Skip to main content
SpringerLink
Log in

Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe

  • Published:
Journal of Biosciences Aims and scope Submit manuscript

Abstract

Short, specific DNA sequences called as Autonomously Replicating Sequence (ARS) elements function as plasmid as well as chromosomal replication origins in yeasts. As compared to ARSs, different chromosomal origins vary greatly in their efficiency and timing of replication probably due to their wider chromosomal context. The two Schizosaccharomyces pombe ARS elements, ars727 and ars2004, represent two extremities in their chromosomal origin activity – ars727 is inactive and late replicating, while ars2004 is a highly active, early-firing origin. To determine the effect of chromosomal context on the activity of these ARS elements, we have cloned them with their extended chromosomal context as well as in the context of each other in both orientations and analysed their replication efficiency by ARS and plasmid stability assays. We found that these ARS elements retain their origin activity in their extended/altered context. However, deletion of a 133-bp region of the previously reported ars727-associated late replication enforcing element (LRE) caused advancement in replication timing of the resulting plasmid. These results confirm the role of LRE in directing plasmid replication timing and suggest that the plasmid origin efficiency of ars2004 or ars727 remains unaltered by the extended chromosomal context.

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

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  • Bell SP and Stillman B 1992 ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357 128–134

    Article  CAS  PubMed  Google Scholar 

  • Bi C and Benham CJ 2004 WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA. Bioinformatics 20 1477–1479

    Article  CAS  PubMed  Google Scholar 

  • Brewer BJ and Fangman WL 1987 The localization of replication origin on ARS plasmids in Saccharomyces cerevisiae. Cell 51 463–471

    Article  CAS  PubMed  Google Scholar 

  • Campbell JL and Newlon CS 1991 hromosomal DNA replication; in The molecular and cellular biology of yeast Saccharomyces (eds) JR Broach, JR Pringle and EW Jones (New York: Cold Spring Harbor Laboratory Press) pp 41–146

    Google Scholar 

  • Clyne RK and Kelly TJ 1995 Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. EMBO J. 14 6348–6357

    CAS  PubMed Central  PubMed  Google Scholar 

  • Dai J, Chuang RY and Kelly TJ 2005 DNA replication origins in the Schizosaccharomyces pombe genome. Proc. Natl. Acad. Sci. USA 102 337–342

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Diffley JFX and Cocker JH 1992 Protein-DNA interactions at a yeast replication origin. Nature 357 169–172

    Article  CAS  PubMed  Google Scholar 

  • Dubey DD, Davis LR, Greenfeder SA, Ong LY, Zhu JG, Broach LR, Newlon CS and Huberman JA 1991 Evidence suggesting that the ARS elements associated with silencers of the yeast mating type locus HML do not function as chromosomal DNA replication origins. Mol. Cell. Biol. 11 5346–5355

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dubey DD, Kim SM, Todorov IT and Huberman JA 1996 Large complex modular structure of a fission yeast DNA replication origin. Curr. Biol. 6 467–473

    Article  CAS  PubMed  Google Scholar 

  • Dubey DD, Srivastava VK, Pratihar AS and Yadava MP 2010 High density of weak replication origins in a 75-kb region of chromosome 2 of fission yeast. Genes Cells 15 1–12

    Article  CAS  PubMed  Google Scholar 

  • Friedman KL, Brewer BJ and Fangman WL 1997 Replication profile of Saccharomyces cerevisiae Chromosome VI. Genes Cells 2 667–678

    Article  CAS  PubMed  Google Scholar 

  • Gietz D, Jean AS, Woods RA and Schiestl RH 1992 Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 20 1425

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hall TA 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 95–98

    CAS  Google Scholar 

  • Hoffman CS and Winston F 1987 A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57 267–272

    Article  CAS  PubMed  Google Scholar 

  • Hsiao CL and Carbon J 1979 High frequency transformation of yeast by plasmid containing the cloned yeast ARG gene. Proc. Natl. Acad. Sci. USA 76 3829–3833

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Huang Y and Kowalski D 2003 WEB-THERMODYN: sequence analysis software for profiling DNA helical stability. Nucleic Acids Res. 31 3819–3821

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Huberman JA, Spotila LD, Nawotka KA, El-Assouli SM and Davis LR 1987 The in vivo replication origin of the yeast 2 micron plasmid. Cell 51 473–481

    Article  CAS  PubMed  Google Scholar 

  • Kim SM and Huberman JA 1999 Influence of a replication enhancer on the hierarchy of origin efficiencies within a cluster of DNA replication origins. J. Mol. Biol. 288 867–882

    Article  CAS  PubMed  Google Scholar 

  • Kim SM and Huberman JA 2001 Regulation of replication timing in fission yeast. EMBO J. 20 6115–6126

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kim SM, Zhang DY and Huberman JA 2001 Multiple redundant sequence elements within the fission yeast ura4 replication origin enhancer. BMC Mol. Biol. 2, e1

    Article  Google Scholar 

  • Lee JK, Moon KY, Jiang Y and Hurwitz J 2001 The Schizosaccharomyces pombe origin recognition complex interacts with multiple AT-rich regions of the replication origin DNA by means of the AT-hook domains of the spOrc4 protein. Proc. Natl. Acad. Sci. USA 98 13589–13594

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Linskens MHK and Huberman JA 1988 Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Biol. Cell 8 4927–4935

    Article  CAS  Google Scholar 

  • Marahrens Y and Stillman B 1992 A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255 817–827

    Article  CAS  PubMed  Google Scholar 

  • Masukata H, Huberman JA, Frattini MG and Kelly TJ 2004 DNA Replication in Schizosaccharomyces pombe; in The molecular biology of Schizosaccharomyces pombe; genetics, genomics and beyond (ed) R Egel (Berlin: Springer Verlag) pp 73–99

    Chapter  Google Scholar 

  • Natale DA, Umek RM and Kowalski D 1993 Ease of DNA unwinding is a conserved property of yeast replication origins. Nucleic Acids Res. 21 555–560

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Newlon CS, Collins I, Dershowitz A, Deshpande AM, Greenfeder SA, Ong LY and Theis JF 1993 Analysis of replication origin function on chromosome III of Saccharomyces cerevisiae. Cold Spring Harb. Symp. Quant. Biol. 58 415–423

    Article  CAS  PubMed  Google Scholar 

  • Okuno Y, Okazaki T and Masukata H 1997 Identification of a predominant chromosomal origin of replication in fission yeast. Nucleic Acids Res. 25 530–536

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Okuno Y, Satos H, Sekiguchi M and Masukata H 1999 Clustered adenine / thymine stretches are essential for function of a fission yeast replication origin. Mol. Cell. Biol. 19 6699–6709

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pohl TJ, Kolor K, Fangmn WL, Brewer BJ and Raghuraman MK 2013 A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae. G3 (Bethesda) 3 1955–1963

    Article  Google Scholar 

  • Potaman VN, Bissler JJ, Hashem VI, Oussatcheva EA, Lu L, Shlyakhtenko LS, Lyubchenko YL, Matsuura T, et al. 2003 Unpaired structures in SCA10 (ATTCT)n. (AGAAT)n repeats. J. Mol. Biol. 326 1095–1111

    Article  CAS  PubMed  Google Scholar 

  • Raghuraman MK and Brewer BJ 2010 Molecular analysis of the replication program in unicellular model organisms. Chromosom. Res. 18 19–34

    Article  CAS  Google Scholar 

  • Sambrook J, Fritsch EF and Maniatis T 1989 Molecular cloning: A laboratory manual (New York: Cold Spring Harbor Laboratory Press)

    Google Scholar 

  • Segurado M, Luis AD and Antequera F 2003 Genome wide distribution of DNA replication origins at A+T-rich islands in Schizosacharomyces pombe. EMBO Rep. 4 1048–1053

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Stinchcomb DT, Struhl K and Davis RW 1979 Isolation and characterization of yeast chromosomal replicator. Nature 282 39–43

    Article  CAS  PubMed  Google Scholar 

  • Yadav MP, Padmanabhan S, Mishra RK, Tripathi VP and Dubey DD 2012 Analysis of stress-induced duplex destabilization (SIDD) properties of replication origins, genes and intergenes in the fission yeast, Schizosaccharomyces pombe. BMC Res. Notes 5 643

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yompakdee C and Huberman JA 2004 Enforcement of late replication origin firing by clusters of short G-rich DNA sequences. J. Biol. Chem. 279 72337–42344

    Article  Google Scholar 

  • Zhu J, Carlson DL, Dubey DD, Sharma K and Huberman JA 1994 Comparison of the two major ARS elements of the ura4 replication origins regions with other ARS elements in the fission yeast, Schizosaccharomyces pombe. Chromosoma 103 414–422

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors are grateful to MM Panicker, NCBS, Bangalore, Rajiva Raman, BHU, Varanasi, and S Ganesh, BSBE, IIT, Kanpur, for extending laboratory support to carry out part of the work. This work was supported by CSIR research grants #38(1075)/03/EMRII & #38(1233)/09/EMRII to DDD. VPT is a recipient of a senior research fellowship from ICMR, New Delhi.

Author information

Author notes

  1. Aditya S Pratihar

    Present address: Department of Biotechnology, Dayanand Academy of Management Studies, Govind Nagar, Kanpur, 208006, India

  2. Mukesh P Yadav

    Present address: E-407, Centre for Cellular & Molecular Biology, Uppal Road, Habsiguda, Hyderabad, Telangana, 500007, India

Authors and Affiliations

  1. Department of Biotechnology, Veer Bahadur Singh Purvanchal University, Jaunpur, 222003, U.P., India

    Vishnu P Tripathi & Dharani D Dubey

Authors
  1. Aditya S Pratihar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vishnu P Tripathi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mukesh P Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dharani D Dubey
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dharani D Dubey.

Additional information

Corresponding editor: Anand Kumar Bachhawat

[Pratihar AS, Tripathi VP, Yadav MP and Dubey DD 2015 Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe. J. Biosci.] DOI 10.1007/s12038-015-9572-y

Supplementary materials pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/dec2015/supp/Pratihar.pdf

Aditya S Pratihar and Vishnu P Tripathi contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 556 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Pratihar, A.S., Tripathi, V.P., Yadav, M.P. et al. Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe . J Biosci 40, 845–853 (2015). https://doi.org/10.1007/s12038-015-9572-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12038-015-9572-y

Keywords

Search

Navigation