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A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival.
Beckley JR, Chen JS, Yang Y, Peng J, Gould KL
(2015) Mol Cell Proteomics 14: 3132-41
MeSH Terms: Cell Membrane, Cell Polarity, Conserved Sequence, Endopeptidases, Humans, Protein Transport, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Substrate Specificity
Show Abstract · Added February 4, 2016
Deubiquitinating enzymes (DUBs), cysteine or metallo- proteases that cleave ubiquitin chains or protein conjugates, are present in nearly every cellular compartment, with overlapping protein domain structure, localization, and functions. We discovered a cohort of DUBs that are involved in membrane trafficking (ubp4, ubp5, ubp9, ubp15, and sst2) and found that loss of all five of these DUBs but not loss of any combination of four, significantly impacted cell viability in the fission yeast Schizosaccharomyces pombe (1). Here, we delineate the collective and individual functions and activities of these five conserved DUBs using comparative proteomics, biochemistry, and microscopy. We find these five DUBs are degenerate rather than redundant at the levels of cell morphology, substrate selectivity, ubiquitin chain specificity, and cell viability under stress. These studies reveal the complexity of interplay among these enzymes, providing a foundation for understanding DUB biology and providing another example of how cells utilize degeneracy to improve survival.
© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
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9 MeSH Terms
Regulation of contractile ring formation and septation in Schizosaccharomyces pombe.
Willet AH, McDonald NA, Gould KL
(2015) Curr Opin Microbiol 28: 46-52
MeSH Terms: Actins, Cell Division, Cell Wall, Cytokinesis, Cytoskeletal Proteins, Gene Expression Regulation, Fungal, Myosins, Profilins, Schizosaccharomyces, Schizosaccharomyces pombe Proteins
Show Abstract · Added February 4, 2016
The fission yeast Schizosaccharomyces pombe has become a powerful model organism for cytokinesis studies, propelled by pioneering genetic screens in the 1980s and 1990s. S. pombe cells are rod-shaped and divide similarly to mammalian cells, utilizing a medially-placed actin-and myosin-based contractile ring. A cell wall division septum is deposited behind the constricting ring, forming the new ends of each daughter cell. Here we discuss recent advances in our understanding of the regulation of contractile ring formation through formin proteins and the role of the division septum in S. pombe cell division.
Copyright © 2015 Elsevier Ltd. All rights reserved.
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10 MeSH Terms
Identification of new players in cell division, DNA damage response, and morphogenesis through construction of Schizosaccharomyces pombe deletion strains.
Chen JS, Beckley JR, McDonald NA, Ren L, Mangione M, Jang SJ, Elmore ZC, Rachfall N, Feoktistova A, Jones CM, Willet AH, Guillen R, Bitton DA, Bähler J, Jensen MA, Rhind N, Gould KL
(2014) G3 (Bethesda) 5: 361-70
MeSH Terms: Cell Division, DNA Damage, Gene Deletion, Genes, Fungal, Schizosaccharomyces
Show Abstract · Added January 20, 2015
Many fundamental biological processes are studied using the fission yeast, Schizosaccharomyces pombe. Here we report the construction of a set of 281 haploid gene deletion strains covering many previously uncharacterized genes. This collection of strains was tested for growth under a variety of different stress conditions. We identified new genes involved in DNA metabolism, completion of the cell cycle, and morphogenesis. This subset of nonessential gene deletions will add to the toolkits available for the study of biological processes in S. pombe.
Copyright © 2015 Chen et al.
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5 MeSH Terms
The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage.
Sabouri N, Capra JA, Zakian VA
(2014) BMC Biol 12: 101
MeSH Terms: DNA Damage, DNA Helicases, DNA Replication, Evolution, Molecular, G-Quadruplexes, Genomic Instability, High-Throughput Nucleotide Sequencing, Protein Structure, Tertiary, Saccharomyces cerevisiae, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Sequence Analysis, DNA
Show Abstract · Added April 18, 2017
BACKGROUND - G-quadruplexes (G4s) are stable non-canonical DNA secondary structures consisting of stacked arrays of four guanines, each held together by Hoogsteen hydrogen bonds. Sequences with the ability to form these structures in vitro, G4 motifs, are found throughout bacterial and eukaryotic genomes. The budding yeast Pif1 DNA helicase, as well as several bacterial Pif1 family helicases, unwind G4 structures robustly in vitro and suppress G4-induced DNA damage in S. cerevisiae in vivo.
RESULTS - We determined the genomic distribution and evolutionary conservation of G4 motifs in four fission yeast species and investigated the relationship between G4 motifs and Pfh1, the sole S. pombe Pif1 family helicase. Using chromatin immunoprecipitation combined with deep sequencing, we found that many G4 motifs in the S. pombe genome were associated with Pfh1. Cells depleted of Pfh1 had increased fork pausing and DNA damage near G4 motifs, as indicated by high DNA polymerase occupancy and phosphorylated histone H2A, respectively. In general, G4 motifs were underrepresented in genes. However, Pfh1-associated G4 motifs were located on the transcribed strand of highly transcribed genes significantly more often than expected, suggesting that Pfh1 has a function in replication or transcription at these sites.
CONCLUSIONS - In the absence of functional Pfh1, unresolved G4 structures cause fork pausing and DNA damage of the sort associated with human tumors.
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12 MeSH Terms
The Cdc15 and Imp2 SH3 domains cooperatively scaffold a network of proteins that redundantly ensure efficient cell division in fission yeast.
Ren L, Willet AH, Roberts-Galbraith RH, McDonald NA, Feoktistova A, Chen JS, Huang H, Guillen R, Boone C, Sidhu SS, Beckley JR, Gould KL
(2015) Mol Biol Cell 26: 256-69
MeSH Terms: Amino Acid Sequence, Cell Cycle Proteins, Cell Division, Cytokinesis, Cytoskeletal Proteins, GTP-Binding Proteins, Gene Regulatory Networks, Guanine Nucleotide Exchange Factors, Immunoblotting, Luminescent Proteins, Microscopy, Confocal, Molecular Sequence Data, Mutation, Protein Binding, Proteome, Proteomics, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Sequence Homology, Amino Acid, Time-Lapse Imaging, src Homology Domains
Show Abstract · Added January 20, 2015
Schizosaccharomyces pombe cdc15 homology (PCH) family members participate in numerous biological processes, including cytokinesis, typically by bridging the plasma membrane via their F-BAR domains to the actin cytoskeleton. Two SH3 domain-containing PCH family members, Cdc15 and Imp2, play critical roles in S. pombe cytokinesis. Although both proteins localize to the contractile ring, with Cdc15 preceding Imp2, only cdc15 is an essential gene. Despite these distinct roles, the SH3 domains of Cdc15 and Imp2 cooperate in the essential process of recruiting other proteins to stabilize the contractile ring. To better understand the connectivity of this SH3 domain-based protein network at the CR and its function, we used a biochemical approach coupled to proteomics to identify additional proteins (Rgf3, Art1, Spa2, and Pos1) that are integrated into this network. Cell biological and genetic analyses of these SH3 partners implicate them in a range of activities that ensure the fidelity of cell division, including promoting cell wall metabolism and influencing cell morphogenesis.
© 2015 Ren et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
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21 MeSH Terms
Structural and functional insights into the N-terminus of Schizosaccharomyces pombe Cdc5.
Collier SE, Voehler M, Peng D, Ohi R, Gould KL, Reiter NJ, Ohi MD
(2014) Biochemistry 53: 6439-51
MeSH Terms: Binding Sites, Catalytic Domain, Cell Cycle Proteins, Gene Deletion, Models, Molecular, Mutant Proteins, Nuclear Magnetic Resonance, Biomolecular, Peptide Fragments, Protein Conformation, Protein Folding, Protein Interaction Domains and Motifs, Protein Stability, RNA Splicing, RNA, Double-Stranded, RNA, Fungal, RNA, Small Nuclear, RNA-Binding Proteins, Recombinant Proteins, Schizosaccharomyces pombe Proteins, Spliceosomes, Titrimetry
Show Abstract · Added January 20, 2015
The spliceosome is a dynamic macromolecular machine composed of five small nuclear ribonucleoparticles (snRNPs), the NineTeen Complex (NTC), and other proteins that catalyze the removal of introns mature to form the mature message. The NTC, named after its founding member Saccharomyces cerevisiae Prp19, is a conserved spliceosome subcomplex composed of at least nine proteins. During spliceosome assembly, the transition to an active spliceosome correlates with stable binding of the NTC, although the mechanism of NTC function is not understood. Schizosaccharomyces pombe Cdc5, a core subunit of the NTC, is an essential protein required for pre-mRNA splicing. The highly conserved Cdc5 N-terminus contains two canonical Myb (myeloblastosis) repeats (R1 and R2) and a third domain (D3) that was previously classified as a Myb-like repeat. Although the N-terminus of Cdc5 is required for its function, how R1, R2, and D3 each contribute to functionality is unclear. Using a combination of yeast genetics, structural approaches, and RNA binding assays, we show that R1, R2, and D3 are all required for the function of Cdc5 in cells. We also show that the N-terminus of Cdc5 binds RNA in vitro. Structural and functional analyses of Cdc5-D3 show that, while this domain does not adopt a Myb fold, Cdc5-D3 preferentially binds double-stranded RNA. Our data suggest that the Cdc5 N-terminus interacts with RNA structures proposed to be near the catalytic core of the spliceosome.
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21 MeSH Terms
Histone H2B ubiquitination promotes the function of the anaphase-promoting complex/cyclosome in Schizosaccharomyces pombe.
Elmore ZC, Beckley JR, Chen JS, Gould KL
(2014) G3 (Bethesda) 4: 1529-38
MeSH Terms: Anaphase-Promoting Complex-Cyclosome, Endopeptidases, Histones, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Ubiquitination
Show Abstract · Added January 20, 2015
Ubiquitination and deubiquitination of proteins are reciprocal events involved in many cellular processes, including the cell cycle. During mitosis, the metaphase to anaphase transition is regulated by the ubiquitin ligase activity of the anaphase-promoting complex/cyclosome (APC/C). Although the E3 ubiquitin ligase function of the APC/C has been well characterized, it is not clear whether deubiquitinating enzymes (DUBs) play a role in reversing APC/C substrate ubiquitination. Here we performed a genetic screen to determine what DUB, if any, antagonizes the function of the APC/C in the fission yeast Schizosaccharomyces pombe. We found that deletion of ubp8, encoding the Spt-Ada-Gcn5-Acetyl transferase (SAGA) complex associated DUB, suppressed temperature-sensitive phenotypes of APC/C mutants cut9-665, lid1-6, cut4-533, and slp1-362. Our analysis revealed that Ubp8 antagonizes APC/C function in a mechanism independent of the spindle assembly checkpoint and proteasome activity. Notably, suppression of APC/C mutants was linked to loss of Ubp8 catalytic activity and required histone H2B ubiquitination. On the basis of these data, we conclude that Ubp8 antagonizes APC/C function indirectly by modulating H2B ubiquitination status.
Copyright © 2014 Elmore et al.
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6 MeSH Terms
Interplay between base excision repair activity and toxicity of 3-methyladenine DNA glycosylases in an E. coli complementation system.
Troll CJ, Adhikary S, Cueff M, Mitra I, Eichman BF, Camps M
(2014) Mutat Res 763-764: 64-73
MeSH Terms: Alkylation, DNA Glycosylases, DNA Repair, Escherichia coli, Genetic Complementation Test, Mutation, Saccharomyces cerevisiae, Schizosaccharomyces, Schizosaccharomyces pombe Proteins
Show Abstract · Added May 27, 2014
DNA glycosylases carry out the first step of base excision repair by removing damaged bases from DNA. The N3-methyladenine (3MeA) DNA glycosylases specialize in alkylation repair and are either constitutively expressed or induced by exposure to alkylating agents. To study the functional and evolutionary significance of constitutive versus inducible expression, we expressed two closely related yeast 3MeA DNA glycosylases - inducible Saccharomyces cerevisiae MAG and constitutive S. pombe Mag1 - in a glycosylase-deficient Escherichia coli strain. In both cases, constitutive expression conferred resistance to alkylating agent exposure. However, in the absence of exogenous alkylation, high levels of expression of both glycosylases were deleterious. We attribute this toxicity to excessive glycosylase activity, since suppressing spMag1 expression correlated with improved growth in liquid culture, and spMag1 mutants exhibiting decreased glycosylase activity showed improved growth and viability. Selection of a random spMag1 mutant library for increased survival in the presence of exogenous alkylation resulted in the selection of hypomorphic mutants, providing evidence for the presence of a genetic barrier to the evolution of enhanced glycosylase activity when constitutively expressed. We also show that low levels of 3MeA glycosylase expression improve fitness in our glycosylase-deficient host, implying that 3MeA glycosylase activity is likely necessary for repair of endogenous lesions. These findings suggest that 3MeA glycosylase activity is evolutionarily conserved for repair of endogenously produced alkyl lesions, and that inducible expression represents a common strategy to rectify deleterious effects of excessive 3MeA activity in the absence of exogenous alkylation challenge.
Copyright © 2014 Elsevier B.V. All rights reserved.
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9 MeSH Terms
Formin-based control of the actin cytoskeleton during cytokinesis.
Bohnert KA, Willet AH, Kovar DR, Gould KL
(2013) Biochem Soc Trans 41: 1750-4
MeSH Terms: Actin Cytoskeleton, Actins, Cytokinesis, Humans, Schizosaccharomyces
Show Abstract · Added March 12, 2014
Cytokinesis, the terminal event in the canonical cell cycle, physically separates daughter cells following mitosis. For cleavage to occur in many eukaryotes, a cytokinetic ring must assemble and constrict between divided genomes. Although dozens of different molecules localize to and participate within the cytokinetic ring, the core machinery comprises linear actin filaments. Accordingly, formins, which nucleate and elongate F-actin (filamentous actin) for the cytokinetic ring, are required for cytokinesis in diverse species. In the present article, we discuss specific modes of formin-based actin regulation during cell division and highlight emerging mechanisms and questions on this topic.
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5 MeSH Terms
SIN-dependent phosphoinhibition of formin multimerization controls fission yeast cytokinesis.
Bohnert KA, Grzegorzewska AP, Willet AH, Vander Kooi CW, Kovar DR, Gould KL
(2013) Genes Dev 27: 2164-77
MeSH Terms: Actin Cytoskeleton, Cytokinesis, Cytoskeletal Proteins, Phosphorylation, Protein Kinases, Protein Multimerization, Protein Structure, Tertiary, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Sequence Deletion
Show Abstract · Added March 7, 2014
Many eukaryotes accomplish cell division by building and constricting a medial actomyosin-based cytokinetic ring (CR). In Schizosaccharomyces pombe, a Hippo-related signaling pathway termed the septation initiation network (SIN) controls CR formation, maintenance, and constriction. However, how the SIN regulates integral CR components was unknown. Here, we identify the essential cytokinetic formin Cdc12 as a key CR substrate of SIN kinase Sid2. Eliminating Sid2-mediated Cdc12 phosphorylation leads to persistent Cdc12 clustering, which prevents CR assembly in the absence of anillin-like Mid1 and causes CRs to collapse when cytokinesis is delayed. Molecularly, Sid2 phosphorylation of Cdc12 abrogates multimerization of a previously unrecognized Cdc12 domain that confers F-actin bundling activity. Taken together, our findings identify a SIN-triggered oligomeric switch that modulates cytokinetic formin function, revealing a novel mechanism of actin cytoskeleton regulation during cell division.
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10 MeSH Terms