Skip to main content
SpringerLink
Log in

Implications of maintenance of mother–bud neck size in diverse vital processes of Saccharomyces cerevisiae

  • Original Article
  • Published:
Current Genetics Aims and scope Submit manuscript

Abstract

The mother–bud neck is defined as the boundary between the mother cell and bud in budding microorganisms, wherein sequential morphological events occur throughout the cell cycle. This study was designed to quantitatively investigate the morphology of the mother–bud neck in budding yeast Saccharomyces cerevisiae. Observation of yeast cells with time-lapse microscopy revealed an increase of mother–bud neck size through the cell cycle. After screening of yeast non-essential gene-deletion mutants with the image processing software CalMorph, we comprehensively identified 274 mutants with broader necks during S/G2 phase. Among these yeasts, we extensively analyzed 19 representative deletion mutants with defects in genes annotated to six gene ontology terms (polarisome, actin reorganization, endosomal tethering complex, carboxy-terminal domain protein kinase complex, DNA replication, and maintenance of DNA trinucleotide repeats). The representative broad-necked mutants exhibited calcofluor white sensitivity, suggesting defects in their cell walls. Correlation analysis indicated that maintenance of mother–bud neck size is important for cellular processes such as cell growth, system robustness, and replicative lifespan. We conclude that neck-size maintenance in budding yeast is regulated by numerous genes and has several aspects that are physiologically significant.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Baladrón V, Ufano S, Dueñas E, Martín-Cuadrado AB, del Rey F, Vázquez de Aldana CR (2002) Eng1p, an endo-1,3-beta-glucanase localized at the daughter side of the septum, is involved in cell separation in Saccharomyces cerevisiae. Eukaryot Cell 1:774–786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barral Y, Mermall V, Mooseker MS, Snyder M (2000) Compartmentalization of the cell cortex by septins is required for maintenance of cell polarity in yeast. Mol Cell 5:841–851

    Article  CAS  PubMed  Google Scholar 

  • Barve G, Sanyal P, Manjithaya R (2018) Septin localization and function during autophagy. Curr Genet. https://doi.org/10.1007/s00294-018-0834-8

    Article  PubMed  Google Scholar 

  • Berman J (2006) Morphogenesis and cell cycle progression in Candida albicans. Curr Opin Microbiol 9:595–601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bi E, Park HO (2012) Cell polarization and cytokinesis in budding yeast. Genetics 191:347–387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blanco N, Reidy M, Arroyo J, Cabib E (2012) Crosslinks in the cell wall of budding yeast control morphogenesis at the mother–bud neck. J Cell Sci 125:5781–5789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Byrne KP, Wolfe KH (2005) The Yeast gene order browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15:1456–1461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cabib E (2004) The septation apparatus, a chitin-requiring machine in budding yeast. Arch Biochem Biophys 426:201–207

    Article  CAS  PubMed  Google Scholar 

  • Cabib E, Blanco N, Arroyo J (2012) Presence of a large β(1–3)glucan linked to chitin at the Saccharomyces cerevisiae mother-bud neck suggests involvement in localized growth control. Eukaryot Cell 11:388–400

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chymkowitch P, Enserink JM (2013) The cell cycle rallies the transcription cycle: Cdc28/Cdk1 is a cell cycle-regulated transcriptional CDK. Transcription 4:3–6

    Article  PubMed  Google Scholar 

  • Cid VJ, Adamikova L, Sanchez M, Molina M, Nombela C (2001) Cell cycle control of septin ring dynamics in the budding yeast. Microbiology 147:1437–1450

    Article  CAS  PubMed  Google Scholar 

  • Colombo D, Maathuis MH (2014) Order-independent constraint-based causal structure learning. J Mach Learn Res 15:3921–3962

    Google Scholar 

  • Enserink JM, Smolka MB, Zhou H, Kolodner RD (2006) Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. J Cell Biol 175:729–741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Evangelista M, Pruyne D, Amberg DC, Boone C, Bretscher A (2002) Formins direct Arp2/3-independent actin filament assembly to polarize cell growth in yeast. Nat Cell Biol 4:260–269

    Article  PubMed  Google Scholar 

  • Gebre AA, Okada H, Kim C, Kubo K, Ohnuki S, Ohya Y (2015) Profiling of the effects of antifungal agents on yeast cells based on morphometric analysis. FEMS Yeast Res 15:fov040

    Article  CAS  PubMed  Google Scholar 

  • Gow NA, Brown AJ, Odds FC (2002) Fungal morphogenesis and host invasion. Curr Opin Microbiol 5:366–371

    Article  CAS  PubMed  Google Scholar 

  • He C, Zhou C, Kennedy BK (2018) The yeast replicative aging model. Biochim Biophys Acta. https://doi.org/10.1016/j.bbadis.2018.02.023

    Article  PubMed Central  Google Scholar 

  • Hiraga S, Robertson ED, Donaldson AD (2006) The Ctf18 RFC-like complex positions yeast telomeres but does not specify their replication time. EMBO J 25:1505–1514

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Howell AS, Lew DJ (2012) Morphogenesis and the cell cycle. Genetics 90:51–77

    Article  CAS  Google Scholar 

  • Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M (2002) Systematic identification of pathways that couple cell growth and division in yeast. Science 297:395–400

    Article  CAS  PubMed  Google Scholar 

  • Kadota J, Yamamoto T, Yoshiuchi S, Bi E, Tanaka K (2004) Septin ring assembly requires concerted action of polarisome components, a PAK kinase Cla4p, and the actin cytoskeleton in Saccharomyces cerevisiae. Mol Biol Cell 15:5329–5345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang H, Lew DJ (2017) How do cells know what shape they are? Curr Genet 63:75–77

    Article  CAS  PubMed  Google Scholar 

  • Klis FM, Mol P, Hellingwerf K, Brul S (2002) Dynamics of cell wall structure in Saccharomyces cerevisiae. FEMS Microbiol Rev 26:239–256

    Article  CAS  PubMed  Google Scholar 

  • Kuranda MJ, Robbins PW (1991) Chitinase is required for cell separation during growth of Saccharomyces cerevisiae. J Biol Chem 266:19758–19767

    CAS  PubMed  Google Scholar 

  • Levy SF, Siegal ML (2008) Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol 6:e264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lippincott J, Shannon KB, Shou W, Deshaies RJ, Li R (2001) The Tem1 small GTPase controls actomyosin and septin dynamics during cytokinesis. J Cell Sci 114:1379–1386

    CAS  PubMed  Google Scholar 

  • Liu B, Larsson L, Caballero A, Hao X, Oling D, Grantham J, Nyström T (2010) The polarisome is required for segregation and retrograde transport of protein aggregates. Cell 140:257–267

    Article  CAS  PubMed  Google Scholar 

  • McCormick MA, Delaney JR, Tsuchiya M et al (2015) A comprehensive analysis of replicative lifespan in 4,698 single-gene deletion strains uncovers conserved mechanisms of aging. Cell Metab 22:895–906

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McMurray MA, Thorner J (2009) Reuse, replace, recycle. Specificity in subunit inheritance and assembly of higher-order septin structures during mitotic and meiotic division in budding yeast. Cell Cycle 8:195–203

    Article  CAS  PubMed  Google Scholar 

  • Meitinger F, Pereira G (2017) The septin-associated kinase Gin4 recruits Gps1 to the site of cell division. Mol Biol Cell 28:883–889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meitinger F, Khmelinskii A, Morlot S, Kurtulmus B, Palani S, Andres-Pons A, Hub B, Knop M, Charvin G, Pereira G (2014) A memory system of negative polarity cues prevents replicative aging. Cell 59:1056–1069

    Article  CAS  Google Scholar 

  • Meitingera F, Palani S (2016) Actomyosin ring driven cytokinesis in budding yeast. Semin Cell Dev Biol 53:19–27

    Article  CAS  Google Scholar 

  • Oh Y, Bi E (2011) Septin structure and function in yeast and beyond. Trends Cell Biol 21:141–148

    Article  CAS  PubMed  Google Scholar 

  • Oh Y, Schreiter JH, Okada H, Wloka C, Okada S, Yan D, Duan X, Bi E (2017) Hof1 and Chs4 interact via F-BAR domain and Sel1-like repeats to control extracellular matrix deposition during cytokinesis. Curr Biol 27:2878–2886

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ohya Y, Sese J, Yukawa M, Sano F et al (2005) High-dimensional and large-scale phenotyping of yeast mutants. Proc Natl Acad Sci USA 102:19015–19020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Okada H, Ohnuki S, Roncero C, Konopka JB, Ohya Y (2014) Distinct roles of cell wall biogenesis in yeast morphogenesis as revealed by multivariate analysis of high-dimensional morphometric data. Mol Biol Cell 25:222–233

    Article  PubMed  PubMed Central  Google Scholar 

  • Onishi M, Ko N, Nishihama R, Pringle JR (2013) Distinct roles of Rho1, Cdc42, and Cyk3 in septum formation and abscission during yeast cytokinesis. J Cell Biol 202:311–329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Piotrowski J, Okada H, Lu F et al (2015) The plant derived, antifungal agent poacic acid targets β-1,3-glucan. Proc Natl Acad Sci USA 112:1490–1497

    Google Scholar 

  • Piotrowski JS, Li SC, Deshpande R et al (2017) Functional annotation of chemical libraries across diverse biological processes. Nat Chem Biol 13:1217–1286a

    Article  CAS  Google Scholar 

  • Powers RW 3rd, Kaeberlein M, Caldwell SD, Kennedy BK, Fields S (2006) Extension of chronological lifespan in yeast by decreased TOR pathway signaling. Genes Dev 20:174–184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ram AF, Klis FM (2006) Identification of fungal cell wall mutants using susceptibility assays based on Calcofluor white and Congo red. Nat Protoc 1:2253–2256

    Article  CAS  PubMed  Google Scholar 

  • Sagot I, Klee SK, Pellman D (2002) Yeast formins regulate cell polarity by controlling the assembly of actin cables. Nat Cell Biol 4:42–50

    Article  CAS  PubMed  Google Scholar 

  • Schmidt M, Varma A, Drgon T, Bowers B, Cabib E (2003) Septins, under Cla4p regulation, and the chitin ring are required for neck integrity in budding yeast. Mol Biol Cell 14:2128–2141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scutari M (2010) Learning Bayesian networks with the bnlearn R package. J Stat Softw 35:1–22

    Article  Google Scholar 

  • Sheu YJ, Santos B, Fortin N, Costigan C, Snyder M (1998) Spa2p interacts with cell polarity proteins and signaling components involved in yeast cell morphogenesis. Mol Cell Biol 18:4053–4069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh P, Li R (2018) Emerging roles for sphingolipids in cellular aging. Curr Genet 64:761–767

    Article  CAS  PubMed  Google Scholar 

  • Snyder M, Gehrun S, Page BD (1991) Studies concerning the temporal and genetic control of cell polarity in Saccharomyces cerevisiae. J Cell Biol 114:515–532

    Article  CAS  PubMed  Google Scholar 

  • Soifer I, Robert L, Amir A (2016) Single-cell analysis of growth in budding yeast and bacteria reveals a common size regulation strategy. Curr Biol 26:356–361

    Article  CAS  PubMed  Google Scholar 

  • Solinger JA, Spang A (2013) Tethering complexes in the endocytic pathway: CORVET and HOPS. FEBS J 280:2743–2757

    Article  CAS  PubMed  Google Scholar 

  • Supek F, Bosnjak M, Skunca N, Smuc T (2011) Revigo summarizes and visualizes long lists of gene ontology terms. PLoS One 6:e21800

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suzuki G, Wang Y, Kubo K, Hirata E, Ohnuki S, Ohya Y (2018) Global study of holistic morphological effectors in the budding yeast Saccharomyces cerevisiae. BMC Genom 19:149

    Article  CAS  Google Scholar 

  • Takizawa PA, DeRisi JL, Wilhelm JE, Vale RD (2000) Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science 290:341–344

    Article  CAS  PubMed  Google Scholar 

  • Tessarz P, Schwarz M, Mogk A, Bukau B (2009) The yeast AAA+ chaperone Hsp104 is part of a network that links the actin cytoskeleton with the inheritance of damaged proteins. Mol Cell Biol 29:3738–3745

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsamardinos I, Brown LE, Aliferis CF (2006) The max–min hill-climbing Bayesian network structure learning algorithm. Mach Learn 65:31–78

    Article  Google Scholar 

  • Warringer J, Ericson E, Fernandez L, Nerman O, Blomberg A (2003) High-resolution yeast phenomics resolves different physiological features in the saline response. Proc Natl Acad Sci USA 100:15724–15729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe M, Watanabe D, Nogami S, Morishita S, Ohya Y (2009) Comprehensive and quantitative analysis of yeast deletion mutants defective in apical and isotropic bud growth. Curr Genet 55:365–380

    Article  CAS  PubMed  Google Scholar 

  • Weiss EL (2012) Mitotic exit and separation of mother and daughter cells. Genetics 192:1165–1202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wloka C, Bi E (2012) Mechanisms of cytokinesis in budding yeast. Cytoskeleton (Hoboken) 69:710–726

    Article  CAS  Google Scholar 

  • Yang M, Ohnuki S, Ohya Y (2014) Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains. BMC Genom 15:932

    Article  Google Scholar 

  • Yvert G, Ohnuki S, Nogami S, Imanaga Y, Fehrmann S, Schacherer J, Ohya Y (2013) Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast. BMC Syst Biol 7:54

    Article  PubMed  PubMed Central  Google Scholar 

  • Zander S, Baumann S, Weidtkamp-Peters S, Feldbrügge M (2016) Endosomal assembly and transport of heteromeric septin complexes promote septin cytoskeleton formation. J Cell Sci 129:2778–2792

    Article  CAS  PubMed  Google Scholar 

  • Zhou C, Slaughter BD, Unruh JR, Eldakak A, Rubinstein B, Li R (2011) Motility and segregation of Hsp104-associated protein aggregates in budding yeast. Cell 147:1186–1196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We would like to thank Bhumil Patel and Brian Kennedy for sharing unpublished data of RLS, and Satoshi Yoshida and staff of Signal Transduction for their helpful discussions. This work was supported by Grants-in-Aid of Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (15H04402 to Y.O., 16H04898 to M.M.), and a National Institutes of Health Grant (GM115420 to E.B.).

Author information

Authors and Affiliations

  1. Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan

    Karen Kubo, Takuya Shimamoto, Shinsuke Ohnuki & Yoshikazu Ohya

  2. Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA

    Hiroki Okada & Erfei Bi

  3. Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan

    Yoshitaka Kimori

  4. Department of Management and Information Sciences, Faculty of Environmental and Information Sciences, Fukui University of Technology, Gakuen, Fukui City, Fukui, 910-8505, Japan

    Yoshitaka Kimori

  5. Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, 739-8530, Japan

    Masaki Mizunuma

  6. AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-8565, Japan

    Yoshikazu Ohya

Authors
  1. Karen Kubo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hiroki Okada
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Takuya Shimamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yoshitaka Kimori
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Masaki Mizunuma
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Erfei Bi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Shinsuke Ohnuki
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yoshikazu Ohya
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yoshikazu Ohya.

Additional information

Communicated by M. Kupiec.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig. S1

Lengths calculated from GFP-Ras2 signals were quantified every 3 or 4 min after bud emergence (0 min). Lines with different colors show approximately linear gamma distributions of the 15 different cells examined. (PDF 773 KB)

Fig. S2

Phenotypic potential of 114 wide-neck mutants detected during M phase and other mutants. Red and gray lines indicate regression lines of the 114 wide-neck mutants and others. * indicate significant differences at P <  0.01, as determined via t test. (PDF 3034 KB)

Table S1

Mutants with abnormal neck size. (XLSX 84 KB)

Table S2

CW-sensitivity and neck-width of the 28 mutants deleted with the genes annotated to the six GO terms. (XLSX 36 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kubo, K., Okada, H., Shimamoto, T. et al. Implications of maintenance of mother–bud neck size in diverse vital processes of Saccharomyces cerevisiae. Curr Genet 65, 253–267 (2019). https://doi.org/10.1007/s00294-018-0872-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00294-018-0872-2

Keywords

Search

Navigation