A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes.

Edward K M Bower,Richard D Morgan,Yvette Luyten,David T F Dryden,Laurie P Cooper,John H White,Gareth A Roberts

doi:10.1093/nar/gky760

Abstract

Restriction Modification (RM) systems prevent the invasion of foreign genetic material into bacterial cells by restriction and protect the host's genetic material by methylation. They are therefore important in maintaining the integrity of the host genome. RM systems are currently classified into four types (I to IV) on the basis of differences in composition, target recognition, cofactors and the manner in which they cleave DNA. Comparing the structures of the different types, similarities can be observed suggesting an evolutionary link between these different types. This work describes the ‘deconstruction’ of a large Type I RM enzyme into forms structurally similar to smaller Type II RM enzymes in an effort to elucidate the pathway taken by Nature to form these different RM enzymes. Based upon the ability to engineer new enzymes from the Type I ‘scaffold’, an evolutionary pathway and the evolutionary pressures required to move along the pathway from Type I RM systems to Type II RM systems are proposed. Experiments to test the evolutionary model are discussed.

Highlights

Prokaryotic restriction-modification (RM) systems provide a major defence against invading foreign DNA [1,2,3,4] and as such their genes are found in over 96% of bacterial genomes and over 99% of archaeal genomes [5,6]
The four variants of the CC398-1 SauSTORF499P Type I Restriction Modification (RM) system shown in Figure 1B and C were constructed
These different lengths were chosen by comparison of the sequence of HsdR with the known sequence and structure of the HsdR protein from the EcoR124I RM system [59,60], Supplementary Figure S1

Summary

Introduction

Prokaryotic restriction-modification (RM) systems provide a major defence against invading foreign DNA [1,2,3,4] and as such their genes are found in over 96% of bacterial genomes and over 99% of archaeal genomes [5,6]. The other constituent part of the RM system is a methyltransferase (MTase), whose action prevents cleavage of host DNA by methylating the target DNA sequence Given their significant role in protecting the host cell, it is surprising that RM systems are not essential to prokaryotic life. There are three classes of RM systems (Types I to III) and one class operating only on methylated DNA and lacking the modification function while retaining the restriction function (Type IV). These Types are separated due to differences in composition, target recognition, cofactors and the manner in which they cleave DNA [18]. The defining characteristic of Type II RM systems, and perhaps the most important in terms of their use to molecular biology, is that their REase cleaves double stranded DNA at fixed, identified positions at or near to the target sequence [19]

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