Restriction Endonucleases

Restriction enzymes are highly specific nucleases which occur ubiquitously among prokaryotic organisms, where they serve to protect bacterial cells against foreign DNA. Many different types of restriction enzymes are known, among them multi-subunit enzymes which depend on ATP or GTP hydrolysis for target site location. The best known representatives, the orthodox type II restriction endonucleases, are homodimers which recognize palindromic sequences, 4 to 8 base pairs in length, and cleave the DNA within or immediately adjacent to the recognition site. In addition to their important biological role (up to 10 % of the genomes of prokaryotic organisms code for restriction/modification systems!), they are among the most important enzymes used for the analysis and recombination of DNA. In addition, they are model systems for the study of protein-nucleic acids interactions and, because of their ubiquitous occurence, also for the understanding of the mechanisms of evolution.

The present book deals with all aspects of restriction endonucleases including nomenclature, diversity, evolution, genetics, structure and function, mechanism of target site location and DNA recognition, enzymology, protein design, and provides a description of the history of the discovery of and the research on restriction enzymes.

Contenu

Survey and Summary A Nomenclature for Restriction Enzymes, DNA Methyltransferases, Homing Endonucleases and Their Genes.- 1 Introduction.- 2 General Rules.- 3 Details of Types and Subtypes.- 3.1 Types I, II, III and IV.- 3.2 Type I.- 3.3 Type II.- 3.4 Type IIP.- 3.5 Type IIA.- 3.6 Type IIB.- 3.7 Type IIC.- 3.8 Type IIE.- 3.9 Type IIF.- 3.10 Type IIG.- 3.11 Type IIH.- 3.12 Type IIM.- 3.13 Type IIS.- 3.14 Type IIT.- 3.15 Nicking Enzymes.- 3.16 Control Proteins.- 3.17 Type III.- 3.18 Type IV.- 3.19 Hypothetical Enzymes.- 3.20 Homing Endonucleases.- 3.21 Adherence to These Conventions and Updates.- References.- Restriction-Modification Systems as Minimal Forms of Life.- 1 Introduction.- 2 Genomics and Mobility of Restriction-Modification Systems.- 2.1 Genomics.- 2.2 Horizontal Gene Transfer Inferred from Evolutionary Analyses.- 2.3 Presence on Mobile Genetic Elements.- 2.4 Genomic Contexts and Genome Comparison.- 2.4.1 Insertion into an Operon-Like Gene Cluster.- 2.4.2 Insertion with Long Target Duplication.- 2.4.3 Substitution Adjacent to a Large Inversion.- 2.4.4 Apparent Transposition.- 2.4.5 Linkage of a Restriction-Modification Gene Complex with Another Restriction-Modification Gene Complex or a Cell Death-Related Gene.- 2.5 Defective Restriction-Modification Gene Complexes.- 3 Attack on the Host Genome and the Selfish Gene Hypothesis.- 3.1 Post-Segregational Host Cell Killing.- 3.2 Comparison with other Post-Segregational Cell Killing Systems.- 3.3 Selfish Gene Hypothesis.- 3.4 Genomics as Explained by the Selfish Gene Hypothesis.- 4 Gene Regulation in the Life Cycle of Restriction-Modification Systems.- 4.1 Gene Organization.- 4.2 Gene Regulation.- 4.2.1 Restriction Gene Downstream of Modification Gene.- 4.2.2 Restriction Gene Upstream of Modification Gene.- 4.2.3 Modification Enzyme as a Regulator.- 4.2.4 Regulatory Proteins.- 4.2.5 Type I Restriction-Modification Systems.- 4.3 Restriction-Modification Gene Complexes May Be Able to Multiply Themselves.- 5 Intra-Genomic Competition Involving Restriction-Modification Gene Complexes.- 5.1 Two Restriction-Modification Systems with the Same Recognition Sequence Can Block the Post-Segregational Killing Potential of Each Other.- 5.2 Solitary Methyltransferases Can Attenuate the Post-Segregational Killing Activity of Restriction-Modification Systems.- 5.3 Resident Restriction-Modification Systems Can Abort the Establishment of a Similar Incoming Restriction-Modification System.- 5.4 Suicidal Defense Against Restriction-Modification Gene Complexes.- 5.5 Defense Against Invaders by Restriction-Modification Systems.- 6 Genome Dynamics and Genome Co-Evolution with Restriction-Modification Gene Complexes.- 6.1 Some Restriction-Modification Gene Complexes and Restriction Sites Are Eliminated from the Genome.- 6.2 Mutagenesis and Anti-Mutagenesis.- 6.3 End Joining.- 6.4 Homologous Recombination by Bacteriophages.- 6.5 Cellular Homologous Recombination in Conflict and Collaboration with Restriction-Modification Gene Complexes.- 6.6 Selfish Genome Rearrangement Model.- 7 Towards Natural Classification of Restriction Enzymes.- 8 Application of the Behavior of Restriction-Modification Gene Complexes as Selfish Elements.- 9 A Hypothesis on the Attack by Restriction-Modification Gene Complexes on the Chromosomes.- 10 Conclusions.- References.- Molecular Phylogenetics of Restriction Endonucleases.- 1 Discovery and Classification of Restriction Enzymes.- 2 Genomic Context of R-M Systems.- 3 Historical Perspective of Comparative Analyses of Restriction Enzymes: Are They Products of Divergent or Convergent Evolution?.- 4 Crystallography of Type II REases: Exploration of the "Midnight Zone of Homology".- 5 Homology Between Restriction Endonucleases and Other Enzymes Acting on Nucleic Acids.- 6 Non-Homologous Active Sites in Homologous Structures.- 7 Cladistic Analysis of the PD-(D/E)xK Superfamily.- 8 Identification of PD-(D/E)xK Domains in Other Nucleases and Prediction of Their Position on the Phylogenetic Tree.- 9 In the End, Convergence Wins: Sequence Analyses Reveal Type II Enzymes Unrelated to the PD-(D/E)XK Superfamily.- 10 Evolutionary Trajectories of Restriction Enzymes: Relationships to Other Polyphyletic Groups of Nucleases.- References.- Sliding or Hopping? How Restriction Enzymes Find Their Way on DNA.- 1 Introduction.- 2 Mechanisms of Facilitated Target Site Location by Proteins on DNA.- 2.1 Sliding.- 2.2 Hopping.- 2.3 Intersegment Transfer.- 3 Critical Factors Determining the Efficiency of Target Site Location by Sliding and Hopping Processes.- 4 Sliding or "Hopping" - A Survey of Experimental Data.- 4.1 Structures of Restriction Endonucleases.- 4.2 Accurate Scanning of the DNA for the Presence of Target Sites.- 4.3 Length Dependence of Linear Diffusion.- 4.4 Processivity of DNA Cleavage.- 4.5 DNA Cleavage by a Covalently Closed EcoRV Variant.- 4.6 Cleavage of Topological Connected Plasmid Molecules.- 5 Conclusions.- References.- The Type I and III Restriction Endonucleases: Structural Elements in Molecular Motors that Process DNA.- 1 Energy-Dependent DNA Processing.- 2 Motor Enzyme Architecture of the ATP-Dependent Restriction Endonucleases.- 2.1 Motor Enzyme Motifs in the Type I and III Restriction Endonucleases.- 2.1.1 Gross Organisation of the Type I HsdR Subunits.- 2.1.2 Gross Organisation of the Type III Res Subunits.- 2.1.3 Core Helicase Motifs in ATP Binding and Catalysis.- 2.1.4 The "Q-Tip Helix" - A New Helicase Motif?.- 2.1.5 The DNA Binding Motifs - Family-Specific Deviations.- 2.2 A Motor Enzyme Fold in the Type I and III Restriction Endonucleases.- 2.3 Macromolecular Assembly of the Type I and III Restriction Endonucleases.- 3 Future Directions.- 3.1 Coupling Chemical Energy to Mechanical Motion.- 3.2 Tools for Nanotechnology Rather Than Biotechnology?.- References.- The Integration of Recognition and Cleavage: X-Ray Structures of Pre-Transition State Complex, Post-Reactive Complex and the DNA-Free Endonuclease.- 1 Introduction.- 2 The Pre-Transition State Complex.- 2.1 General Features.- 2.2 DNA Numbering Scheme.- 2.3 Secondary Structure.- 2.4 The EcoRI Kink.- 2.5 Recognition Overview.- 2.6 Sequence-Specific Hydrogen Bonds.- 2.7 Sequence-Specific Interactions Via Bound Water.- 2.8 Sequence-Specific Van der Waals Interactions.- 2.9 Redundancy of Direct Sequence-Specific Interactions.- 2.10 Bound Solvent.- 2.11 "Buried" DNA Phosphate Groups.- 2.12 Solvent-Mediated Contacts to the DNA Bases Flanking the Recognition Site.- 2.13 DNA Minor Groove.- 2.14 Contrasting the 1.85 and 2.7 Å Pre-Transition State Complexes.- 3 The Post-Reactive Complex and the Cleavage Mechanism.- 3.…