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In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
Published on: March 25, 2020
Characterization of Vsr endonucleases from Neisseria meningitidis
Milena Bażlekowa1, Monika Adamczyk-Popławska1, Agnieszka Kwiatek1
1Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
Abstract:
DNA methylation is a common modification occurring in all living organisms. 5-methylcytosine, which is produced in a reaction catalysed by C5-methyltransferases, can spontaneously undergo deamination to thymine, leading to the formation of T:G mismatches and C→T transitions. In Escherichia coli K-12, such mismatches are corrected by the Very Short Patch (VSP) repair system, with Vsr endonuclease as the key enzyme. Neisseria meningitidis possesses genes that encode DNA methyltransferases, including C5-methyltransferases. We report on the mutagenic potential of the meningococcal C5-methyltransferases M.NmeDI and M.NmeAI resulting from deamination of 5-methylcytosine. N. meningitidis strains also possess genes encoding potential Vsr endonucleases. Phylogenetic analysis of meningococcal Vsr endonucleases indicates that they belong to two phylogenetically distinct groups (type I or type II Vsr endonucleases). N. meningitidis serogroup C (FAM18) is a representative of meningococcal strains that carry two Vsr endonuclease genes (V.Nme18IIP and V.Nme18VIP). The V.Nme18VIP (type II) endonuclease cut DNA containing T:G mismatches in all tested nucleotide contexts. V.Nme18IIP (type I) is not active in vitro, but the change of Tyr69 to His69 in the amino acid sequence of the protein restores its endonucleolytic activity. The presence of tyrosine in position 69 is a characteristic feature of type I meningococcal Vsr proteins, while type II Vsr endonucleases possess His69. In addition to the T:G mismatches, V.Nme18VIP and V.Nme18IIPY69H recognize and digest DNA with T:T or U:G mispairs. Thus, for the first time, we demonstrate that the VSP repair system may have a wider significance and broader substrate specificity than DNA lesions that only result from 5-methylcytosine deamination.
Insights
DNA methylation can cause mutations. The study investigates meningococcal C5-methyltransferases and their Very Short Patch (VSP) repair system, revealing broader substrate specificity for DNA repair enzymes.
Area of Science:
- Molecular Biology
- Genetics
- Microbial Pathogenesis
Background:
- DNA methylation is a fundamental biological process with implications for genome stability.
- Deamination of 5-methylcytosine leads to C→T transitions, a common mutagenic event.
- The Very Short Patch (VSP) repair system, involving Vsr endonuclease, corrects these mismatches in bacteria like Escherichia coli.
Purpose of the Study:
- To investigate the mutagenic potential of Neisseria meningitidis C5-methyltransferases (M.NmeDI and M.NmeAI).
- To characterize the Vsr endonucleases encoded by N. meningitidis and their substrate specificities.
- To explore the broader role and substrate range of the VSP repair system in N. meningitidis.
Main Methods:
- Analysis of meningococcal C5-methyltransferases for mutagenic activity.
- Phylogenetic analysis of N. meningitidis Vsr endonucleases.
- In vitro characterization of Vsr endonuclease activity on various DNA mismatches.
- Site-directed mutagenesis to restore activity in a non-functional Vsr endonuclease.
Main Results:
- Meningococcal C5-methyltransferases contribute to C→T transition mutations via 5-methylcytosine deamination.
- N. meningitidis possesses two distinct types of Vsr endonucleases (type I and type II).
- The type II Vsr endonuclease (V.Nme18VIP) efficiently repairs T:G mismatches.
- A specific mutation (Tyr69 to His69) restored activity to the type I Vsr endonuclease (V.Nme18IIP).
- Both active Vsr endonucleases recognized and digested T:T and U:G mispairs in addition to T:G mismatches.
Conclusions:
- The VSP repair system in N. meningitidis exhibits broader substrate specificity than previously understood.
- Meningococcal Vsr endonucleases can repair DNA lesions beyond those arising solely from 5-methylcytosine deamination.
- This study expands the known functions of the VSP repair pathway in maintaining genome integrity.
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