Family under Phytohormone and Abiotic Stresses in Apple ( Malus domestica). Int J Mol Sci 2023; 24:16414. [PMID: 38003604 PMCID: PMC10671573 DOI: 10.3390/ijms242216414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Ubiquitination participates in plant hormone signaling and stress response to adversity. SKP1-Like, a core component of the SCF (Skp1-Cullin-F-box) complex, is the final step in catalyzing the ubiquitin-mediated protein degradation pathway. However, the SKP1-Like gene family has not been well characterized in response to apple abiotic stresses and hormonal treatments. This study revealed that 17 MdSKP1-Like gene family members with the conserved domain of SKP1 were identified in apples and were unevenly distributed on eight chromosomes. The MdSKP1-Like genes located on chromosomes 1, 10, and 15 were highly homologous. The MdSKP1-like genes were divided into three subfamilies according to the evolutionary affinities of monocotyledons and dicotyledons. MdSKP1-like members of the same group or subfamily show some similarity in gene structure and conserved motifs. The predicted results of protein interactions showed that members of the MdSKP1-like family have strong interactions with members of the F-Box family of proteins. A selection pressure analysis showed that MdSKP1-Like genes were in purifying selection. A chip data analysis showed that MdSKP1-like14 and MdSKP1-like15 were higher in flowers, whereas MdSKP1-like3 was higher in fruits. The upstream cis-elements of MdSKP1-Like genes contained a variety of elements related to light regulation, drought, low temperature, and many hormone response elements, etc. Meanwhile, qRT-PCR also confirmed that the MdSKP1-Like gene is indeed involved in the response of the apple to hormonal and abiotic stress treatments. This research provides evidence for regulating MdSKP1-Like gene expression in response to hormonal and abiotic stresses to improve apple stress resistance.
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Affiliation(s)
| | | | | | | | | | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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3
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Guzman UH, Aksnes H, Ree R, Krogh N, Jakobsson ME, Jensen LJ, Arnesen T, Olsen JV. Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae. Nat Commun 2023; 14:4517. [PMID: 37500638 PMCID: PMC10374663 DOI: 10.1038/s41467-023-40224-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Protein N-terminal (Nt) acetylation is one of the most abundant modifications in eukaryotes, covering ~50-80 % of the proteome, depending on species. Cells with defective Nt-acetylation display a wide array of phenotypes such as impaired growth, mating defects and increased stress sensitivity. However, the pleiotropic nature of these effects has hampered our understanding of the functional impact of protein Nt-acetylation. The main enzyme responsible for Nt-acetylation throughout the eukaryotic kingdom is the N-terminal acetyltransferase NatA. Here we employ a multi-dimensional proteomics approach to analyze Saccharomyces cerevisiae lacking NatA activity, which causes global proteome remodeling. Pulsed-SILAC experiments reveals that NatA-deficient strains consistently increase degradation of ribosomal proteins compared to wild type. Explaining this phenomenon, thermal proteome profiling uncovers decreased thermostability of ribosomes in NatA-knockouts. Our data are in agreement with a role for Nt-acetylation in promoting stability for parts of the proteome by enhancing the avidity of protein-protein interactions and folding.
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Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Magnus E Jakobsson
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Biosciences, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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4
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James SW, Palmer J, Keller NP, Brown ML, Dunworth MR, Francisco SG, Watson KG, Titchen B, Achimovich A, Mahoney A, Artemiou JP, Buettner KG, Class M, Sydenstricker AL, Anglin SL. A reciprocal translocation involving Aspergillus nidulans snxAHrb1/Gbp2 and gyfA uncovers a new regulator of the G2-M transition and reveals a role in transcriptional repression for the setBSet2 histone H3-lysine-36 methyltransferase. Genetics 2022; 222:iyac130. [PMID: 36005881 PMCID: PMC9526064 DOI: 10.1093/genetics/iyac130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
Aspergillus nidulans snxA, an ortholog of Saccharomyces cerevisiae Hrb1/Gbp2 messenger RNA shuttle proteins, is-in contrast to budding yeast-involved in cell cycle regulation, in which snxA1 and snxA2 mutations as well as a snxA deletion specifically suppress the heat sensitivity of mutations in regulators of the CDK1 mitotic induction pathway. snxA mutations are strongly cold sensitive, and at permissive temperature snxA mRNA and protein expression are strongly repressed. Initial attempts to identify the causative snxA mutations revealed no defects in the SNXA protein. Here, we show that snxA1/A2 mutations resulted from an identical chromosome I-II reciprocal translocation with breakpoints in the snxA first intron and the fourth exon of a GYF-domain gene, gyfA. Surprisingly, a gyfA deletion and a reconstructed gyfA translocation allele suppressed the heat sensitivity of CDK1 pathway mutants in a snxA+ background, demonstrating that 2 unrelated genes, snxA and gyfA, act through the CDK1-CyclinB axis to restrain the G2-M transition, and for the first time identifying a role in G2-M regulation for a GYF-domain protein. To better understand snxA1/A2-reduced expression, we generated suppressors of snxA cold sensitivity in 2 genes: (1) loss of the abundant nucleolar protein Nsr1/nucleolin bypassed the requirement for snxA and (2) loss of the Set2 histone H3 lysine36 (H3K36) methyltransferase or a nonmethylatable histone H3K36L mutant rescued hypomorphic snxA mutants by restoring full transcriptional proficiency, indicating that methylation of H3K36 acts normally to repress snxA transcription. These observations are in line with known Set2 functions in preventing excessive and cryptic transcription of active genes.
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Affiliation(s)
- Steven W James
- Department of Biology, Gettysburg College, Gettysburg, PA 17325, USA
| | - Jonathan Palmer
- Data Analytics, Genencor Technology Center, IFF, Palo Alto, CA, 94306, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Morgan L Brown
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Dunworth
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Sarah G Francisco
- Department of Otolaryngology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Katherine G Watson
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, USA
| | - Breanna Titchen
- Department of Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Alecia Achimovich
- Department of Chemistry, Gettysburg College, Gettysburg, PA 17325, USA
| | - Andrew Mahoney
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | - Kyra G Buettner
- School of Medicine, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Madelyn Class
- School of Medicine, Temple University, Philadelphia, PA 19140, USA
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5
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Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T, Knop M. Up-regulation of ubiquitin-proteasome activity upon loss of NatA-dependent N-terminal acetylation. Life Sci Alliance 2021; 5:5/2/e202000730. [PMID: 34764209 PMCID: PMC8605321 DOI: 10.26508/lsa.202000730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Inactivation of N-terminal acetyltransferase A is found to alter Rpn4 as well as E3 ligase abundance, causing up-regulation of Ubiquitin–proteasome activity. In this context, Tom1 is also identified as a novel chain-elongating enzyme of the UFD-pathway. N-terminal acetylation is a prominent protein modification, and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system, we observed increased ubiquitin proteasome system activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin–independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain-elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11, K29, and K48 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christian Reinbold
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Laura Armbruster
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany .,Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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6
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Dhakal S, Macreadie I. Protein Homeostasis Networks and the Use of Yeast to Guide Interventions in Alzheimer's Disease. Int J Mol Sci 2020; 21:E8014. [PMID: 33126501 PMCID: PMC7662794 DOI: 10.3390/ijms21218014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's Disease (AD) is a progressive multifactorial age-related neurodegenerative disorder that causes the majority of deaths due to dementia in the elderly. Although various risk factors have been found to be associated with AD progression, the cause of the disease is still unresolved. The loss of proteostasis is one of the major causes of AD: it is evident by aggregation of misfolded proteins, lipid homeostasis disruption, accumulation of autophagic vesicles, and oxidative damage during the disease progression. Different models have been developed to study AD, one of which is a yeast model. Yeasts are simple unicellular eukaryotic cells that have provided great insights into human cell biology. Various yeast models, including unmodified and genetically modified yeasts, have been established for studying AD and have provided significant amount of information on AD pathology and potential interventions. The conservation of various human biological processes, including signal transduction, energy metabolism, protein homeostasis, stress responses, oxidative phosphorylation, vesicle trafficking, apoptosis, endocytosis, and ageing, renders yeast a fascinating, powerful model for AD. In addition, the easy manipulation of the yeast genome and availability of methods to evaluate yeast cells rapidly in high throughput technological platforms strengthen the rationale of using yeast as a model. This review focuses on the description of the proteostasis network in yeast and its comparison with the human proteostasis network. It further elaborates on the AD-associated proteostasis failure and applications of the yeast proteostasis network to understand AD pathology and its potential to guide interventions against AD.
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Affiliation(s)
| | - Ian Macreadie
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia;
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7
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Exploring the Complexity of Protein-Level Dosage Compensation that Fine-Tunes Stoichiometry of Multiprotein Complexes. PLoS Genet 2020; 16:e1009091. [PMID: 33112847 PMCID: PMC7652333 DOI: 10.1371/journal.pgen.1009091] [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: 07/18/2019] [Revised: 11/09/2020] [Accepted: 08/31/2020] [Indexed: 11/19/2022] Open
Abstract
Proper control of gene expression levels upon various perturbations is a fundamental aspect of cellular robustness. Protein-level dosage compensation is one mechanism buffering perturbations to stoichiometry of multiprotein complexes through accelerated proteolysis of unassembled subunits. Although N-terminal acetylation- and ubiquitin-mediated proteasomal degradation by the Ac/N-end rule pathway enables selective compensation of excess subunits, it is unclear how widespread this pathway contributes to stoichiometry control. Here we report that dosage compensation depends only partially on the Ac/N-end rule pathway. Our analysis of genetic interactions between 18 subunits and 12 quality control factors in budding yeast demonstrated that multiple E3 ubiquitin ligases and N-acetyltransferases are involved in dosage compensation. We find that N-acetyltransferases-mediated compensation is not simply predictable from N-terminal sequence despite their sequence specificity for N-acetylation. We also find that the compensation of Pop3 and Bet4 is due in large part to a minor N-acetyltransferase NatD. Furthermore, canonical NatD substrates histone H2A/H4 were compensated even in its absence, suggesting N-acetylation-independent stoichiometry control. Our study reveals the complexity and robustness of the stoichiometry control system. Quality control of multiprotein complexes is important for maintaining homeostasis in cellular systems that are based on functional complexes. Proper stoichiometry of multiprotein complexes is achieved by the balance between protein synthesis and degradation. Recent studies showed that translation efficiency tends to scale with stoichiometry of their subunits. On the other hand, although protein N-terminal acetylation- and ubiquitin-mediated proteolysis pathway is involved in selective degradation of excess subunits, it is unclear how widespread this pathway contributes to stoichiometry control due to the lack of a systematic investigation using endogenous proteins. To better understand the landscape of the stoichiometry control system, we examined genetic interactions between 18 subunits and 12 quality control factors (E3 ubiquitin ligases and N-acetyltransferases), in total 114 combinations. Our data suggest that N-acetyltransferases are partially responsible for stoichiometry control and that N-acetylation-independent pathway is also involved in selective degradation of excess subunits. Therefore, this study reveals the complexity and robustness of the stoichiometry control system. Further dissection of this complexity will help to understand the mechanisms buffering gene expression perturbations and shaping proteome stoichiometry.
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8
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Yao M, Rahman SU, Wang A, Ma T, Raza SHA, Mehmood R, Liu Y, Tao S. Evolutionary Analysis of the F-Box Gene Family in Saccharomycetaceae. DNA Cell Biol 2019; 38:333-340. [PMID: 30801225 DOI: 10.1089/dna.2018.4271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
F-box proteins are a core component of Skp1-Cul1-F-box (SCF) ubiquitin/ligase complexes and are involved in a lot of cellular processes in yeasts. However, the current knowledge of the molecular evolution of the F-box gene family in yeasts remains unclear. In this study, 136 F-box genes were identified in 10 yeast species of the Saccharomycetaceae. In addition to the F-box domain, the other six domains were identified in these F-box proteins. The evolutionary history of F-box gene numbers in 10 Saccharomycetaceae yeasts was reconstructed. Whole-genome duplication, interspersed repeats, and gene loss events were inferred. These events contributed to F-box gene number variation in the 10 yeast species. Eighty-seven and 33 positively selected sites were detected in program Selecton and Datamonkey web-server, respectively. Three of them were considered the significant positively selected sites, and 23 of them had changed radically in amino acid properties by using TreeSAAP. We investigated F-box gene number variation and underlying mechanisms, and selection patterns, all of which were beneficial to deeply understand genome evolution and figure out the function of the F-box proteins.
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Affiliation(s)
- Mingyue Yao
- 1 College of Enology, Northwest A&F University, Yangling, China
| | - Siddiq Ur Rahman
- 2 State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
- 3 Bioinformatics Center, Northwest A&F University, Yangling, China
- 4 Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Ailan Wang
- 2 State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
- 3 Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Tao Ma
- 1 College of Enology, Northwest A&F University, Yangling, China
| | | | - Rashid Mehmood
- 6 Department of Computer Sciences and Information Technology, University of Kotli, Kotli, Pakistan
| | - Yanlin Liu
- 1 College of Enology, Northwest A&F University, Yangling, China
| | - Shiheng Tao
- 2 State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
- 3 Bioinformatics Center, Northwest A&F University, Yangling, China
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9
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Control of Eukaryotic DNA Replication Initiation-Mechanisms to Ensure Smooth Transitions. Genes (Basel) 2019; 10:genes10020099. [PMID: 30700044 PMCID: PMC6409694 DOI: 10.3390/genes10020099] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/06/2023] Open
Abstract
DNA replication differs from most other processes in biology in that any error will irreversibly change the nature of the cellular progeny. DNA replication initiation, therefore, is exquisitely controlled. Deregulation of this control can result in over-replication characterized by repeated initiation events at the same replication origin. Over-replication induces DNA damage and causes genomic instability. The principal mechanism counteracting over-replication in eukaryotes is a division of replication initiation into two steps—licensing and firing—which are temporally separated and occur at distinct cell cycle phases. Here, we review this temporal replication control with a specific focus on mechanisms ensuring the faultless transition between licensing and firing phases.
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10
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Niekamp JM, Evans MD, Scott AR, Smaldino PJ, Rubenstein EM. TOM1 confers resistance to the aminoglycoside hygromycin B in Saccharomyces cerevisiae. MICROPUBLICATION BIOLOGY 2019; 2019:10.17912/micropub.biology.000193. [PMID: 32083242 PMCID: PMC7031815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Julia M Niekamp
- Ball State University, Department of Biology, Muncie, IN 47306
| | - Melissa D Evans
- Ball State University, Department of Biology, Muncie, IN 47306
| | - Abigail R Scott
- Ball State University, Department of Biology, Muncie, IN 47306
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11
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Nakatsukasa K, Sone M, Alemayehu DH, Okumura F, Kamura T. The HECT-type ubiquitin ligase Tom1 contributes to the turnover of Spo12, a component of the FEAR network, in G2/M phase. FEBS Lett 2018; 592:1716-1724. [PMID: 29683484 DOI: 10.1002/1873-3468.13066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 11/11/2022]
Abstract
The ubiquitin-proteasome system plays a crucial role in cell cycle progression. A previous study suggested that Spo12, a component of the Cdc14 early anaphase release (FEAR) network, is targeted for degradation by the APC/CCdh1 complex in G1 phase. In the present study, we demonstrate that the Hect-type ubiquitin ligase Tom1 contributes to the turnover of Spo12 in G2/M phase. Coimmunoprecipitation analysis confirmed that Tom1 and Spo12 interact. Overexpression of Spo12 is cytotoxic in the absence of Tom1. Notably, Spo12 is degraded in S phase even in the absence of Tom1 and Cdh1, suggesting that an additional E3 ligase(s) also mediates Spo12 degradation. Together, we propose that several distinct degradation pathways control the level of Spo12 during the cell cycle.
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Affiliation(s)
- Kunio Nakatsukasa
- Division of Biological Science, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Megumi Sone
- Division of Biological Science, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Dawit Hailu Alemayehu
- Division of Biological Science, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Fumihiko Okumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Takumi Kamura
- Division of Biological Science, Graduate School of Science, Nagoya University, Aichi, Japan
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12
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Nair SC, Xu R, Pattaradilokrat S, Wu J, Qi Y, Zilversmit M, Ganesan S, Nagarajan V, Eastman RT, Orandle MS, Tan JC, Myers TG, Liu S, Long CA, Li J, Su XZ. A Plasmodium yoelii HECT-like E3 ubiquitin ligase regulates parasite growth and virulence. Nat Commun 2017; 8:223. [PMID: 28790316 PMCID: PMC5548792 DOI: 10.1038/s41467-017-00267-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/12/2017] [Indexed: 01/18/2023] Open
Abstract
Infection of mice with strains of Plasmodium yoelii parasites can result in different pathology, but molecular mechanisms to explain this variation are unclear. Here we show that a P. yoelii gene encoding a HECT-like E3 ubiquitin ligase (Pyheul) influences parasitemia and host mortality. We genetically cross two lethal parasites with distinct disease phenotypes, and identify 43 genetically diverse progeny by typing with microsatellites and 9230 single-nucleotide polymorphisms. A genome-wide quantitative trait loci scan links parasite growth and host mortality to two major loci on chromosomes 1 and 7 with LOD (logarithm of the odds) scores = 6.1 and 8.1, respectively. Allelic exchange of partial sequences of Pyheul in the chromosome 7 locus and modification of the gene expression alter parasite growth and host mortality. This study identifies a gene that may have a function in parasite growth, virulence, and host–parasite interaction, and therefore could be a target for drug or vaccine development. Many strains of Plasmodium differ in virulence, but factors that control these distinctions are not known. Here the authors comparatively map virulence loci using the offspring from a P. yoelii YM and N67 genetic cross, and identify a putative HECT E3 ubiquitin ligase that may explain the variance.
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Affiliation(s)
- Sethu C Nair
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ruixue Xu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Sittiporn Pattaradilokrat
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yanwei Qi
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Martine Zilversmit
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard T Eastman
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marlene S Orandle
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John C Tan
- The Eck Institute of Global Health, Department of Biological Sciences, University of Notre Dame, Indiana, 46556, USA
| | - Timothy G Myers
- Genomic Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shengfa Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Carole A Long
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Xin-Zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA. .,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China.
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13
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Defenouillère Q, Namane A, Mouaikel J, Jacquier A, Fromont-Racine M. The ribosome-bound quality control complex remains associated to aberrant peptides during their proteasomal targeting and interacts with Tom1 to limit protein aggregation. Mol Biol Cell 2017; 28:1165-1176. [PMID: 28298488 PMCID: PMC5415013 DOI: 10.1091/mbc.e16-10-0746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 11/16/2022] Open
Abstract
The RQC complex involved in protein quality control mechanisms also exists as a ribosome-unbound complex during the escort of aberrant peptides to the proteasome. The E3 ubiquitin ligase Tom1 is a newly identified partner of this light version of the RQC complex and is required for aggregate prevention. Protein quality control mechanisms eliminate defective polypeptides to ensure proteostasis and to avoid the toxicity of protein aggregates. In eukaryotes, the ribosome-bound quality control (RQC) complex detects aberrant nascent peptides that remain stalled in 60S ribosomal particles due to a dysfunction in translation termination. The RQC complex polyubiquitylates aberrant polypeptides and recruits a Cdc48 hexamer to extract them from 60S particles in order to escort them to the proteasome for degradation. Whereas the steps from stalled 60S recognition to aberrant peptide polyubiquitylation by the RQC complex have been described, the mechanism leading to proteasomal degradation of these defective translation products remains unknown. We show here that the RQC complex also exists as a ribosome-unbound complex during the escort of aberrant peptides to the proteasome. In addition, we identify a new partner of this light version of the RQC complex, the E3 ubiquitin ligase Tom1. Tom1 interacts with aberrant nascent peptides and is essential to limit their accumulation and aggregation in the absence of Rqc1; however, its E3 ubiquitin ligase activity is not required. Taken together, these results reveal new roles for Tom1 in protein quality control, aggregate prevention, and, therefore, proteostasis maintenance.
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Affiliation(s)
- Quentin Defenouillère
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France.,Sorbonne Universités, UPMC Paris 6, Complexité Du Vivant, 75252 Paris Cedex 05, France
| | - Abdelkader Namane
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - John Mouaikel
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - Alain Jacquier
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
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14
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Al-Zain A, Schroeder L, Sheglov A, Ikui AE. Cdc6 degradation requires phosphodegron created by GSK-3 and Cdk1 for SCFCdc4 recognition in Saccharomyces cerevisiae. Mol Biol Cell 2015. [PMID: 25995377 DOI: 10.1091/mbc.e14-07-1213/asset/images/large/mbc-26-2609-g005.jpeg] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To ensure genome integrity, DNA replication takes place only once per cell cycle and is tightly controlled by cyclin-dependent kinase (Cdk1). Cdc6p is part of the prereplicative complex, which is essential for DNA replication. Cdc6 is phosphorylated by cyclin-Cdk1 to promote its degradation after origin firing to prevent DNA rereplication. We previously showed that a yeast GSK-3 homologue, Mck1 kinase, promotes Cdc6 degradation in a SCF(Cdc4)-dependent manner, therefore preventing rereplication. Here we present evidence that Mck1 directly phosphorylates a GSK-3 consensus site in the C-terminus of Cdc6. The Mck1-dependent Cdc6 phosphorylation required priming by cyclin/Cdk1 at an adjacent CDK consensus site. The sequential phosphorylation by Mck1 and Clb2/Cdk1 generated a Cdc4 E3 ubiquitin ligase-binding motif to promote Cdc6 degradation during mitosis. We further revealed that Cdc6 degradation triggered by Mck1 kinase was enhanced upon DNA damage caused by the alkylating agent methyl methanesulfonate and that the resulting degradation was mediated through Cdc4. Thus, Mck1 kinase ensures proper DNA replication, prevents DNA damage, and maintains genome integrity by inhibiting Cdc6.
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Affiliation(s)
- Amr Al-Zain
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
| | - Lea Schroeder
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
| | - Alina Sheglov
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
| | - Amy E Ikui
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
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15
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Zakari M, Trimble Ross R, Peak A, Blanchette M, Seidel C, Gerton JL. The SMC Loader Scc2 Promotes ncRNA Biogenesis and Translational Fidelity. PLoS Genet 2015; 11:e1005308. [PMID: 26176819 PMCID: PMC4503661 DOI: 10.1371/journal.pgen.1005308] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/28/2015] [Indexed: 11/18/2022] Open
Abstract
The Scc2-Scc4 complex is essential for loading the cohesin complex onto DNA. Cohesin has important roles in chromosome segregation, DSB repair, and chromosome condensation. Here we report that Scc2 is important for gene expression in budding yeast. Scc2 and the transcriptional regulator Paf1 collaborate to promote the production of Box H/ACA snoRNAs which guide pseudouridylation of RNAs including ribosomal RNA. Mutation of SCC2 was associated with defects in the production of ribosomal RNA, ribosome assembly, and splicing. While the scc2 mutant does not have a general defect in protein synthesis, it shows increased frameshifting and reduced cap-independent translation. These findings suggest Scc2 normally promotes a gene expression program that supports translational fidelity. We hypothesize that translational dysfunction may contribute to the human disorder Cornelia de Lange syndrome, which is caused by mutations in NIPBL, the human ortholog of SCC2.
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Affiliation(s)
- Musinu Zakari
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Universite Pierre et Marie Curie (Paris VI), Paris, France
| | - Rhonda Trimble Ross
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Allison Peak
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Chris Seidel
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, Kansas, United States of America
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16
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Al-Zain A, Schroeder L, Sheglov A, Ikui AE. Cdc6 degradation requires phosphodegron created by GSK-3 and Cdk1 for SCFCdc4 recognition in Saccharomyces cerevisiae. Mol Biol Cell 2015; 26:2609-19. [PMID: 25995377 PMCID: PMC4501359 DOI: 10.1091/mbc.e14-07-1213] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 05/12/2015] [Indexed: 11/11/2022] Open
Abstract
DNA replication has to be tightly regulated to ensure genome integrity such that DNA replication takes place only once per cell cycle. The Cdc6 sequential phosphorylation by GSK-3 and Cdk1 creates a binding site for Cdc4 ubiquitin ligase to promote Cdc6 degradation. To ensure genome integrity, DNA replication takes place only once per cell cycle and is tightly controlled by cyclin-dependent kinase (Cdk1). Cdc6p is part of the prereplicative complex, which is essential for DNA replication. Cdc6 is phosphorylated by cyclin-Cdk1 to promote its degradation after origin firing to prevent DNA rereplication. We previously showed that a yeast GSK-3 homologue, Mck1 kinase, promotes Cdc6 degradation in a SCFCdc4-dependent manner, therefore preventing rereplication. Here we present evidence that Mck1 directly phosphorylates a GSK-3 consensus site in the C-terminus of Cdc6. The Mck1-dependent Cdc6 phosphorylation required priming by cyclin/Cdk1 at an adjacent CDK consensus site. The sequential phosphorylation by Mck1 and Clb2/Cdk1 generated a Cdc4 E3 ubiquitin ligase–binding motif to promote Cdc6 degradation during mitosis. We further revealed that Cdc6 degradation triggered by Mck1 kinase was enhanced upon DNA damage caused by the alkylating agent methyl methanesulfonate and that the resulting degradation was mediated through Cdc4. Thus, Mck1 kinase ensures proper DNA replication, prevents DNA damage, and maintains genome integrity by inhibiting Cdc6.
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Affiliation(s)
- Amr Al-Zain
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
| | - Lea Schroeder
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
| | - Alina Sheglov
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
| | - Amy E Ikui
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210
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17
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Kim DH, Koepp DM. Analyzing cell cycle-dependent degradation and ubiquitination in budding yeast. Methods Mol Biol 2014; 1170:343-56. [PMID: 24906322 DOI: 10.1007/978-1-4939-0888-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Cell cycle progression is tightly regulated to prevent uncontrolled growth and division. Specific cell cycle factors are responsible for driving the cell from one cell cycle stage to the next. Many of these proteins are targeted for degradation by the ubiquitin proteasome system when their function is no longer required or may disrupt cell cycle progression. Here we describe a series of experiments used to study the ubiquitin-mediated degradation of cell cycle proteins. This collection of assays may be used to determine the requirement for individual proteins in the degradation and ubiquitination of cell cycle proteins in Saccharomyces cerevisiae.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
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18
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Abstract
Cell division is controlled by a highly regulated program to accurately duplicate and segregate chromosomes. An important feature of the cell cycle regulatory program is that key cell cycle proteins are present and active during specific cell cycle stages but are later removed or inhibited to maintain appropriate timing. The ubiquitin-proteasome system has emerged as an important mechanism to target cell cycle proteins for degradation at critical junctures during cell division. Two key E3 ubiquitin ligase complexes that target key cell cycle proteins are the Skp1-Cul1-F-box protein complex and the anaphase-promoting complex/cyclosome. This chapter focuses on the role of these E3 ubiquitin ligases and how ubiquitin-dependent degradation of central cell cycle regulatory proteins advances the cell cycle.
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Affiliation(s)
- Deanna M Koepp
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA,
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19
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Ghosh A, Cannon JF. Analysis of protein phosphatase-1 and aurora protein kinase suppressors reveals new aspects of regulatory protein function in Saccharomyces cerevisiae. PLoS One 2013; 8:e69133. [PMID: 23894419 PMCID: PMC3718817 DOI: 10.1371/journal.pone.0069133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/01/2013] [Indexed: 01/31/2023] Open
Abstract
Protein phosphatase-1 (PP1) controls many processes in eukaryotic cells. Modulation of mitosis by reversing phosphorylation of proteins phosphorylated by aurora protein kinase is a critical function for PP1. Overexpression of the sole PP1, Glc7, in budding yeast, Saccharomyces cerevisiae, is lethal. This work shows that lethality requires the function of Glc7 regulatory proteins Sds22, Reg2, and phosphorylated Glc8. This finding shows that Glc7 overexpression induced cell death requires a specific subset of the many Glc7-interacting proteins and therefore is likely caused by promiscuous dephosphorylation of a variety of substrates. Additionally, suppression can occur by reducing Glc7 protein levels by high-copy Fpr3 without use of its proline isomerase domain. This divulges a novel function of Fpr3. Most suppressors of GLC7 overexpression also suppress aurora protein kinase, ipl1, temperature-sensitive mutations. However, high-copy mutant SDS22 genes show reciprocal suppression of GLC7 overexpression induced cell death or ipl1 temperature sensitivity. Sds22 binds to many proteins besides Glc7. The N-terminal 25 residues of Sds22 are sufficient to bind, directly or indirectly, to seven proteins studied here including the spindle assembly checkpoint protein, Bub3. These data demonstrate that Sds22 organizes several proteins in addition to Glc7 to perform functions that counteract Ipl1 activity or lead to hyper Glc7 induced cell death. These data also emphasize that Sds22 targets Glc7 to nuclear locations distinct from Ipl1 substrates.
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Affiliation(s)
- Anuprita Ghosh
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - John F. Cannon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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