New Recognition Mode for a TG Mismatch: The Atomic Structure of a Very Short Patch Repair Endonuclease-DNA Complex

2000 ◽  
Vol 65 (0) ◽  
pp. 233-240 ◽  
Author(s):  
S.E. TSUTAKAWA ◽  
K. MORIKAWA
Keyword(s):  
Atomic Structure ◽  
Patch Repair ◽  
Very Short Patch Repair ◽  
Dna Complex

scholarly journals Neisseria gonorrhoeae FA1090 Carries Genes Encoding Two Classes of Vsr Endonucleases

2010 ◽  
Vol 192 (15) ◽  
pp. 3951-3960 ◽  
Author(s):  
Agnieszka Kwiatek ◽  
Maciej Łuczkiewicz ◽  
Katarzyna Bandyra ◽  
Daniel C. Stein ◽  
Andrzej Piekarowicz
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Sequence Similarity ◽  
Hydrolytic Activity ◽  
Patch Repair ◽  
Repair System ◽  
Sequence Specificity ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Nucleotide Context ◽  
Very Short Patch Repair

ABSTRACT A very short patch repair system prevents mutations resulting from deamination of 5-methylcytosine to thymine. The Vsr endonuclease is the key enzyme of this system, providing sequence specificity. We identified two genes encoding Vsr endonucleases V.NgoAXIII and V.NgoAXIV from Neisseria gonorrhoeae FA1090 based on DNA sequence similarity to genes encoding Vsr endonucleases from other bacteria. After expression of the gonococcal genes in Escherichia coli, the proteins were biochemically characterized and the endonucleolytic activities and specificities of V.NgoAXIII and V.NgoAXIV were determined. V.NgoAXIII was found to be multispecific and to recognize T:G mismatches in every nucleotide context tested, whereas V.NgoAXIV recognized T:G mismatches in the following sequences: GTGG, CTGG, GTGC, ATGC, and CTGC. Alanine mutagenesis of conserved residues showed that Asp50 and His68 of V.NgoAXIII and Asp51 and His69 of V.NgoAXIV are essential for hydrolytic activity. Glu25, His64, and Asp97 of V.NgoAXIV and Glu24, Asp63, and Asp97 of V.NgoAXIII are important but not crucial for the activity of V.NgoAXIII and V.NgoAXIV. However, Glu24 and Asp63 are also important for the specificity of V.NgoAXIII. On the basis of our results concerning features of Vsr endonucleases expressed by N. gonorrhoeae FA1090, we postulate that at least two types of Vsr endonucleases can be distinguished.

scholarly journals Very-Short-Patch Repair in Escherichia coli Requires the dam Adenine Methylase

2001 ◽  
Vol 183 (12) ◽  
pp. 3631-3635 ◽  
Author(s):  
Derek C. Bell ◽  
Claire G. Cupples
Keyword(s):  
Escherichia Coli ◽  
Mismatch Repair ◽  
Patch Repair ◽  
Very Short Patch Repair

ABSTRACT Strains of Escherichia coli which lack thedam-encoded adenine methylase are mutators due to a reduction in the efficiency of postreplication mismatch repair. In this study, we show that Dam− strains are also defective in very-short-patch repair, the system which corrects T/G mismatches arising from the deamination of 5-methylcytosine. This defect is associated with decreased levels of Vsr, the endonuclease which initiates short-patch repair. We also show that production of thedcm-encoded cytosine methylase is unaffected in Dam− strains. Since the dcm andvsr genes are cotranscribed, the regulation of Vsr by Dam is probably posttranscriptional.

scholarly journals Crystallographic and Functional Studies of Very Short Patch Repair Endonuclease

1999 ◽  
Vol 3 (5) ◽  
pp. 621-628 ◽  
Author(s):  
Susan E Tsutakawa ◽  
Takanori Muto ◽  
Tomohiko Kawate ◽  
Hisato Jingami ◽  
Naoki Kunishima ◽  
...  
Keyword(s):  
Patch Repair ◽  
Functional Studies ◽  
Very Short Patch Repair

scholarly journals An orphan DNA (cytosine-5-)-methyltransferase in Vibrio cholerae

Microbiology ◽  
2006 ◽  
Vol 152 (4) ◽  
pp. 1055-1062 ◽  
Author(s):  
Sanjib Banerjee ◽  
Rukhsana Chowdhury
Keyword(s):  
Stationary Phase ◽  
Restriction Endonuclease ◽  
Vibrio Cholerae ◽  
Spontaneous Mutation ◽  
Patch Repair ◽  
Pcr Analysis ◽  
Methyl Cytosine ◽  
Vsp Repair ◽  
Very Short Patch Repair ◽  
Spontaneous Mutation Frequency

5-Methyl cytosine (m5C) was detected in genomic DNA of the enteric pathogen Vibrio cholerae by HPLC analysis and immunoblotting with m5C-specific antibody. Although cleavage with the restriction endonuclease EcoRII revealed the absence of a Dcm homologue in V. cholerae, analysis of the genome sequence indicated the presence of a gene, designated in this study as vchM, which encodes a DNA (cytosine-5-)-methyltransferase (m5C-MTase) designated M.Vch. M.Vch is not associated with a restriction endonuclease or a mismatch very short patch repair (Vsr)-like endonuclease and is hence an ‘orphan’ or solitary MTase, although analysis of a phylogenetic tree indicated that related cytosine MTases are all components of restriction-modification systems. M.Vch recognizes and methylates the first 5′ C in the degenerate sequence 5′-RCCGGY-3′. RT-PCR analysis suggested that vchM gene expression is increased during the stationary phase of growth. During stationary phase, the spontaneous mutation frequency in the V. cholerae wild-type strain was significantly higher than in the corresponding vchM mutant strain, suggesting that the presence of M.Vch and the absence of a very short patch (VSP) repair-like system imposes upon V. cholerae a mutator phenotype.

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