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Journal articles on the topic 'Fission Yeast Splicing'

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Author: Grafiati
Published: 6 September 2023

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1

TANG, Zhaohua, Norbert F. KÄUFER, and Ren-Jang LIN. "Interactions between two fission yeast serine/arginine-rich proteins and their modulation by phosphorylation." Biochemical Journal 368, no. 2 (December 1, 2002): 527–34. http://dx.doi.org/10.1042/bj20021133.

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The unexpected low number of genes in the human genome has triggered increasing attention to alternative pre-mRNA splicing, and serine/arginine-rich (SR) proteins have been correlated with the complex alternative splicing that is a characteristic of metazoans. SR proteins interact with RNA and splicing protein factors, and they also undergo reversible phosphorylation, thereby regulating constitutive and alternative splicing in mammals and Drosophila. However, it is not clear whether the features of SR proteins and alternative splicing are present in simple and genetically tractable organisms, such as yeasts. In the present study, we show that the SR-like proteins Srp1 and Srp2, found in the fission yeast Schizosaccharomyces pombe, interact with each other and the interaction is modulated by protein phosphorylation. By using Srp1 as bait in a yeast two-hybrid analysis, we specifically isolated Srp2 from a random screen. This Srp interaction was confirmed by a glutathione-S-transferase pull-down assay. We also found that the Srp1—Srp2 complex was phosphorylated at a reduced efficiency by a fission yeast SR-specific kinase, Dis1-suppression kinase (Dsk1). Conversely, Dsk1-mediated phosphorylation inhibited the formation of the Srp complex. These findings offer the first example in fission yeast for interactions between SR-related proteins and the modulation of the interactions by specific protein phosphorylation, suggesting that a mammalian-like SR protein function may exist in fission yeast.
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Moldón, Alberto, Jordi Malapeira, Natalia Gabrielli, Madelaine Gogol, Blanca Gómez-Escoda, Tsvetomira Ivanova, Chris Seidel, and José Ayté. "Promoter-driven splicing regulation in fission yeast." Nature 455, no. 7215 (September 24, 2008): 997–1000. http://dx.doi.org/10.1038/nature07325.

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3

Baumann, Peter, Elaine Podell, and Thomas R. Cech. "Human Pot1 (Protection of Telomeres) Protein: Cytolocalization, Gene Structure, and Alternative Splicing." Molecular and Cellular Biology 22, no. 22 (November 15, 2002): 8079–87. http://dx.doi.org/10.1128/mcb.22.22.8079-8087.2002.

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ABSTRACT Fission yeast Pot1 (protection of telomeres) is a single-stranded telomeric DNA binding protein with a critical role in ensuring chromosome stability. A putative human homolog (hPot1) was previously identified, based on moderate sequence similarity with fission yeast Pot1 and telomere end-binding proteins from ciliated protozoa. Using indirect immunofluorescence, we show here that epitope-tagged hPot1 localizes to telomeres in interphase nuclei of human cells, consistent with a direct role in telomere end protection. The hPOT1 gene contains 22 exons, most of which are present in all cDNAs examined. However, four exons are subject to exon skipping in some transcripts, giving rise to five splice variants. Four of these are ubiquitously expressed, whereas the fifth appears to be specific to leukocytes. The resultant proteins vary significantly in their ability to form complexes with single-stranded telomeric DNA as judged by electrophoretic mobility shift assays. In addition to these splice variants, the Pot1 family is expanded by the identification of six more genes from diverse species. Pot1-like proteins have now been found in plants, animals, yeasts, and microsporidia.
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Sarmah, Bhaskarjyoti, Niranjan Chakraborty, Subhra Chakraborty, and Asis Datta. "Plant pre-mRNA splicing in fission yeast, Schizosaccharomyces pombe." Biochemical and Biophysical Research Communications 293, no. 4 (May 2002): 1209–16. http://dx.doi.org/10.1016/s0006-291x(02)00364-9.

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5

Bayne, E. H., M. Portoso, A. Kagansky, I. C. Kos-Braun, T. Urano, K. Ekwall, F. Alves, J. Rappsilber, and R. C. Allshire. "Splicing Factors Facilitate RNAi-Directed Silencing in Fission Yeast." Science 322, no. 5901 (October 24, 2008): 602–6. http://dx.doi.org/10.1126/science.1164029.

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6

Tang, Zhaohua, Amy Tsurumi, Sarah Alaei, Christopher Wilson, Cathleen Chiu, Jessica Oya, and Benson Ngo. "Dsk1p kinase phosphorylates SR proteins and regulates their cellular localization in fission yeast." Biochemical Journal 405, no. 1 (June 13, 2007): 21–30. http://dx.doi.org/10.1042/bj20061523.

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Evolutionarily conserved SR proteins (serine/arginine-rich proteins) are important factors for alternative splicing and their activity is modulated by SRPKs (SR protein-specific kinases). We previously identified Dsk1p (dis1-suppressing protein kinase) as the orthologue of human SRPK1 in fission yeast. In addition to its similarity of gene structure to higher eukaryotes, fission yeast Schizosaccharomyces pombe is a unicellular eukaryotic organism in which alternative splicing takes place. In the present study, we have revealed for the first time that SR proteins, Srp1p and Srp2p, are the in vivo substrates of Dsk1p in S. pombe. Moreover, the cellular localization of the SR proteins and Prp2p splicing factor is dependent on dsk1+: Dsk1p is required for the efficient nuclear localization of Srp2p and Prp2p, while it promotes the cytoplasmic distribution of Srp1p, thereby differentially influencing the destinations of these proteins in the cell. The present study offers the first biochemical and genetic evidence for the in vivo targets of the SRPK1 orthologue, Dsk1p, in S. pombe and the significant correlation between Dsk1p-mediated phosphorylation and the cellular localization of the SR proteins, providing information about the physiological functions of Dsk1p. Furthermore, the results demonstrate that the regulatory function of SRPKs in the nuclear targeting of SR proteins is conserved from fission yeast to human, indicating a general mechanism of reversible phosphorylation to control the activities of SR proteins in RNA metabolism through cellular partitioning.
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7

Dhoondia, Zuzer, Hesham Elewa, Marva Malik, Zahidur Arif, Roger Pique-Regi, and Athar Ansari. "A termination-independent role of Rat1 in cotranscriptional splicing." Nucleic Acids Research 49, no. 10 (May 12, 2021): 5520–36. http://dx.doi.org/10.1093/nar/gkab339.

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Abstract Rat1 is a 5′→3′ exoribonuclease in budding yeast. It is a highly conserved protein with homologs being present in fission yeast, flies, worms, mice and humans. Rat1 and its human homolog Xrn2 have been implicated in multiple nuclear processes. Here we report a novel role of Rat1 in mRNA splicing. We observed an increase in the level of unspliced transcripts in mutants of Rat1. Accumulation of unspliced transcripts was not due to the surveillance role of Rat1 in degrading unspliced mRNA, or an indirect effect of Rat1 function in termination of transcription or on the level of splicing factors in the cell, or due to an increased elongation rate in Rat1 mutants. ChIP-Seq analysis revealed Rat1 crosslinking to the introns of a subset of yeast genes. Mass spectrometry and coimmunoprecipitation revealed an interaction of Rat1 with the Clf1, Isy1, Yju2, Prp43 and Sub2 splicing factors. Furthermore, recruitment of splicing factors on the intron was compromised in the Rat1 mutant. Based on these findings we propose that Rat1 has a novel role in splicing of mRNA in budding yeast. Rat1, however, is not a general splicing factor as it crosslinks to only long introns with an average length of 400 nucleotides.
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8

Romfo, Charles M., Consuelo J. Alvarez, Willem J. van Heeckeren, Christopher J. Webb, and Jo Ann Wise. "Evidence for Splice Site Pairing via Intron Definition in Schizosaccharomyces pombe." Molecular and Cellular Biology 20, no. 21 (November 1, 2000): 7955–70. http://dx.doi.org/10.1128/mcb.20.21.7955-7970.2000.

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ABSTRACT Schizosaccharomyces pombe pre-mRNAs are generally multi-intronic and share certain features with pre-mRNAs fromDrosophila melanogaster, in which initial splice site pairing can occur via either exon or intron definition. Here, we present three lines of evidence suggesting that, despite these similarities, fission yeast splicing is most likely restricted to intron definition. First, mutating either or both splice sites flanking an internal exon in the S. pombe cdc2 gene produced almost exclusively intron retention, in contrast to the exon skipping observed in vertebrates. Second, we were unable to induce skipping of the internal microexon in fission yeast cgs2, whereas the default splicing pathway excludes extremely small exons in mammals. Because nearly quantitative removal of the downstream intron incgs2 could be achieved by expanding the microexon, we propose that its retention is due to steric occlusion. Third, several cryptic 5′ junctions in the second intron of fission yeastcdc2 are located within the intron, in contrast to their generally exonic locations in metazoa. The effects of expanding and contracting this intron are as predicted by intron definition; in fact, even highly deviant 5′ junctions can compete effectively with the standard 5′ splice site if they are closer to the 3′ splicing signals. Taken together, our data suggest that pairing of splice sites inS. pombe most likely occurs exclusively across introns in a manner that favors excision of the smallest segment possible.
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9

Banerjee, Shataparna, Piyush Khandelia, Geetha Melangath, Samirul Bashir, Vijaykrishna Nagampalli, and Usha Vijayraghavan. "Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly." Molecular and Cellular Biology 33, no. 16 (June 10, 2013): 3125–36. http://dx.doi.org/10.1128/mcb.00007-13.

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The multiple short introns inSchizosaccharomyces pombegenes with degeneratecissequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of theS. pombe slu7+(spslu7+) gene product, known fromSaccharomyces cerevisiaeand humanin vitroreactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3′ splice site choice during the second reaction. By using a missense mutant of this essentialS. pombefactor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3′ splice site distance, intron length, and the impact of its A/U content at the 5′ end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest inspslu7-2revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions withspprp1+, a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly.
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10

Selicky, Tomas, Matus Jurcik, Barbora Mikolaskova, Alexandra Pitelova, Nina Mayerova, Miroslava Kretova, Michaela Osadska, et al. "Defining the Functional Interactome of Spliceosome-Associated G-patch Protein Gpl1 in the Fission Yeast Schizosaccharomyces pombe." International Journal of Molecular Sciences 23, no. 21 (October 24, 2022): 12800. http://dx.doi.org/10.3390/ijms232112800.

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Pre-mRNA splicing plays a fundamental role in securing protein diversity by generating multiple transcript isoforms from a single gene. Recently, it has been shown that specific G-patch domain-containing proteins are critical cofactors involved in the regulation of splicing processes. In this study, using the knock-out strategy, affinity purification and the yeast-two-hybrid assay, we demonstrated that the spliceosome-associated G-patch protein Gpl1 of the fission yeast S. pombe mediates interactions between putative RNA helicase Gih35 (SPAC20H4.09) and WD repeat protein Wdr83, and ensures their binding to the spliceosome. Furthermore, RT-qPCR analysis of the splicing efficiency of deletion mutants indicated that the absence of any of the components of the Gpl1-Gih35-Wdr83 complex leads to defective splicing of fet5 and pwi1, the reference genes whose unspliced isoforms harboring premature stop codons are targeted for degradation by the nonsense-mediated decay (NMD) pathway. Together, our results shed more light on the functional interactome of G-patch protein Gpl1 and revealed that the Gpl1-Gih35-Wdr83 complex plays an important role in the regulation of pre-mRNA splicing in S. pombe.
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11

Potashkin, Judith, and David Frendewey. "Splicing of the U6 RNA precursor is impaired in fission yeast pre-mRNA splicing mutants." Nucleic Acids Research 17, no. 19 (1989): 7821–31. http://dx.doi.org/10.1093/nar/17.19.7821.

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12

Schwelnus, Wiebke, Kathrin Richert, Florian Opitz, Thomas Groß, Yasuaki Habara, Tokio Tani, and Norbert F. Käufer. "Fission yeast Prp4p kinase regulates pre‐mRNA splicing by phosphorylating a non‐SR‐splicing factor." EMBO reports 2, no. 1 (January 2001): 35–41. http://dx.doi.org/10.1093/embo-reports/kve009.

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13

Jang, Young Joo, Young Sook Kil, Jee Hee Ahn, Jae Hoon Ji, Jong Seok Lim, M. Won, and Hyang Sook Yoo. "Overexpression Phenotypes of Plk1 and Ndrg2 in Schizosaccharomyces Pombe: Fission Yeast System for Mammalian Gene Study." Key Engineering Materials 277-279 (January 2005): 1–6. http://dx.doi.org/10.4028/www.scientific.net/kem.277-279.1.

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The fission yeast, Schizosaccharomyces pombe is a single-celled free-living fungus that shares many features with cells of more complicated eukaryotes. Many of the genes required for the cell-cycle control, proteolysis, protein modification, and RNA splicing are highly conserved with those of higher eukaryotes. Moreover, fission yeast has the merit of genetics and its genetic system is already well characterized. As such, the current study evaluated the use of a fission yeast system as a tool for the functional study of mammalian genes and attempted to set up an assay system for novel genes. Since the phenotypes of a deletion mutant and the overexpression of a gene are generally analyzed for a functional study of specific genes in yeast, the present study used overexpression phenotypes to study the functions of mammalian genes. Therefore, based on using a thiamine-repressive promoter, two mammalian genes were expressed in fission yeast, and their overexpressed phenotypes compared with those in mammalian cells. The phenotypes resulting from overexpression were analyzed using a FACS, which analyzes the DNA contents, and a microscope. One of the selected genes was the mammalian Polo-like kinase 1 (Plk1), which is activated and plays a role in the mitotic phase of the cell division cycle. The overexpression of various constructs of Plk1 in the HeLa cells caused cell cycle defects, suggesting that the ectopic Plk1s blocked the endogenous Plk1 in the cells. As expected, when the constructs were overexpressed in the fission yeast system, the cells were arrested in mitosis and defected at the end of mitosis. As such, this data suggests that the Plk1-overexpressed phenotypes were similar in the mammalian cells and the fission yeast, thereby enabling the mammalian Plk1 functions to be approximated in the fission yeast. The other selected gene was the N-Myc downstream-regulated gene 2 (ndrg2), which is upregulated during cell differentiation, yet still not well characterized. When the ndrg2 gene was overexpressed in the fission yeast, the cells contained multi-septa. The septa were positioned well, yet their number increased per cell. Therefore, this gene was speculated to block cell division in the last stage of the cell cycle, making the phenotype potentially useful for explaining cell growth and differentiation in mammalian cells. Accordingly, fission yeast is demonstrated to be an appropriate species for the functional study of mammalian genes.
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14

YADAV, SUDHANSHU, AMIT SONKAR, NAFEES AHAMAD, and SHAKIL AHMED. "Mutant allele of rna14 in fission yeast affects pre-mRNA splicing." Journal of Genetics 95, no. 2 (June 2016): 389–97. http://dx.doi.org/10.1007/s12041-016-0652-z.

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15

Bernard, P., J. Drogat, S. Dheur, S. Genier, and J. P. Javerzat. "Splicing Factor Spf30 Assists Exosome-Mediated Gene Silencing in Fission Yeast." Molecular and Cellular Biology 30, no. 5 (December 22, 2009): 1145–57. http://dx.doi.org/10.1128/mcb.01317-09.

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16

Takahashi, K., H. Yamada, and M. Yanagida. "Fission yeast minichromosome loss mutants mis cause lethal aneuploidy and replication abnormality." Molecular Biology of the Cell 5, no. 10 (October 1994): 1145–58. http://dx.doi.org/10.1091/mbc.5.10.1145.

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Precise chromosome transmission in cell division cycle is maintained by a number of genes. The attempt made in the present study was to isolate temperature-sensitive (ts) fission yeast mutants that display high loss rates of minichromosomes at permissive or semipermissive temperature (designated mis). By colony color assay of 539 ts strains that contain a minichromosome, we have identified 12 genetic loci (mis1-mis12) and determined their phenotypes at restrictive temperature. Seven of them are related to cell cycle block phenotype at restrictive temperature, three of them in mitosis. Unequal distribution of regular chromosomes in the daughters is extensive in mis6 and mis12. Cells become inviable after rounds of cell division due to missegregation. The phenotype of mis5 is DNA replication defect and hypersensitivity to UV ray and hydroxyurea. mis5+ encodes a novel member of the ubiquitous MCM family required for the onset of replication. The mis5+ gene is essential for viability and functionally distinct from other previously identified members in fission yeast, cdc21+, nda1+, and nda4+. The mis11 mutant phenotype was the cell division block with reduced cell size. Progression of the G1 and G2 phases is blocked in mis11. The cloned mis11+ gene is identical to prp2+, which is essential for RNA splicing and similar to a mammalian splicing factor U2AF65.
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17

Kim, Dae-Myung. "The Multifunctional Protein, Snd1, Involved in tRNA Splicing of the Fission Yeast." Journal of the Korea Entertainment Industry Association 10, no. 6 (December 31, 2016): 439. http://dx.doi.org/10.21184/jkeia.2016.12.10.6.439.

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18

Kishida, Masao, Tsutomu Nagai, Yukinobu Nakaseko, and Chikashi Shimoda. "Meiosis-dependent mRNA splicing of the fission yeast Schizosaccharomyces pombe mes1 + gene." Current Genetics 25, no. 6 (June 1994): 497–503. http://dx.doi.org/10.1007/bf00351668.

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19

Fair, Benjamin Jung, and Jeffrey A. Pleiss. "The power of fission: yeast as a tool for understanding complex splicing." Current Genetics 63, no. 3 (September 14, 2016): 375–80. http://dx.doi.org/10.1007/s00294-016-0647-6.

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20

Potashkin, Judith, Daemyung Kim, Mark Fons, Tim Humphrey, and David Frendewey. "Cell-division-cycle defects associated with fission yeast pre-mRNA splicing mutants." Current Genetics 34, no. 3 (September 16, 1998): 153–63. http://dx.doi.org/10.1007/s002940050381.

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21

Webb, C. J. "Exonic splicing enhancers in fission yeast: functional conservation demonstrates an early evolutionary origin." Genes & Development 19, no. 2 (January 15, 2005): 242–54. http://dx.doi.org/10.1101/gad.1265905.

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22

Averbeck, Nicole, Sham Sunder, Nicole Sample, Jo Ann Wise, and Janet Leatherwood. "Negative Control Contributes to an Extensive Program of Meiotic Splicing in Fission Yeast." Molecular Cell 18, no. 4 (May 2005): 491–98. http://dx.doi.org/10.1016/j.molcel.2005.04.007.

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23

Wentz-Hunter, K. "The small subunit of the splicing factor U2AF is conserved in fission yeast." Nucleic Acids Research 24, no. 10 (May 15, 1996): 1849–54. http://dx.doi.org/10.1093/nar/24.10.1849.

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24

Lundgren, K., S. Allan, S. Urushiyama, T. Tani, Y. Ohshima, D. Frendewey, and D. Beach. "A connection between pre-mRNA splicing and the cell cycle in fission yeast: cdc28+ is allelic with prp8+ and encodes an RNA-dependent ATPase/helicase." Molecular Biology of the Cell 7, no. 7 (July 1996): 1083–94. http://dx.doi.org/10.1091/mbc.7.7.1083.

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The fission-yeast gene cdc28+ was originally identified in a screen for temperature-sensitive mutants that exhibit a cell-division cycle arrest and was found to be required for mitosis. We undertook a study of this gene to understand more fully the general requirements for entry into mitosis. Cells carrying the conditional lethal cdc28-P8 mutation divide once and arrest in G2 after being shifted to the restrictive temperature. We cloned the cdc28+ gene by complementation of the temperature-sensitive growth arrest in cdc28-P8. DNA sequence analysis indicated that cdc28+ encodes a member of the DEAH-box family of putative RNA-dependent ATPases or helicases. The Cdc28 protein is most similar to the Prp2, Prp16, and Prp22 proteins from budding yeast, which are required for the splicing of mRNA precursors. Consistent with this similarity, the cdc28-P8 mutant accumulates unspliced precursors at the restrictive temperature. Independently, we isolated a temperature-sensitive pre-mRNA splicing mutant prp8-1 that exhibits a cell-cycle phenotype identical to that of cdc28-P8. We have shown that cdc28 and prp8 are allelic. These results suggest a connection between pre-mRNA splicing and progression through the cell cycle.
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25

Kaufer, N. F. "SURVEY AND SUMMARY: Analysis of the splicing machinery in fission yeast: a comparison with budding yeast and mammals." Nucleic Acids Research 28, no. 16 (August 15, 2000): 3003–10. http://dx.doi.org/10.1093/nar/28.16.3003.

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26

Habara, Y. "The fission yeast prp10(+) gene involved in pre-mRNA splicing encodes a homologue of highly conserved splicing factor, SAP155." Nucleic Acids Research 26, no. 24 (December 15, 1998): 5662–69. http://dx.doi.org/10.1093/nar/26.24.5662.

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27

Melangath, Geetha, Titash Sen, Rakesh Kumar, Pushpinder Bawa, Subha Srinivasan, and Usha Vijayraghavan. "Functions for fission yeast splicing factors SpSlu7 and SpPrp18 in alternative splice-site choice and stress-specific regulated splicing." PLOS ONE 12, no. 12 (December 13, 2017): e0188159. http://dx.doi.org/10.1371/journal.pone.0188159.

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28

Ohi, Melanie D., Andrew J. Link, Liping Ren, Jennifer L. Jennings, W. Hayes McDonald, and Kathleen L. Gould. "Proteomics Analysis Reveals Stable Multiprotein Complexes in Both Fission and Budding Yeasts Containing Myb-Related Cdc5p/Cef1p, Novel Pre-mRNA Splicing Factors, and snRNAs." Molecular and Cellular Biology 22, no. 7 (April 1, 2002): 2011–24. http://dx.doi.org/10.1128/mcb.22.7.2011-2024.2002.

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ABSTRACT Schizosaccharomyces pombe Cdc5p and its Saccharomyces cerevisiae ortholog, Cef1p, are essential Myb-related proteins implicated in pre-mRNA splicing and contained within large multiprotein complexes. Here we describe the tandem affinity purification (TAP) of Cdc5p- and Cef1p-associated complexes. Using transmission electron microscopy, we show that the purified Cdc5p complex is a discrete structure. The components of the S. pombe Cdc5p/S. cerevisiae Cef1p complexes (termed Cwfs or Cwcs, respectively) were identified using direct analysis of large protein complex (DALPC) mass spectrometry (A. J. Link et al., Nat. Biotechnol. 17:676-682, 1999). At least 26 proteins were detected in the Cdc5p/Cef1p complexes. Comparison of the polypeptides identified by S. pombe Cdc5p purification with those identified by S. cerevisiae Cef1p purification indicates that these two yeast complexes are nearly identical in composition. The majority of S. pombe Cwf proteins and S. cerevisiae Cwc proteins are known pre-mRNA splicing factors including core Sm and U2 and U5 snRNP components. In addition, the complex contains the U2, U5, and U6 snRNAs. Previously uncharacterized proteins were also identified, and we provide evidence that several of these novel factors are involved in pre-mRNA splicing. Our data represent the first comprehensive analysis of CDC5-associated proteins in yeasts, describe a discrete highly conserved complex containing novel pre-mRNA splicing factors, and demonstrate the power of DALPC for identification of components in multiprotein complexes.
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Webb, Christopher J., and Jo Ann Wise. "The Splicing Factor U2AF Small Subunit Is Functionally Conserved between Fission Yeast and Humans." Molecular and Cellular Biology 24, no. 10 (May 15, 2004): 4229–40. http://dx.doi.org/10.1128/mcb.24.10.4229-4240.2004.

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ABSTRACT The small subunit of U2AF, which functions in 3′ splice site recognition, is more highly conserved than its heterodimeric partner yet is less thoroughly investigated. Remarkably, we find that the small subunit of Schizosaccharomyces pombe U2AF (U2AFSM) can be replaced in vivo by its human counterpart, demonstrating that the conservation extends to function. Precursor mRNAs accumulate in S. pombe following U2AFSM depletion in a time frame consistent with a role in splicing. A comprehensive mutational analysis reveals that all three conserved domains are required for viability. Notably, however, a tryptophan in the pseudo-RNA recognition motif implicated in a key contact with the large subunit by crystallographic data is dispensable whereas amino acids implicated in RNA recognition are critical. Mutagenesis of the two zinc-binding domains demonstrates that they are neither equivalent nor redundant. Finally, two- and three-hybrid analyses indicate that mutations with effects on large-subunit interactions are rare whereas virtually all alleles tested diminished RNA binding by the heterodimer. In addition to demonstrating extraordinary conservation of U2AF small-subunit function, these results provide new insights into the roles of individual domains and residues.
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Tang, Zhaohua, Tiffany Kuo, Jenny Shen, and Ren-Jang Lin. "Biochemical and Genetic Conservation of Fission Yeast Dsk1 and Human SR Protein-Specific Kinase 1." Molecular and Cellular Biology 20, no. 3 (February 1, 2000): 816–24. http://dx.doi.org/10.1128/mcb.20.3.816-824.2000.

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ABSTRACT Arginine/serine-rich (RS) domain-containing proteins and their phosphorylation by specific protein kinases constitute control circuits to regulate pre-mRNA splicing and coordinate splicing with transcription in mammalian cells. We present here the finding that similar SR networks exist in Schizosaccharomyces pombe. We previously showed that Dsk1 protein, originally described as a mitotic regulator, displays high activity in phosphorylating S. pombe Prp2 protein (spU2AF59), a homologue of human U2AF65. We now demonstrate that Dsk1 also phosphorylates two recently identified fission yeast proteins with RS repeats, Srp1 and Srp2, in vitro. The phosphorylated proteins bear the same phosphoepitope found in mammalian SR proteins. Consistent with its substrate specificity, Dsk1 forms kinase-competent complexes with those proteins. Furthermore,dsk1 + gene determines the phenotype ofprp2 + overexpression, providing in vivo evidence that Prp2 is a target for Dsk1. The dsk1-null mutant strain became severely sick with the additional deletion of a related kinase gene. Significantly, human SR protein-specific kinase 1 (SRPK1) complements the growth defect of the double-deletion mutant. In conjunction with the resemblance of dsk1 + andSRPK1 in sequence homology, biochemical properties, and overexpression phenotypes, the complementation result indicates that SRPK1 is a functional homologue of Dsk1. Collectively, our studies illustrate the conserved SR networks in S. pombe consisting of RS domain-containing proteins and SR protein-specific kinases and thus establish the importance of the networks in eucaryotic organisms.
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31

Wilkinson, Caroline R. M., Gunnar A. G. Dittmar, Melanie D. Ohi, Peter Uetz, Nic Jones, and Daniel Finley. "Ubiquitin-like Protein Hub1 Is Required for Pre-mRNA Splicing and Localization of an Essential Splicing Factor in Fission Yeast." Current Biology 14, no. 24 (December 2004): 2283–88. http://dx.doi.org/10.1016/j.cub.2004.11.058.

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32

Wilkinson, Caroline R. M., Gunnar A. G. Dittmar, Melanie D. Ohi, Peter Uetz, Nic Jones, and Daniel Finley. "Ubiquitin-like Protein Hub1 Is Required for pre-mRNA Splicing and Localization of an Essential Splicing Factor in Fission Yeast." Current Biology 16, no. 24 (December 2006): 2488. http://dx.doi.org/10.1016/j.cub.2006.12.004.

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33

Kallgren, Scott P., Stuart Andrews, Xavier Tadeo, Haitong Hou, James J. Moresco, Patricia G. Tu, John R. Yates, Peter L. Nagy, and Songtao Jia. "The Proper Splicing of RNAi Factors Is Critical for Pericentric Heterochromatin Assembly in Fission Yeast." PLoS Genetics 10, no. 5 (May 29, 2014): e1004334. http://dx.doi.org/10.1371/journal.pgen.1004334.

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34

Lo, Chor-Wai, Daisuke Kaida, Shinichi Nishimura, Akihisa Matsuyama, Yoko Yashiroda, Hiroshi Taoka, Ken Ishigami, et al. "Inhibition of splicing and nuclear retention of pre-mRNA by spliceostatin A in fission yeast." Biochemical and Biophysical Research Communications 364, no. 3 (December 2007): 573–77. http://dx.doi.org/10.1016/j.bbrc.2007.10.029.

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35

Carnahan, Robert H., Anna Feoktistova, Liping Ren, Sherry Niessen, John R. Yates, and Kathleen L. Gould. "Dim1p Is Required for Efficient Splicing and Export of mRNA Encoding Lid1p, a Component of the Fission Yeast Anaphase-Promoting Complex." Eukaryotic Cell 4, no. 3 (March 2005): 577–87. http://dx.doi.org/10.1128/ec.4.3.577-587.2005.

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ABSTRACT Schizosaccharomyces pombe Dim1p is required for maintaining the steady-state level of the anaphase-promoting complex or cyclosome (APC/C) component Lid1p and thus for maintaining the steady-state level and activity of the APC/C. To gain further insight into Dim1p function, we have investigated the mechanism whereby Dim1p influences Lid1p levels. We show that S. pombe cells lacking Dim1p or Saccharomyces cerevisiae cells lacking its ortholog, Dib1p, are defective in generalized pre-mRNA splicing in vivo, a result consistent with the identification of Dim1p as a component of the purified yeast U4/U6.U5 tri-snRNP complex. Moreover, we find that Dim1p is part of a complex with the splicing factor Prp1p. However, although Dim1p is required for efficient splicing of lid1 + pre-mRNA, circumventing the necessity for this particular function of Dim1p is insufficient for restoring normal Lid1p levels. Finally, we provide evidence that Dim1p also participates in the nuclear export of lid1 + mRNA and that it is likely the combined loss of both of these two Dim1p functions which compromises Lid1p levels in the absence of proper Dim1p function. These data indicate that a mechanism acting at the level of mRNA impacts the functioning of the APC/C, a critical complex in controlling mitotic progression.
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36

Malapeira, Jordi, Alberto Moldón, Elena Hidalgo, Gerald R. Smith, Paul Nurse, and José Ayté. "A Meiosis-Specific Cyclin Regulated by Splicing Is Required for Proper Progression through Meiosis." Molecular and Cellular Biology 25, no. 15 (August 1, 2005): 6330–37. http://dx.doi.org/10.1128/mcb.25.15.6330-6337.2005.

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ABSTRACT The meiotic cell cycle is modified from the mitotic cell cycle by having a premeiotic S phase which leads to high levels of recombination, a reductional pattern of chromosome segregation at the first division, and a second division with no intervening DNA synthesis. Cyclin-dependent kinases are essential for progression through the meiotic cell cycle, as for the mitotic cycle. Here we show that a fission yeast cyclin, Rem1, is present only during meiosis. Cells lacking Rem1 have impaired meiotic recombination, and Rem1 is required for premeiotic DNA synthesis when Cig2 is not present. rem1 expression is regulated at the level of both transcription and splicing, with Mei4 as a positive and Cig2 a negative factor of rem1 splicing. This regulation ensures the timely appearance of the different cyclins during meiosis, which is required for the proper progression through the meiotic cell cycle. We propose that the meiosis-specific B-type cyclin Rem1 has a central role in bringing about progression through meiosis.
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37

Webb, Christopher J., Sujata Lakhe-Reddy, Charles M. Romfo, and Jo Ann Wise. "Analysis of Mutant Phenotypes and Splicing Defects Demonstrates Functional Collaboration between the Large and Small Subunits of the Essential Splicing Factor U2AF In Vivo." Molecular Biology of the Cell 16, no. 2 (February 2005): 584–96. http://dx.doi.org/10.1091/mbc.e04-09-0768.

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The heterodimeric splicing factor U2AF plays an important role in 3′ splice site selection, but the division of labor between the two subunits in vivo remains unclear. In vitro assays led to the proposal that the human large subunit recognizes 3′ splice sites with extensive polypyrimidine tracts independently of the small subunit. We report in vivo analysis demonstrating that all five domains of spU2AFLGare essential for viability; a partial deletion of the linker region, which forms the small subunit interface, produces a severe growth defect and an aberrant morphology. A small subunit zinc-binding domain mutant confers a similar phenotype, suggesting that the heterodimer functions as a unit during splicing in Schizosaccharomyces pombe. As this is not predicted by the model for metazoan 3′ splice site recognition, we sought introns for which the spU2AFLGand spU2AFSMmake distinct contributions by analyzing diverse splicing events in strains harboring mutations in each partner. Requirements for the two subunits are generally parallel and, moreover, do not correlate with the length or strength of the 3′ pyrimidine tract. These and other studies performed in fission yeast support a model for 3′ splice site recognition in which the two subunits of U2AF functionally collaborate in vivo.
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38

Sridharan, Vinod, and Ravinder Singh. "A Conditional Role of U2AF in Splicing of Introns with Unconventional Polypyrimidine Tracts." Molecular and Cellular Biology 27, no. 20 (August 20, 2007): 7334–44. http://dx.doi.org/10.1128/mcb.00627-07.

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ABSTRACT Recognition of polypyrimidine (Py) tracts typically present between the branch point and the 3′ splice site by the large subunit of the essential splicing factor U2AF is a key early step in pre-mRNA splicing. Diverse intronic sequence arrangements exist, however, including 3′ splice sites lacking recognizable Py tracts, which raises the question of how general the requirement for U2AF is for various intron architectures. Our analysis of fission yeast introns in vivo has unexpectedly revealed that whereas introns lacking Py tracts altogether remain dependent on both subunits of U2AF, introns with long Py tracts, unconventionally positioned upstream of branch points, are unaffected by U2AF inactivation. Nevertheless, mutation of these Py tracts causes strong dependence on the large subunit U2AF59. We also find that Py tract diversity influences the requirement for the conserved C-terminal domain of U2AF59 (RNA recognition motif 3), which has been implicated in protein-protein interactions with other splicing factors. Together, these results suggest that in addition to Py tract binding by U2AF, supplementary mechanisms of U2AF recruitment and 3′ splice site identification exist to accommodate diverse intron architectures, which have gone unappreciated in biochemical studies of model pre-mRNAs.
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39

Ochotorena, Iciar L., Dai Hirata, Kin-ichiro Kominami, Judith Potashkin, Fikret Sahin, Kelly Wentz-Hunter, Kathleen L. Gould, et al. "Conserved Wat1/Pop3 WD-repeat protein of fission yeast secures genome stability through microtubule integrity and may be involved in mRNA maturation." Journal of Cell Science 114, no. 16 (August 15, 2001): 2911–20. http://dx.doi.org/10.1242/jcs.114.16.2911.

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Accurate chromosome segregation is dependent upon the integrity of mitotic spindles, which pull each pair of sister chromatids towards opposite poles. In this study, we have characterised fission yeast pop3-5235, a diploidising mutant that is impaired in genome stability. Pop3 is the same as Wat1, a conserved protein containing 7 WD repeats. Pop3/Wat1 has also been isolated from a two-hybrid screen as a binding partner to Prp2, the large subunit of the essential splicing factor U2AF. In wat1 mutants, the cellular amount of α-tubulin is decreased to very low levels, which results in compromised microtubules and spindles, consequently leading to unequal chromosome separation. Further analysis shows that, in spite of the binding between Wat1 and Prp2, Wat1 may not be involved directly in splicing reactions per se. Instead, we find that Wat1 is required for the maintenance of α-tubulin mRNA levels; moreover, transcript levels of genes other than the α-tubulin gene are also equally decreased in this mutant. Wild-type Wat1, but not the mutant protein, forms a large complex in the cell with several other proteins, suggesting that Wat1 functions as a structural linker in the complex. The results suggest that Wat1 plays a role in mRNA maturation as a coupling protein between splicing and synthesis and/or stabilisation.
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40

Reich, C., and J. A. Wise. "Evolutionary origin of the U6 small nuclear RNA intron." Molecular and Cellular Biology 10, no. 10 (October 1990): 5548–52. http://dx.doi.org/10.1128/mcb.10.10.5548-5552.1990.

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U6 is the most conserved of the five small nuclear RNAs known to participate in pre-mRNA splicing. In the fission yeast Schizosaccharomyces pombe, the single-copy gene encoding this RNA is itself interrupted by an intron (T. Tani and Y. Ohshima, Nature (London) 337:87-90, 1989). Here we report analysis of the U6 genes from all four Schizosaccharomyces species, revealing that each is interrupted at an identical position by a homologous intron; in other groups, including ascomycete and basidiomycete fungi, as well as more distantly related organisms, the U6 gene is colinear with the RNA. The most parsimonious interpretation of our data is that the ancestral U6 gene did not contain an intron, but rather, it was acquired via a single relatively recent insertional event.
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41

Reich, C., and J. A. Wise. "Evolutionary origin of the U6 small nuclear RNA intron." Molecular and Cellular Biology 10, no. 10 (October 1990): 5548–52. http://dx.doi.org/10.1128/mcb.10.10.5548.

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U6 is the most conserved of the five small nuclear RNAs known to participate in pre-mRNA splicing. In the fission yeast Schizosaccharomyces pombe, the single-copy gene encoding this RNA is itself interrupted by an intron (T. Tani and Y. Ohshima, Nature (London) 337:87-90, 1989). Here we report analysis of the U6 genes from all four Schizosaccharomyces species, revealing that each is interrupted at an identical position by a homologous intron; in other groups, including ascomycete and basidiomycete fungi, as well as more distantly related organisms, the U6 gene is colinear with the RNA. The most parsimonious interpretation of our data is that the ancestral U6 gene did not contain an intron, but rather, it was acquired via a single relatively recent insertional event.
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42

McKinney, R., Kelly Wentz-Hunter, Henning Schmidt, and J. Potashkin. "Molecular characterization of a novel fission yeast gene spUAP2 that interacts with the splicing factor spU2AF 59." Current Genetics 32, no. 5 (November 28, 1997): 323–30. http://dx.doi.org/10.1007/s002940050284.

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43

McDonald, W. Hayes, Ryoma Ohi, Natalia Smelkova, David Frendewey, and Kathleen L. Gould. "Myb-Related Fission Yeast cdc5p Is a Component of a 40S snRNP-Containing Complex and Is Essential for Pre-mRNA Splicing." Molecular and Cellular Biology 19, no. 8 (August 1, 1999): 5352–62. http://dx.doi.org/10.1128/mcb.19.8.5352.

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ABSTRACT Myb-related cdc5p is required for G2/M progression in the yeast Schizosaccharomyces pombe. We report here that all detectable cdc5p is stably associated with a multiprotein 40S complex. Immunoaffinity purification has allowed the identification of 10 cwf (complexed with cdc5p) proteins. Two (cwf6p and cwf10p) are members of the U5 snRNP; one (cwf9p) is a core snRNP protein. cwf8p is the apparent ortholog of the Saccharomyces cerevisiaesplicing factor Prp19p. cwf1 + is allelic to theprp5 + gene defined by the S. pombesplicing mutant, prp5-1, and there is a strong negative genetic interaction between cdc5-120 andprp5-1. Five cwfs have not been recognized previously as important for either pre-mRNA splicing or cell cycle control. Further characterization of cwf1p, cwf2p, cwf3p, and cwf4p demonstrates that they are encoded by essential genes, cosediment with cdc5p at 40S, and coimmunoprecipitate with cdc5p. We further show that cdc5p associates with the U2, U5, and U6 snRNAs and that cells lackingcdc5 + function are defective in pre-mRNA splicing. These data raise the possibility that the cdc5p complex is an intermediate in the assembly or disassembly of an active S. pombe spliceosome.
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44

Gallo, G. J., H. Prentice, and R. E. Kingston. "Heat shock factor is required for growth at normal temperatures in the fission yeast Schizosaccharomyces pombe." Molecular and Cellular Biology 13, no. 2 (February 1993): 749–61. http://dx.doi.org/10.1128/mcb.13.2.749-761.1993.

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Schizosaccharomyces pombe is becoming an increasingly useful organism for the study of cellular processes, since in certain respects, such as the cell cycle and splicing, it is similar to metazoans. Previous biochemical studies have shown that the DNA binding ability of S. pombe heat shock factor (HSF) is fully induced only under stressed conditions, in a manner similar to that of Drosophila melanogaster and humans but differing from the constitutive binding by HSF in the budding yeasts. We report the isolation of the cDNA and gene for the HSF from S. pombe. S. pombe HSF has a domain structure that is more closely related to the structure of human and D. melanogaster HSFs than to the structure of the budding yeast HSFs, further arguing that regulation of HSF in S. pombe is likely to reflect regulation in metazoans. Surprisingly, the S. pombe HSF gene is required for growth at normal temperatures. We show that the S. pombe HSF gene can be replaced by the D. melanogaster HSF gene and that strains containing either of these genes behave similarly to transiently heat-shocked strains with respect to viability and the level of heat-induced transcripts from heat shock promoters. Strains containing the D. melanogaster HSF gene, however, have lower growth rates and show altered morphology at normal growth temperatures. These data demonstrate the functional conservation of domains of HSF that are required for response to heat shock. They further suggest a general role for HSF in growth of eukaryotic cells under normal (nonstressed) growth conditions.
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45

Gallo, G. J., H. Prentice, and R. E. Kingston. "Heat shock factor is required for growth at normal temperatures in the fission yeast Schizosaccharomyces pombe." Molecular and Cellular Biology 13, no. 2 (February 1993): 749–61. http://dx.doi.org/10.1128/mcb.13.2.749.

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Schizosaccharomyces pombe is becoming an increasingly useful organism for the study of cellular processes, since in certain respects, such as the cell cycle and splicing, it is similar to metazoans. Previous biochemical studies have shown that the DNA binding ability of S. pombe heat shock factor (HSF) is fully induced only under stressed conditions, in a manner similar to that of Drosophila melanogaster and humans but differing from the constitutive binding by HSF in the budding yeasts. We report the isolation of the cDNA and gene for the HSF from S. pombe. S. pombe HSF has a domain structure that is more closely related to the structure of human and D. melanogaster HSFs than to the structure of the budding yeast HSFs, further arguing that regulation of HSF in S. pombe is likely to reflect regulation in metazoans. Surprisingly, the S. pombe HSF gene is required for growth at normal temperatures. We show that the S. pombe HSF gene can be replaced by the D. melanogaster HSF gene and that strains containing either of these genes behave similarly to transiently heat-shocked strains with respect to viability and the level of heat-induced transcripts from heat shock promoters. Strains containing the D. melanogaster HSF gene, however, have lower growth rates and show altered morphology at normal growth temperatures. These data demonstrate the functional conservation of domains of HSF that are required for response to heat shock. They further suggest a general role for HSF in growth of eukaryotic cells under normal (nonstressed) growth conditions.
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46

Cipakova, Ingrid, Matus Jurcik, Veronika Rubintova, Marianna Borbova, Barbora Mikolaskova, Jan Jurcik, Jana Bellova, Peter Barath, Juraj Gregan, and Lubos Cipak. "Identification of proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1 in the fission yeast Schizosaccharomyces pombe." Cell Cycle 18, no. 14 (June 20, 2019): 1532–36. http://dx.doi.org/10.1080/15384101.2019.1632126.

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47

Sasaki-Haraguchi, Noriko, Takeshi Ikuyama, Shogo Yoshii, Tomoko Takeuchi-Andoh, David Frendewey, and Tokio Tani. "Cwf16p Associating with the Nineteen Complex Ensures Ordered Exon Joining in Constitutive Pre-mRNA Splicing in Fission Yeast." PLOS ONE 10, no. 8 (August 24, 2015): e0136336. http://dx.doi.org/10.1371/journal.pone.0136336.

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48

Mertins, P., and D. Gallwitz. "Nuclear pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe strictly requires an intron-contained, conserved sequence element." EMBO Journal 6, no. 6 (June 1987): 1757–63. http://dx.doi.org/10.1002/j.1460-2075.1987.tb02428.x.

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49

Mikolaskova, Barbora, Matus Jurcik, Ingrid Cipakova, Tomas Selicky, Jan Jurcik, Silvia Bagelova Polakova, Erika Stupenova, et al. "Identification of Nrl1 Domains Responsible for Interactions with RNA-Processing Factors and Regulation of Nrl1 Function by Phosphorylation." International Journal of Molecular Sciences 22, no. 13 (June 29, 2021): 7011. http://dx.doi.org/10.3390/ijms22137011.

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Pre-mRNA splicing is a key process in the regulation of gene expression. In the fission yeast Schizosaccharomyces pombe, Nrl1 regulates splicing and expression of several genes and non-coding RNAs, and also suppresses the accumulation of R-loops. Here, we report analysis of interactions between Nrl1 and selected RNA-processing proteins and regulation of Nrl1 function by phosphorylation. Bacterial two-hybrid system (BACTH) assays revealed that the N-terminal region of Nrl1 is important for the interaction with ATP-dependent RNA helicase Mtl1 while the C-terminal region of Nrl1 is important for interactions with spliceosome components Ctr1, Ntr2, and Syf3. Consistent with this result, tandem affinity purification showed that Mtl1, but not Ctr1, Ntr2, or Syf3, co-purifies with the N-terminal region of Nrl1. Interestingly, mass-spectrometry analysis revealed that in addition to previously identified phosphorylation sites, Nrl1 is also phosphorylated on serines 86 and 112, and that Nrl1-TAP co-purifies with Cka1, the catalytic subunit of casein kinase 2. In vitro assay showed that Cka1 can phosphorylate bacterially expressed Nrl1 fragments. An analysis of non-phosphorylatable nrl1 mutants revealed defects in gene expression and splicing consistent with the notion that phosphorylation is an important regulator of Nrl1 function. Taken together, our results provide insights into two mechanisms that are involved in the regulation of the spliceosome-associated factor Nrl1, namely domain-specific interactions between Nrl1 and RNA-processing proteins and post-translational modification of Nrl1 by phosphorylation.
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50

Urushiyama, Seiichi, Tokio Tani, and Yasumi Ohshima. "The Prpl + Gene Required for Pre-mRNA Splicing in Schizosaccharomyces pombe Encodes a Protein That Contains TPR Motifs and Is Similar to Prp6p of Budding Yeast." Genetics 147, no. 1 (September 1, 1997): 101–15. http://dx.doi.org/10.1093/genetics/147.1.101.

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Abstract The prp (pre-mRNA processing) mutants of the fission yeast Schizosaccharomyces pombe have a defect in pre-mRNA splicing and accumulate mRNA precursors at a restrictive temperature. One of the prp mutants, prp1-4, also has a defect in poly(A)+ RNA transport. The prp1 + gene encodes a protein of 906 amino acid residues that contains 19 repeats of 34 amino acids termed tetratrico peptide repeat (TPR) motifs, which were proposed to mediate protein-protein interactions. The amino acid sequence of Prplp shares 29.6% identity and 50.6% similarity with that of the PRP6 protein of Saccharomyces cerevisiae, which is a component of the U4/U6 snRNP required for spliceosome assembly. No functional complementation was observed between S. pombe prp1 + and S. cerevisiae PRP6. We examined synthetic lethality of prp1-4 with the other known prp mutations in S. pombe. The results suggest that Prp1p interacts either physically or functionally with Prp4p, Prp6p and Prp13p. Interestingly, the prp1 + gene was found to be identical with the zer1 + gene that functions in cell cycle control. These results suggest that Prp1p/Zer1p is either directly or indirectly involved in cell cycle progression and/or poly(A)+ RNA nuclear export, in addition to pre-mRNA splicing.
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