通过点突变实现限制内切酶序列特异性的进化。
Evolution of sequence specificity in a restriction endonuclease by a point mutation.
作者信息
Saravanan Matheshwaran, Vasu Kommireddy, Nagaraja Valakunja
机构信息
Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
出版信息
Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10344-7. doi: 10.1073/pnas.0804974105. Epub 2008 Jul 22.
Abstract
Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.
摘要
限制性内切酶（REases）保护细菌免受外来DNA的入侵，并具有极高的序列特异性。REases起源于祖先蛋白，并通过基因重组、基因复制、复制滑移和转座事件进化出新的序列特异性。也有人推测它们是从非特异性内切酶进化而来，通过点突变获得高度的序列特异性。我们在此描述了一个通过单点突变从高度混杂的REase产生极其位点特异性REase的例子。
相似文献
1
Evolution of sequence specificity in a restriction endonuclease by a point mutation.通过点突变实现限制内切酶序列特异性的进化。
Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10344-7. doi: 10.1073/pnas.0804974105. Epub 2008 Jul 22.
2
Generation of a manganese specific restriction endonuclease with nicking activity.生成一种具有切割活性的锰特异性限制内切酶。
Biochemistry. 2010 Sep 28;49(38):8425-33. doi: 10.1021/bi101035k.
3
The link between restriction endonuclease fidelity and oligomeric state: a study with Bse634I.限制内切酶保真度与寡聚状态之间的联系：Bse634I 的研究。
FEBS Lett. 2012 Sep 21;586(19):3324-9. doi: 10.1016/j.febslet.2012.07.009. Epub 2012 Jul 22.
4
Ca(2+)-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease.钙离子介导的位点特异性DNA切割及KpnI限制性内切核酸酶混杂活性的抑制
J Biol Chem. 2004 Nov 26;279(48):49736-40. doi: 10.1074/jbc.M409483200. Epub 2004 Sep 16.
5
A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy.通过折叠识别预测，并经定点诱变和圆二色光谱验证的限制性内切酶NlaIV与DNA复合物的理论模型。
Protein Eng Des Sel. 2005 Apr;18(4):181-9. doi: 10.1093/protein/gzi019. Epub 2005 Apr 22.
6
Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities.相关的双功能限制内切酶-甲基转移酶三联体：TspDTI、Tth111II/TthHB27I 和 TsoI，具有不同的特异性。
BMC Mol Biol. 2012 Apr 10;13:13. doi: 10.1186/1471-2199-13-13.
7
PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes.PspGI，一种来自嗜热古菌嗜热栖热袍菌的II型限制性内切酶：旨在研究其与几种嗜温限制性酶进化关系的结构与功能研究。
J Mol Biol. 2003 Jun 20;329(5):913-29. doi: 10.1016/s0022-2836(03)00523-0.
8
Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII.结合生物信息学和定点诱变推断同源性“模糊地带”的关系：限制性内切酶Bsp6I和PvuII的案例研究
Nucleic Acids Res. 2005 Jan 31;33(2):661-71. doi: 10.1093/nar/gki213. Print 2005.
9
Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium.IIs型限制酶的新型亚型。BfiI核酸内切酶与鼠伤寒沙门氏菌的耐EDTA核酸酶Nuc具有相似性。
J Biol Chem. 2000 Oct 6;275(40):30878-85. doi: 10.1074/jbc.M003350200.
10
A putative Type IIS restriction endonuclease GeoICI from Geobacillus sp.--A robust, thermostable alternative to mezophilic prototype BbvI.来自嗜热栖热菌属的一种假定的IIS型限制性内切酶GeoICI——一种比嗜温原型BbvI更强大、更耐热的替代酶。
J Biosci. 2016 Mar;41(1):27-38. doi: 10.1007/s12038-016-9595-z.
引用本文的文献
1
The defensome of complex bacterial communities.复杂细菌群落的防御组。
Nat Commun. 2024 Mar 8;15(1):2146. doi: 10.1038/s41467-024-46489-0.
2
Modified nucleoside triphosphates in bacterial research for and live-cell applications.用于细菌研究及活细胞应用的修饰核苷三磷酸。
RSC Chem Biol. 2020 Dec 1;1(5):333-351. doi: 10.1039/d0cb00078g. Epub 2020 Sep 14.
3
Promiscuous DNA cleavage by HpyAII endonuclease is modulated by the HNH catalytic residues.HpyAII 内切酶的乱切活性由 HNH 催化残基调节。
Biosci Rep. 2020 Sep 30;40(9). doi: 10.1042/BSR20201633.
4
Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases.活性位点残基的身份决定了 LAGLIDADG 归巢内切核酸酶的切割偏好性。
Nucleic Acids Res. 2018 Dec 14;46(22):11990-12007. doi: 10.1093/nar/gky976.
5
The ascent of man(made oxidoreductases).人类（制造）氧化还原酶的进化。
Curr Opin Struct Biol. 2018 Aug;51:149-155. doi: 10.1016/j.sbi.2018.04.008. Epub 2018 May 10.
6
Restriction endonuclease triggered bacterial apoptosis as a mechanism for long time survival.限制内切酶引发细菌凋亡作为长期存活的一种机制。
Nucleic Acids Res. 2017 Aug 21;45(14):8423-8434. doi: 10.1093/nar/gkx576.
7
Increasing cleavage specificity and activity of restriction endonuclease KpnI.提高限制内切酶 KpnI 的酶切特异性和活性。
Nucleic Acids Res. 2013 Nov;41(21):9812-24. doi: 10.1093/nar/gkt734. Epub 2013 Aug 19.
8
Massively parallel characterization of restriction endonucleases.大规模平行鉴定限制酶。
Nucleic Acids Res. 2013 Jun;41(11):e119. doi: 10.1093/nar/gkt257. Epub 2013 Apr 19.
9
Diverse functions of restriction-modification systems in addition to cellular defense.限制修饰系统除了具有细胞防御功能外，还有多种功能。
Microbiol Mol Biol Rev. 2013 Mar;77(1):53-72. doi: 10.1128/MMBR.00044-12.
10
Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria.滥交限制是一种细胞防御策略，使细菌具有适应性优势。
Proc Natl Acad Sci U S A. 2012 May 15;109(20):E1287-93. doi: 10.1073/pnas.1119226109. Epub 2012 Apr 16.
本文引用的文献
1
Rational design of a chimeric endonuclease targeted to NotI recognition site.靶向NotI识别位点的嵌合核酸内切酶的合理设计。
Protein Eng Des Sel. 2007 Oct;20(10):497-504. doi: 10.1093/protein/gzm049. Epub 2007 Oct 20.
2
Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.限制性内切酶BmrI的催化结构域作为一种切割模块，用于构建具有新型底物特异性的内切酶。
Nucleic Acids Res. 2007;35(18):6238-48. doi: 10.1093/nar/gkm665. Epub 2007 Sep 13.
3
Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease.锌离子在维持一种多功能核酸内切酶的结构完整性和诱导DNA序列特异性方面的双重作用。
J Biol Chem. 2007 Nov 2;282(44):32320-6. doi: 10.1074/jbc.M705927200. Epub 2007 Sep 4.
4
Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains.通过靶标识别结构域的重排产生II型限制性内切酶的DNA切割特异性
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10358-63. doi: 10.1073/pnas.0610365104. Epub 2007 Jun 6.
5
R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+.R.KpnI是一种HNH超家族限制性内切酶，在存在Ca2+和Mg2+的情况下，对非规范序列表现出不同的识别能力。
Nucleic Acids Res. 2007;35(8):2777-86. doi: 10.1093/nar/gkm114. Epub 2007 Apr 11.
6
REBASE--enzymes and genes for DNA restriction and modification.REBASE——DNA 限制与修饰的酶及基因
Nucleic Acids Res. 2007 Jan;35(Database issue):D269-70. doi: 10.1093/nar/gkl891.
7
Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.II型限制性内切酶R.KpnI是HNH核酸酶超家族的成员。
Nucleic Acids Res. 2004 Nov 23;32(20):6129-35. doi: 10.1093/nar/gkh951. Print 2004.
8
Ca(2+)-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease.钙离子介导的位点特异性DNA切割及KpnI限制性内切核酸酶混杂活性的抑制
J Biol Chem. 2004 Nov 26;279(48):49736-40. doi: 10.1074/jbc.M409483200. Epub 2004 Sep 16.
9
Isolation of BsoBI restriction endonuclease variants with altered substrate specificity.具有改变的底物特异性的BsoBI限制性内切酶变体的分离。
J Mol Biol. 2003 Jul 4;330(2):359-72. doi: 10.1016/s0022-2836(03)00595-3.
10
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.限制酶、DNA甲基转移酶、归巢内切酶及其基因的命名法。
Nucleic Acids Res. 2003 Apr 1;31(7):1805-12. doi: 10.1093/nar/gkg274.
Zotero 插件