DNA Replication: Yeast

Shanna J Smith, City of Hope Beckman Research Institute, Duarte, California, USA
Caroline M Li, City of Hope Beckman Research Institute, Duarte, California, USA
Mustafa Raoof, City of Hope Beckman Research Institute, Duarte, California, USA
Robert G Lingeman, City of Hope Beckman Research Institute, Duarte, California, USA
Robert J Hickey, City of Hope Beckman Research Institute, Duarte, California, USA
Linda H Malkas, City of Hope Beckman Research Institute, Duarte, California, USA

Published online: September 2018

DOI: 10.1002/9780470015902.a0027975

Abstract

DNA replication is a complex biological process essential to maintaining the fidelity of genetic information passed to subsequent generations, while allowing for the mutations necessary for natural selection. The cellular machinery required for DNA replication must be precisely controlled throughout the cycle. A variety of DNA polymerases have proofreading and repairing capabilities to avoid catastrophic errors, thus maintaining genomic stability. Much of the mechanism involved in this process is evolutionarily conserved. Because yeast is a relatively simple and inexpensive organism to work with, much of our understanding of DNA replication in eukaryotes originates from experiments with yeast. The most thoroughly characterized model yeast systems are Saccharomyces cerevisiae (budding yeast) and Saccharomyces pombe (fission yeast).

Key Concepts

  • Yeast is a good model organism for simplifying and characterising cellular processes, such as DNA replication.
  • The two most commonly used yeast models are S. cerevisiae and S. pombe.
  • DNA replication is a complex biological process essential to genomic replication.
  • DNA replication is a process that involves timely organisation of proteins and is regulated during the cell cycle by cyclin‐dependent protein kinases.
  • Termination of DNA replication in yeast is generally not sequence specific, except in special circumstances in the cellular process.

Keywords: Saccharomyces cerevisiae; Saccharomyces pombe; cell cycle; initiation; elongation; termination; replication complex; autonomous replicating sequence (ARS)

Figure 1. Initiation of DNA replication in S. cerevisiae. The DNA replication origins in S. cerevisiae are autonomously replicating sequences (ARS) consisting of element A (a conserved 11 bp AT‐rich sequence or ACS), B1, and B2 on the DNA. Element A and B1 is required for ORC binding. B2 is proposed to have a dsDNA unwinding element that is needed for MCM binding. Some origins have element B3, where the transcription factor Abf1 binds. At the G1 phase, CDK levels are low, and the double hexamer of MCM is inactive. Binding of inactive MCM (Mcm2‐7) requires ORC, Cdc6 and Cdt1. At high CDK levels, the double hexamer MCM is activated as the core component of the CMG complex. The CMG complex consists of: Cdc45, MCM and GINS (Sld5, Psf1, Psf2 and Psf3).
Figure 2. DNA duplex unwinding and replication fork formation in S. pombe. Origin recognition complex (ORC) associated with chromatin marks the ARS elements. Upon the initiation of replication, the MCM recruits Cdc18 (homologue of S. cerevisiae Cdc 6) and Cdt1 to the origin, thereby forming the prereplicative complex (pre‐RC). At the G1 – S transition, Sna41 (homologue of S. cerevisiae Cdc45) associates with the pre‐RC as a result of the action of several protein kinases (not shown) forming the preinitiation complex (pre‐IC). In the S phase, the two activated CMG helicase structures will move in opposite directions down the dsDNA strand, unwinding dsDNA via ATP hydrolysis, and creating two DNA replication forks.
Figure 3. Simplified model of leading‐ and lagging‐strand synthesis during elongation. DNA synthesis moves away from the DNA replication origin in two opposite DNA replication forks. As the CMG complex (Cdc45, MCM2‐7, GINS) opens double‐helical DNA, topoisomerases relieve torsional strain in DNA. Yellow bars represent RNA–DNA primers synthesised by Pol α. DNA synthesis by Pol ϵ at the leading strand is increased in the presence of PCNA. Pol δ is the major polymerase that synthesises DNA at the lagging strand and is very processive in the presence of PCNA. Many molecules of RPA bind to exposed ssDNA.
Figure 4. Comparison of the programmed termination of rDNA in S. cerevisiae and S. pombe. One complete origin to origin unit is shown for each type of yeast. (a) In S. cerevisiae, Fob1 binds to identical Ter sequences on the rDNA strand. (b) In S. pombe, Sap1 binds to Ter1, while Reb1 binds to Ter2 and Ter3 on the rDNA strand. An additional factor, Rtf1, has been shown bind to Ter site RTS1. The direction of replication is shown with black arrows below each strand. The T‐bar in the opposite direction indicates replication fork stalling.
close

References

Barberis M, Spiesser TW and Klipp E (2010) Replication origins and timing of temporal replication in budding yeast: how to solve the conundrum? Current Genomics 11: 199–211.

Bastia D and Zaman S (2014) Mechanism and physiological significance of programmed replication termination. Seminars in Cell and Developmental Biology 30: 165–173.

Bell SP and Labib K (2016) Chromosome duplication in Saccharomyces cerevisiae. Genetics 203: 1027–1067.

Biswas S and Bastia D (2008) Mechanistic insights into replication termination as revealed by investigations of the Reb1‐Ter3 complex of Schizosaccharomyces pombe. Molecular and Cellular Biology 28: 6844–6857.

Budd ME and Campbell JL (2013) Dna2 is involved in CA strand resection and nascent lagging strand completion at native yeast telomeres. The Journal of Biological Chemistry 288: 29414–29429.

Chang F, May CD, Hoggard T, et al. (2011) High‐resolution analysis of four efficient yeast replication origins reveals new insights into the ORC and putative MCM binding elements. Nucleic Acids Research 39: 6523–6535.

Chuang RY and Kelly TJ (1999) The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT‐hooks. Proceedings of the National Academy of Sciences of the United States of America 96: 2656–2661.

Clyne RK and Kelly TJ (1995) Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. The EMBO Journal 14: 6348–6357.

Dai J, Chuang RY and Kelly TJ (2005) DNA replication origins in the Schizosaccharomyces pombe genome. Proceedings of the National Academy of Sciences of the United States of America 102: 337–342.

Doublie S and Zahn KE (2014) Structural insights into eukaryotic DNA replication. Frontiers in Microbiology 5: 444.

Duina AA, Miller ME and Keeney JB (2014) Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system. Genetics 197: 33–48.

Evrin C, Clarke P, Zech J, et al. (2009) A double‐hexameric MCM2‐7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication. Proceedings of the National Academy of Sciences of the United States of America 106: 20240–20245.

Gadaleta MC and Noguchi E (2017) Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome. Genes 8: 98.

Gilbert DM (2001) Making sense of eukaryotic DNA replication origins. Science 294: 96–100.

Graham JE, Marians KJ and Kowalczykowski SC (2017) Independent and stochastic action of DNA polymerases in the replisome. Cell 169: 1201–1213 e1217.

Guan L, He P, Yang F, et al. (2017) Sap1 is a replication‐initiation factor essential for the assembly of pre‐replicative complex in the fission yeast Schizosaccharomyces pombe. Journal of Biological Chemistry 292: 6056–6075.

Hogg M, Osterman P, Bylund GO, et al. (2014) Structural basis for processive DNA synthesis by yeast DNA polymerase varepsilon. Nature Structural & Molecular Biology 21: 49–55.

Kemmerich FE, Daldrop P, Pinto C, et al. (2016) Force regulated dynamics of RPA on a DNA fork. Nucleic Acids Research 44: 5837–5848.

Kim SM and Huberman JA (2001) Regulation of replication timing in fission yeast. The EMBO Journal 20: 6115–6126.

Kitamura E, Blow JJ and Tanaka TU (2006) Live‐cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell 125: 1297–1308.

Kong D and DePamphilis ML (2002) Site‐specific ORC binding, pre‐replication complex assembly and DNA synthesis at Schizosaccharomyces pombe replication origins. The EMBO Journal 21: 5567–5576.

Krings G and Bastia D (2006) Molecular architecture of a eukaryotic DNA replication terminus‐terminator protein complex. Molecular and Cellular Biology 26: 8061–8074.

Krishna TS, Kong XP, Gary S, Burgers PM and Kuriyan J (1994) Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79: 1233–1243.

Levikova M and Cejka P (2015) The Saccharomyces cerevisiae Dna2 can function as a sole nuclease in the processing of Okazaki fragments in DNA replication. Nucleic Acids Research 43: 7888–7897.

Lewis JS, Spenkelink LM, Schauer GD, et al. (2017) Single‐molecule visualization of Saccharomyces cerevisiae leading‐strand synthesis reveals dynamic interaction between MTC and the replisome. Proceedings of the National Academy of Sciences of the United States of America 114: 10630–10635.

Li H and Stillman B (2012) The origin recognition complex: a biochemical and structural view. Sub‐Cellular Biochemistry 62: 37–58.

Liu B, Hu J, Wang J and Kong D (2017) Direct visualization of RNA‐DNA primer removal from Okazaki fragments provides support for flap cleavage and exonucleolytic pathways in eukaryotic cells. The Journal of Biological Chemistry 292: 4777–4788.

Maric M, Mukherjee P, Tatham MH, Hay R and Labib K (2017) Ufd1‐Npl4 recruit Cdc48 for disassembly of ubiquitylated CMG helicase at the End of chromosome replication. Cell Reports 18: 3033–3042.

Maundrell K, Hutchison A and Shall S (1988) Sequence analysis of ARS elements in fission yeast. The EMBO Journal 7: 2203–2209.

Maundrell K, Wright APH, Piper M and Shall S (1985) Evaluation of heterologous ARS activity in S. cerevisiae using cloned DNA from S. pombe. Nucleic Acids Research 13: 3711–3722.

Mejia‐Ramirez E, Sanchez‐Gorostiaga A, Krimer DB, Schvartzman JB and Hernandez P (2005) The mating type switch‐activating protein Sap1 is required for replication fork arrest at the rRNA genes of fission yeast. Molecular and Cellular Biology 25: 8755–8761.

Muzi‐Falconi M, Giannattasio M, Foiani M and Plevani P (2003) The DNA polymerase alpha‐primase complex: multiple functions and interactions. TheScientificWorldJOURNAL 3: 21–33.

Nguyen VQ, Co C and Li JJ (2001) Cyclin‐dependent kinases prevent DNA re‐replication through multiple mechanisms. Nature 411: 1068–1073.

Park H, Francesconi S and Wang TS (1993) Cell cycle expression of two replicative DNA polymerases alpha and delta from Schizosaccharomyces pombe. Molecular Biology of the Cell 4: 145–157.

Patel PK, Arcangioli B, Baker SP, Bensimon A and Rhind N (2006) DNA replication origins fire stochastically in fission yeast. Molecular Biology of the Cell 17: 308–316.

Perez‐Arnaiz P, Bruck I, Colbert MK and Kaplan DL (2017) An intact Mcm10 coiled‐coil interaction surface is important for origin melting, helicase assembly and the recruitment of Pol‐alpha to Mcm2‐7. Nucleic Acids Research 45: 7261–7275.

Pignede G, Bouvier D, de Recondo AM and Baldacci G (1991) Characterization of the POL3 gene product from Schizosaccharomyces pombe indicates inter‐species conservation of the catalytic subunit of DNA polymerase delta. Journal of Molecular Biology 222: 209–218.

Ravoityte B and Wellinger RE (2017) Non‐canonical replication initiation: you're fired!. Genes 8. DOI: 10.3390/genes8020054.

Riera A, Barbon M, Noguchi Y, et al. (2017) From structure to mechanism‐understanding initiation of DNA replication. Genes & Development 31: 1073–1088.

Sakaguchi J and Yamamoto M (1982) Cloned ural locus of Schizosaccharomyces pombe propagates autonomously in this yeast assuming a polymeric form. Proceedings of the National Academy of Sciences of the United States of America 79: 7819–7823.

Segurado M, de Luis A and Antequera F (2003) Genome‐wide distribution of DNA replication origins at A+T‐rich islands in Schizosaccharomyces pombe. EMBO Reports 4: 1048–1053.

Simon AC, Zhou JC, Perera RL, et al. (2014) A Ctf4 trimer couples the CMG helicase to DNA polymerase alpha in the eukaryotic replisome. Nature 510: 293–297.

Stillman B (1994) Initiation of chromosomal DNA replication in eukaryotes. Lessons from lambda. The Journal of Biological Chemistry 269: 7047–7050.

Sun J, Yuan Z, Bai L and Li H (2017) Cryo‐EM of dynamic protein complexes in eukaryotic DNA replication. Protein Science : A Publication of the Protein Society 26: 40–51.

Tanaka S and Araki H (2013) Helicase activation and establishment of replication forks at chromosomal origins of replication. Cold Spring Harbor Perspectives in Biology 5: a010371.

Waga S and Stillman B (1994) Anatomy of a DNA replication fork revealed by reconstitution of SV40 DNA replication in vitro. Nature 369: 207–212.

Waseem NH, Labib K, Nurse P and Lane DP (1992) Isolation and analysis of the fission yeast gene encoding polymerase delta accessory protein PCNA. The EMBO Journal 11: 5111–5120.

Yanow SK, Lygerou Z and Nurse P (2001) Expression of Cdc18/Cdc6 and Cdt1 during G(2) phase induces initiation of DNA replication. The Embo Journal 20: 4648–4656.

Yeeles JT, Janska A, Early A and Diffley JF (2017) How the eukaryotic replisome achieves rapid and efficient DNA replication. Molecular Cell 65: 105–116.

Zhou JC, Janska A, Goswami P, et al. (2017) CMG‐Pol epsilon dynamics suggests a mechanism for the establishment of leading‐strand synthesis in the eukaryotic replisome. Proceedings of the National Academy of Sciences of the United States of America 114: 4141–4146.

Further Reading

Alberts B, Johnson A, Lewis J, et al. (2015) DNA replication, repair, and recombination. In: Molecular Biology of the Cell, 6th edn, chap. 5, pp. 237–298. New York and Abingdon: Garland Science.

Burke D, Dawson D and Stearns T (2000) Methods in Yeast Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Errico A and Constanzo V (2010) Differences in the DNA replication of unicellular eukaryotes and metazoans: known unknowns. EMBO Reports 11 (4): 270–278.

Newlon C (1996) DNA replication in yeast. In: DNA Replication in Eukaryotic Cells. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN: 0-87969-459-9/96.

Tan C and Tomkins J (2015) Information processing differences between bacteria and eukarya – Implications for the myth of eukaryogenesis. Answers Research Journal 8: 143–162.

Related Sub-Topics:

DNA Structure and Function | DNA Damage and Repair | Techniques and Tools in Molecular Biology | Genomes and Chromosomes
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: DNA Replication: Yeast
 
How to Cite close
Smith, Shanna J, Li, Caroline M, Raoof, Mustafa, Lingeman, Robert G, Hickey, Robert J, and Malkas, Linda H(Sep 2018) DNA Replication: Yeast. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0027975]