TstI, a Type II Restriction-modification Protein with DNA Recognition, Cleavage and Methylation Functions in a Single Polypeptide

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2014 Mar 18

PMID 24634443

Citations 7

Authors

Rachel M Smith

Christian Pernstich

Stephen E Halford

Affiliations

Soon will be listed here.

Abstract

Type II restriction-modification systems cleave and methylate DNA at specific sequences. However, the Type IIB systems look more like Type I than conventional Type II schemes as they employ the same protein for both restriction and modification and for DNA recognition. Several Type IIB proteins, including the archetype BcgI, are assemblies of two polypeptides: one with endonuclease and methyltransferase roles, another for DNA recognition. Conversely, some IIB proteins express all three functions from separate segments of a single polypeptide. This study analysed one such single-chain protein, TstI. Comparison with BcgI showed that the one- and the two-polypeptide systems differ markedly. Unlike the heterologous assembly of BcgI, TstI forms a homotetramer. The tetramer bridges two recognition sites before eventually cutting the DNA in both strands on both sides of the sites, but at each site the first double-strand break is made long before the second. In contrast, BcgI cuts all eight target bonds at two sites in a single step. TstI also differs from BcgI in either methylating or cleaving unmodified sites at similar rates. The site may thus be modified before TstI can make the second double-strand break. TstI MTase acts best at hemi-methylated sites.

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References

Makarova K, Wolf Y, Koonin E . Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res. 2013; 41(8):4360-77. PMC: 3632139. DOI: 10.1093/nar/gkt157. View

Kong H, Roemer S, Benner J, Wilson G, Nwankwo D . Characterization of BcgI, a new kind of restriction-modification system. J Biol Chem. 1994; 269(1):683-90. View

Smith R, Diffin F, Savery N, Josephsen J, Szczelkun M . DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGI. Nucleic Acids Res. 2009; 37(21):7206-18. PMC: 2790903. DOI: 10.1093/nar/gkp790. View

Kong H, Morgan R, Maunus R, Schildkraut I . A unique restriction endonuclease, BcgI, from Bacillus coagulans. Nucleic Acids Res. 1993; 21(4):987-91. PMC: 309233. DOI: 10.1093/nar/21.4.987. View

Borgaro J, Benner N, Zhu Z . Fidelity index determination of DNA methyltransferases. PLoS One. 2013; 8(5):e63866. PMC: 3646050. DOI: 10.1371/journal.pone.0063866. View

Jurenaite-Urbanaviciene S, Serksnaite J, Kriukiene E, Giedriene J, Venclovas C, Lubys A . Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains. Proc Natl Acad Sci U S A. 2007; 104(25):10358-63. PMC: 1965518. DOI: 10.1073/pnas.0610365104. View

Sisakova E, van Aelst K, Diffin F, Szczelkun M . The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their recognition sites. Nucleic Acids Res. 2012; 41(2):1071-80. PMC: 3553950. DOI: 10.1093/nar/gks1209. View

Mucke M, Kruger D, Reuter M . Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res. 2003; 31(21):6079-84. PMC: 275478. DOI: 10.1093/nar/gkg836. View

Kong H . Analyzing the functional organization of a novel restriction modification system, the BcgI system. J Mol Biol. 1998; 279(4):823-32. DOI: 10.1006/jmbi.1998.1821. View

10.

Vipond I, Halford S . Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Biochemistry. 1995; 34(4):1113-9. DOI: 10.1021/bi00004a002. View

11.

Kong H, Smith C . Does BcgI, a unique restriction endonuclease, require two recognition sites for cleavage?. Biol Chem. 1998; 379(4-5):605-9. View

12.

Marshall J, Smith R, Ganguly S, Halford S . Concerted action at eight phosphodiester bonds by the BcgI restriction endonuclease. Nucleic Acids Res. 2011; 39(17):7630-40. PMC: 3177199. DOI: 10.1093/nar/gkr453. View

13.

Embleton M, Siksnys V, Halford S . DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J Mol Biol. 2001; 311(3):503-14. DOI: 10.1006/jmbi.2001.4892. View

14.

Sears L, Zhou B, Aliotta J, Morgan R, Kong H . BaeI, another unusual BcgI-like restriction endonuclease. Nucleic Acids Res. 1996; 24(18):3590-2. PMC: 146138. DOI: 10.1093/nar/24.18.3590. View

15.

Arber W, Linn S . DNA modification and restriction. Annu Rev Biochem. 1969; 38:467-500. DOI: 10.1146/annurev.bi.38.070169.002343. View

16.

Smith R, Marshall J, Jacklin A, Retter S, Halford S, Sobott F . Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA. Nucleic Acids Res. 2012; 41(1):391-404. PMC: 3592470. DOI: 10.1093/nar/gks1023. View

17.

Zaremba M, Sasnauskas G, Urbanke C, Siksnys V . Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations. J Mol Biol. 2005; 348(2):459-78. DOI: 10.1016/j.jmb.2005.02.037. View

18.

Marshall J, Halford S . The type IIB restriction endonucleases. Biochem Soc Trans. 2010; 38(2):410-6. DOI: 10.1042/BST0380410. View

19.

Cheng X, Roberts R . AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 2001; 29(18):3784-95. PMC: 55914. DOI: 10.1093/nar/29.18.3784. View

20.

Szczelkun M, Halford S . Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J. 1996; 15(6):1460-9. PMC: 450051. View