scholarly journals Type III restriction-modification enzymes: a historical perspective

2013 ◽  
Vol 42 (1) ◽  
pp. 45-55 ◽  
Author(s):  
Desirazu N. Rao ◽  
David T. F. Dryden ◽  
Shivakumara Bheemanaik
Keyword(s):  
Historical Perspective ◽  
Type Iii ◽  
Restriction Modification

scholarly journals Transcriptional Phase Variation of a Type III Restriction-Modification System in Helicobacter pylori

2002 ◽  
Vol 184 (23) ◽  
pp. 6615-6623 ◽  
Author(s):  
Nicolette de Vries ◽  
Dirk Duinsbergen ◽  
Ernst J. Kuipers ◽  
Raymond G. J. Pot ◽  
Patricia Wiesenekker ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Phase Variation ◽  
Transcriptional Level ◽  
Length Variation ◽  
Phase Variable ◽  
Modification System ◽  
Type Iii ◽  
Restriction Modification System ◽  
H Pylori ◽  
Restriction Modification

ABSTRACT Phase variation is important in bacterial pathogenesis, since it generates antigenic variation for the evasion of immune responses and provides a strategy for quick adaptation to environmental changes. In this study, a Helicobacter pylori clone, designated MOD525, was identified that displayed phase-variable lacZ expression. The clone contained a transcriptional lacZ fusion in a putative type III DNA methyltransferase gene (mod, a homolog of the gene JHP1296 of strain J99), organized in an operon-like structure with a putative type III restriction endonuclease gene (res, a homolog of the gene JHP1297), located directly upstream of it. This putative type III restriction-modification system was common in H. pylori, as it was present in 15 out of 16 clinical isolates. Phase variation of the mod gene occurred at the transcriptional level both in clone MOD525 and in the parental H. pylori strain 1061. Further analysis showed that the res gene also displayed transcriptional phase variation and that it was cotranscribed with the mod gene. A homopolymeric cytosine tract (C tract) was present in the 5′ coding region of the res gene. Length variation of this C tract caused the res open reading frame (ORF) to shift in and out of frame, switching the res gene on and off at the translational level. Surprisingly, the presence of an intact res ORF was positively correlated with active transcription of the downstream mod gene. Moreover, the C tract was required for the occurrence of transcriptional phase variation. Our finding that translation and transcription are linked during phase variation through slipped-strand mispairing is new for H. pylori.

Phase variation in a type III restriction-modification system of Helicobacter pylori

2000 ◽  
Vol 118 (4) ◽  
pp. A736 ◽  
Author(s):  
Nicolette Vries de ◽  
Dirk Duinsbergen ◽  
Ernst J. Kuipers ◽  
Patricia Wiesenekker ◽  
Christina M. Vandenbroucke-Grauls ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Phase Variation ◽  
Modification System ◽  
Type Iii ◽  
Restriction Modification System ◽  
Restriction Modification

Molecular identification and characterization of type III restriction-modification (R-M) gene cluster in Campylobacter lari

2013 ◽  
Vol 63 (4) ◽  
pp. 1629-1637 ◽  
Author(s):  
Takuya Nakajima ◽  
Keiko Matsubara ◽  
Hitomi Ueno ◽  
Shizuko Kagawa ◽  
John E. Moore ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Molecular Identification ◽  
M Gene ◽  
Type Iii ◽  
Campylobacter Lari ◽  
Identification And Characterization ◽  
Restriction Modification

scholarly journals Structural and functional diversity among Type III restriction-modification systems that confer host DNA protection via methylation of the N4 atom of cytosine

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0253267
Author(s):  
Iain A. Murray ◽  
Yvette A. Luyten ◽  
Alexey Fomenkov ◽  
Nan Dai ◽  
Ivan R. Corrêa ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Methyltransferase ◽  
Protein A ◽  
Single Copy ◽  
Atpase Subunit ◽  
Type Iii ◽  
Host Protection ◽  
Rich Diversity ◽  
Restriction Modification ◽  
Restriction Modification Systems

We report a new subgroup of Type III Restriction-Modification systems that use m4C methylation for host protection. Recognition specificities for six such systems, each recognizing a novel motif, have been determined using single molecule real-time DNA sequencing. In contrast to all previously characterized Type III systems which modify adenine to m6A, protective methylation of the host genome in these new systems is achieved by the N4-methylation of a cytosine base in one strand of an asymmetric 4 to 6 base pair recognition motif. Type III systems are heterotrimeric enzyme complexes containing a single copy of an ATP-dependent restriction endonuclease-helicase (Res) and a dimeric DNA methyltransferase (Mod). The Type III Mods are beta-class amino-methyltransferases, examples of which form either N6-methyl adenine or N4-methyl cytosine in Type II RM systems. The Type III m4C Mod and Res proteins are diverged, suggesting ancient origin or that m4C modification has arisen from m6A MTases multiple times in diverged lineages. Two of the systems, from thermophilic organisms, required expression of both Mod and Res to efficiently methylate an E. coli host, unlike previous findings that Mod alone is proficient at modification, suggesting that the division of labor between protective methylation and restriction activities is atypical in these systems. Two of the characterized systems, and many homologous putative systems, appear to include a third protein; a conserved putative helicase/ATPase subunit of unknown function and located 5’ of the mod gene. The function of this additional ATPase is not yet known, but close homologs co-localize with the typical Mod and Res genes in hundreds of putative Type III systems. Our findings demonstrate a rich diversity within Type III RM systems.

scholarly journals Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleases

2011 ◽  
Vol 39 (2) ◽  
pp. 589-594 ◽  
Author(s):  
Mark D. Szczelkun
Keyword(s):  
Long Range ◽  
Atp Hydrolysis ◽  
Helicase Domain ◽  
Dna Translocation ◽  
Base Pairs ◽  
Range Interaction ◽  
Type Iii ◽  
Long Range Interaction ◽  
Atp Binding And Hydrolysis ◽  
Restriction Modification

To cleave DNA, the Type III RM (restriction–modification) enzymes must communicate the relative orientation of two recognition sequences, which may be separated by many thousands of base pairs. This long-range interaction requires ATP hydrolysis by a helicase domain, and both active (DNA translocation) and passive (DNA sliding) modes of motion along DNA have been proposed. Potential roles for ATP binding and hydrolysis by the helicase domains are discussed, with a focus on bipartite ATPases that act as molecular switches.

Sign in / Sign up

Export Citation Format

Share Document