Inhaltsangabe
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 Ph
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