BACKGROUND: Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell-cycle progression, but no specific roles have been described and their target genes have been only partially mapped. METHODOLOGY/PRINCIPAL FINDINGS: Using a combination of transcriptome profiling under various conditions and genome-wide analysis of CSL-DNA interactions, we identify genes regulated directly and indirectly by CSL proteins in fission yeast. We show that the expression of stress-response genes and genes that are expressed periodically during the cell cycle is deregulated upon genetic manipulation of cbf11 and/or cbf12. Accordingly, the coordination of mitosis and cytokinesis is perturbed in cells with genetically manipulated CSL protein levels, together with other specific defects in cell-cycle progression. Cbf11 activity is nutrient-dependent and Δcbf11-associated defects are mitigated by inactivation of the protein kinase A (Pka1) and stress-activated MAP kinase (Sty1p38) pathways. Furthermore, Cbf11 directly regulates a set of lipid metabolism genes and Δcbf11 cells feature a stark decrease in the number of storage lipid droplets. CONCLUSIONS/SIGNIFICANCE: Our results provide a framework for a more detailed understanding of the role of CSL proteins in the regulation of cell-cycle progression in fission yeast.

Department of Cell Biology Faculty of Science Charles University Prague Prague Czech Republic

Research Department of Genetics Evolution and Environment and UCL Cancer Institute University College London London United Kingdom

Research Department of Genetics Evolution and Environment and UCL Cancer Institute University College London London United Kingdom; Department of Cell Biology Faculty of Science Charles University Prague Prague Czech Republic

Erratum v

PLoS One. 2024 Feb 15;19(2):e0299200. doi: 10.1371/journal.pone.0299200. PubMed

Zobrazit více v PubMed

Gould KL (2004) Protein Kinases Driving the Cell Cycle In: Egel R, editor. The Molecular Biology of Schizosaccharomyces pombe. Springer; pp. 27–40.

Rustici G, Mata J, Kivinen K, Lió P, Penkett CJ, Burns G, et al. (2004) Periodic gene expression program of the fission yeast cell cycle. Nat Genet 36: 809–817. 10.1038/ng1377 PubMed DOI

Peng X, Karuturi RKM, Miller LD, Lin K, Jia Y, Kondu P, et al. (2005) Identification of cell cycle-regulated genes in fission yeast. Mol Biol Cell 16: 1026–1042. 10.1091/mbc.E04-04-0299 PubMed DOI PMC

Oliva A, Rosebrock A, Ferrezuelo F, Pyne S, Chen H, Skiena S, et al. (2005) The cell cycle-regulated genes of Schizosaccharomyces pombe . PLoS Biol 3: e225 10.1371/journal.pbio.0030225 PubMed DOI PMC

Aligianni S, Lackner DH, Klier S, Rustici G, Wilhelm BT, Marguerat S, et al. (2009) The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback. PLoS Genet 5: e1000626 10.1371/journal.pgen.1000626 PubMed DOI PMC

De Bruin RAM, Kalashnikova TI, Aslanian A, Wohlschlegel J, Chahwan C, Yates JR 3rd, et al. (2008) DNA replication checkpoint promotes G1-S transcription by inactivating the MBF repressor Nrm1. Proc Natl Acad Sci U S A 105: 11230–11235. 10.1073/pnas.0801106105 PubMed DOI PMC

Zilahi E, Salimova E, Simanis V, Sipiczki M (2000) The S. pombe sep1 gene encodes a nuclear protein that is required for periodic expression of the cdc15 gene. FEBS Lett 481: 105–108. PubMed

Martín-Cuadrado AB, Dueñas E, Sipiczki M, Vázquez de Aldana CR, del Rey F (2003) The endo-beta-1,3-glucanase eng1p is required for dissolution of the primary septum during cell separation in Schizosaccharomyces pombe . J Cell Sci 116: 1689–1698. 10.1242/jcs.00377 PubMed DOI

Bulmer R, Pic-Taylor A, Whitehall SK, Martin KA, Millar JBA, Quinn J, et al. (2004) The forkhead transcription factor Fkh2 regulates the cell division cycle of Schizosaccharomyces pombe . Eukaryot Cell 3: 944–954. 10.1128/EC.3.4.944-954.2004 PubMed DOI PMC

Buck V, Ng SS, Ruiz-Garcia AB, Papadopoulou K, Bhatti S, Samuel JM, et al. (2004) Fkh2p and Sep1p regulate mitotic gene transcription in fission yeast. J Cell Sci 117: 5623–5632. 10.1242/jcs.01473 PubMed DOI

Lowndes NF, McInerny CJ, Johnson AL, Fantes PA, Johnston LH (1992) Control of DNA synthesis genes in fission yeast by the cell-cycle gene cdc10+ . Nature 355: 449–453. 10.1038/355449a0 PubMed DOI

Papadopoulou K, Chen J-S, Mead E, Feoktistova A, Petit C, Agarwal M, et al. (2010) Regulation of cell cycle-specific gene expression in fission yeast by the Cdc14p-like phosphatase Clp1p. J Cell Sci 123: 4374–4381. 10.1242/jcs.073056 PubMed DOI

Takayama Y, Takahashi K (2007) Differential regulation of repeated histone genes during the fission yeast cell cycle. Nucleic Acids Res 35: 3223–3237. 10.1093/nar/gkm213 PubMed DOI PMC

Bushel PR, Heard NA, Gutman R, Liu L, Peddada SD, Pyne S (2009) Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. BMC Syst Biol 3: 93 10.1186/1752-0509-3-93 PubMed DOI PMC

Pursglove SE, Mackay JP (2005) CSL: a notch above the rest. Int J Biochem Cell Biol 37: 2472–2477. 10.1016/j.biocel.2005.06.013 PubMed DOI

Joshi I, Minter LM, Telfer J, Demarest RM, Capobianco AJ, Aster JC, et al. (2009) Notch signaling mediates G1/S cell-cycle progression in T cells via cyclin D3 and its dependent kinases. Blood 113: 1689–1698. 10.1182/blood-2008-03-147967 PubMed DOI PMC

Sarmento LM, Huang H, Limon A, Gordon W, Fernandes J, Tavares MJ, et al. (2005) Notch1 modulates timing of G1-S progression by inducing SKP2 transcription and p27 Kip1 degradation. J Exp Med 202: 157–168. 10.1084/jem.20050559 PubMed DOI PMC

Ronchini C, Capobianco AJ (2001) Induction of cyclin D1 transcription and CDK2 activity by Notch(ic): implication for cell cycle disruption in transformation by Notch(ic). Mol Cell Biol 21: 5925–5934. 10.1128/MCB.21.17.5925 PubMed DOI PMC

Rangarajan A, Talora C, Okuyama R, Nicolas M, Mammucari C, Oh H, et al. (2001) Notch signaling is a direct determinant of keratinocyte growth arrest and entry into differentiation. EMBO J 20: 3427–3436. 10.1093/emboj/20.13.3427 PubMed DOI PMC

Převorovský M, Půta F, Folk P (2007) Fungal CSL transcription factors. BMC Genomics 8: 233 10.1186/1471-2164-8-233 PubMed DOI PMC

Převorovský M, Atkinson SR, Ptáčková M, McLean JR, Gould K, Folk P, et al. (2011) N-termini of fungal CSL transcription factors are disordered, enriched in regulatory motifs and inhibit DNA binding in fission yeast. PLoS One 6: e23650 10.1371/journal.pone.0023650 PubMed DOI PMC

Převorovský M, Groušl T, Staňurová J, Ryneš J, Nellen W, Půta F, et al. (2009) Cbf11 and Cbf12, the fission yeast CSL proteins, play opposing roles in cell adhesion and coordination of cell and nuclear division. Exp Cell Res 315: 1533–1547. 10.1016/j.yexcr.2008.12.001 PubMed DOI

Oravcová M, Teska M, Půta F, Folk P, Převorovský M (2013) Fission Yeast CSL Proteins Function as Transcription Factors. PLoS One 8: e59435 10.1371/journal.pone.0059435 PubMed DOI PMC

Kwon EG, Laderoute A, Chatfield-Reed K, Vachon L, Karagiannis J, Chua G (2012) Deciphering the Transcriptional-Regulatory Network of Flocculation in Schizosaccharomyces pombe . PLoS Genet 8: e1003104 10.1371/journal.pgen.1003104 PubMed DOI PMC

Vachon L, Wood J, Kwon E-JG, Laderoute A, Chatfield-Reed K, Karagiannis J, et al. (2013) Functional characterization of fission yeast transcription factors by overexpression analysis. Genetics 194: 873–884. 10.1534/genetics.113.150870 PubMed DOI PMC

Hayles J, Wood V, Jeffery L, Hoe K- L, Kim D-U, Park HO, et al. (2013) A genome-wide resource of cell cycle and cell shape genes of fission yeast. Open Biol 3: 130053 10.1098/rsob.130053 PubMed DOI PMC

Wells ML, Huang W, Li L, Gerrish KE, Fargo DC, Ozsolak F, et al. (2012) Posttranscriptional regulation of cell-cell interaction protein-encoding transcripts by Zfs1p in Schizosaccharomyces pombe . Mol Cell Biol 32: 4206–4214. 10.1128/MCB.00325-12 PubMed DOI PMC

Navarro FJ, Nurse P (2012) A systematic screen reveals new elements acting at the G2/M cell cycle control. Genome Biol 13: R36 10.1186/gb-2012-13-5-r36 PubMed DOI PMC

Beltraminelli N, Murone M, Simanis V (1999) The S. pombe zfs1 gene is required to prevent septation if mitotic progression is inhibited. J Cell Sci 112 Pt 18: 3103–3114. PubMed

Moreno S, Klar A, Nurse P (1991) Molecular genetic analysis of fission yeast Schizosaccharomyces pombe . Methods Enzymol 194: 795–823. doi: 10.1534/genetics.107.076315 PubMed DOI

Bähler J, Wu JQ, Longtine MS, Shah NG, McKenzie A, Steever AB, et al. (1998) Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe . Yeast 14: 943–951. 10.1002/(SICI)1097-0061(199807)14:10<943::AID-YEA292>3.0.CO;2-Y PubMed DOI

Moreno MB, Durán A, Ribas JC (2000) A family of multifunctional thiamine-repressible expression vectors for fission yeast. Yeast 16: 861–872. 10.1002/1097-0061(20000630)16:9<861::AID-YEA577>3.0.CO;2-9 PubMed DOI

Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9: 671–675. 10.1038/nmeth.2089 PubMed DOI PMC

Rostron KA, Rolph CE, Lawrence CL (2015) Nile red fluorescence screening facilitating neutral lipid phenotype determination in budding yeast, Saccharomyces cerevisiae, and the fission yeast Schizosaccharomyces pombe . Antonie Van Leeuwenhoek 108: 97–106. 10.1007/s10482-015-0467-6 PubMed DOI

Van Driessche B, Tafforeau L, Hentges P, Carr AM, Vandenhaute J (2005) Additional vectors for PCR-based gene tagging in Saccharomyces cerevisiae and Schizosaccharomyces pombe using nourseothricin resistance. Yeast 22: 1061–1068. 10.1002/yea.1293 PubMed DOI

Gregan J, Rabitsch PK, Rumpf C, Novatchkova M, Schleiffer A, Nasmyth K (2006) High-throughput knockout screen in fission yeast. Nat Protoc 1: 2457–2464. 10.1038/nprot.2006.385 PubMed DOI PMC

Lyne R, Burns G, Mata J, Penkett CJ, Rustici G, Chen D, et al. (2003) Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics 4: 27 10.1186/1471-2164-4-27 PubMed DOI PMC

Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48: 240–248. 10.1016/j.ymeth.2009.03.001 PubMed DOI PMC

Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. 10.1093/bioinformatics/btp324 PubMed DOI PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC

Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform 14: 178–192. 10.1093/bib/bbs017 PubMed DOI PMC

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137 10.1186/gb-2008-9-9-r137 PubMed DOI PMC

Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28–36. PubMed

Sazer S, Sherwood SW (1990) Mitochondrial growth and DNA synthesis occur in the absence of nuclear DNA replication in fission yeast. J Cell Sci 97 (Pt 3): 509–516. PubMed

Knutsen JHJ, Rein ID, Rothe C, Stokke T, Grallert B, Boye E (2011) Cell-cycle analysis of fission yeast cells by flow cytometry. PLoS One 6: e17175 10.1371/journal.pone.0017175 PubMed DOI PMC

Chua G (2013) Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network. Biochem Soc Trans 41: 1696–1700. 10.1042/BST20130224 PubMed DOI

Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bähler J (2006) The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast 23: 261–277. 10.1002/yea.1351 PubMed DOI PMC

Mata J, Lyne R, Burns G, Bähler J (2002) The transcriptional program of meiosis and sporulation in fission yeast. Nat Genet 32: 143–147. 10.1038/ng951 PubMed DOI

Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, et al. (2003) Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14: 214–229. 10.1091/mbc.E02-08-0499 PubMed DOI PMC

Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, et al. (2012) PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res 40: D695–D699. 10.1093/nar/gkr853 PubMed DOI PMC

De Groot PWJ, Hellingwerf KJ, Klis FM (2003) Genome-wide identification of fungal GPI proteins. Yeast 20: 781–796. 10.1002/yea.1007 PubMed DOI

Iso T, Kedes L, Hamamori Y (2003) HES and HERP families: multiple effectors of the Notch signaling pathway. J Cell Physiol 194: 237–255. 10.1002/jcp.10208 PubMed DOI

Smith DA, Toone WM, Chen D, Bahler J, Jones N, Morgan BA, et al. (2002) The Srk1 protein kinase is a target for the Sty1 stress-activated MAPK in fission yeast. J Biol Chem 277: 33411–33421. 10.1074/jbc.M204593200 PubMed DOI

Petersen J, Nurse P (2007) TOR signalling regulates mitotic commitment through the stress MAP kinase pathway and the Polo and Cdc2 kinases. Nat Cell Biol 9: 1263–1272. 10.1038/ncb1646 PubMed DOI

Harigaya Y, Yamamoto M (2007) Molecular mechanisms underlying the mitosis-meiosis decision. Chromosome Res 15: 523–537. 10.1007/s10577-007-1151-0 PubMed DOI

Tun T, Hamaguchi Y, Matsunami N, Furukawa T, Honjo T, Kawaichi M (1994) Recognition sequence of a highly conserved DNA binding protein RBP-J kappa. Nucleic Acids Res 22: 965–971. PubMed PMC

Del Bianco C, Vedenko A, Choi SH, Berger MF, Shokri L, Bulyk ML, et al. (2010) Notch and MAML-1 complexation do not detectably alter the DNA binding specificity of the transcription factor CSL. PLoS One 5: e15034 10.1371/journal.pone.0015034 PubMed DOI PMC

Gupta DR, Paul SK, Oowatari Y, Matsuo Y, Kawamukai M (2011) Complex formation, phosphorylation, and localization of protein kinase A of Schizosaccharomyces pombe upon glucose starvation. Biosci Biotechnol Biochem 75: 1456–1465. 10.1271/bbb.110125 PubMed DOI

Jin M, Fujita M, Culley BM, Apolinario E, Yamamoto M, Maundrell K, et al. (1995) sck1, a high copy number suppressor of defects in the cAMP-dependent protein kinase pathway in fission yeast, encodes a protein homologous to the Saccharomyces cerevisiae SCH9 kinase. Genetics 140: 457–467. PubMed PMC

López-Maury L, Marguerat S, Bähler J (2008) Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet 9: 583–593. 10.1038/nrg2398 PubMed DOI

Shiozaki K, Russell P (1995) Cell-cycle control linked to extracellular environment by MAP kinase pathway in fission yeast. Nature 378: 739–743. 10.1038/378739a0 PubMed DOI

Maeda T, Watanabe Y, Kunitomo H, Yamamoto M (1994) Cloning of the pka1 gene encoding the catalytic subunit of the cAMP-dependent protein kinase in Schizosaccharomyces pombe . J Biol Chem 269: 9632–9637. PubMed

Byrne SM, Hoffman CS (1993) Six git genes encode a glucose-induced adenylate cyclase activation pathway in the fission yeast Schizosaccharomyces pombe . J Cell Sci 105 (Pt 4: 1095–1100. PubMed PMC

Davidson MK, Shandilya HK, Hirota K, Ohta K, Wahls WP (2004) Atf1-Pcr1-M26 complex links stress-activated MAPK and cAMP-dependent protein kinase pathways via chromatin remodeling of cgs2+ . J Biol Chem 279: 50857–50863. 10.1074/jbc.M409079200 PubMed DOI PMC

Machanick P, Bailey TL (2011) MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27: 1696–1697. 10.1093/bioinformatics/btr189 PubMed DOI PMC

Atilla-Gokcumen GE, Muro E, Relat-Goberna J, Sasse S, Bedigian A, Coughlin ML, et al. (2014) Dividing cells regulate their lipid composition and localization. Cell 156: 428–439. 10.1016/j.cell.2013.12.015 PubMed DOI PMC

Saitoh S, Takahashi K, Nabeshima K, Yamashita Y, Nakaseko Y, Hirata A, et al. (1996) Aberrant mitosis in fission yeast mutants defective in fatty acid synthetase and acetyl CoA carboxylase. J Cell Biol 134: 949–961. PubMed PMC

Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast

Perturbed fatty-acid metabolism is linked to localized chromatin hyperacetylation, increased stress-response gene expression and resistance to oxidative stress

Repression of a large number of genes requires interplay between homologous recombination and HIRA

Mitotic defects in fission yeast lipid metabolism 'cut' mutants are suppressed by ammonium chloride

CSL protein regulates transcription of genes required to prevent catastrophic mitosis in fission yeast