Homing Endonucleases And Inteins

by Belfort, Marlene; Stoddard, Barry L.; Wood, David W.; Derbyshire, Victoria

• ISBN13: 9783540251064
• ISBN10: 3540251065
• Format: Hardcover
• Copyright: 2005-12-22
• Publisher: Springer Nature

Summary

This book provides the first and only comprehensive description and detailed summary of the genetics, structure, function, mechanisms of action, evolution and engineering of homing endonucleases and inteins. These two unique protein superfamilies, which are tied together through their frequent fusion and coevolution, have generated considerable excitement for their fundamental, structural, and functional properties, their evolution as parasitic elements, and their widespread applications as gene targeting agents and as instruments for the generation of modified proteins and novel protein combinations.

Table of Contents

Back to Basics: Structure, Function, Evolution and Application of Homing Endonucleases and Inteins	1	(10)
MARLENE BELFORT
1 Introduction: Back to Basics	1	(1)
2 What Is a Homing Endonuclease?	2	(2)
3 What Is an Intein?	4	(1)
4 Inteins and Homing Endonucleases as Molecular Mosaics	4	(2)
5 Applications: "Turning Junk into Gold"	6	(3)
5.1 Site-Specific Group I Intron and Intein Endonucleases	6	(1)
5.2 Gene Targeting by a Group II Intron RNP Complex	6	(2)
5.3 "Inteins...Nature's Gift to the Protein Chemist"	8	(1)
6 The Message	9	(1)
References	10	(1)
Homing Endonucleases and the Yeast Mitochondrial co Locus - A Historical Perspective	11	(22)
BERNARD DUJON
1 The First Years of Yeast Mitochondrial Genetics	11	(2)
2 Genetic and Molecular Characterization of the co Locus	13	(4)
3 The Problems of Mitochondrial Intronic Reading Frames and Their Products	17	(1)
4 Group I and Group II Introns, and RNA Splicing	18	(1)
5 First Clues to the Function of the Translation Product of the w Intronic Reading Frame	19	(2)
6 Expressing the ω Intron-Encoded Protein in a Heterologous System	21	(1)
7 The Unusual Enzymatic Properties of the Group I Intron-Encoded Homing Endonuclease I-SceI	22	(1)
8 The First Additional Homing Endonucleases Discovered after I-SceI	23	(1)
9 Use of the I-SceI Endonuclease in Heterologous Systems	24	(2)
10 Epilogue	26	(1)
References	26	(7)
The LAGLIDADG Homing Endonuclease Family	33	(16)
BRETT CHEVALIER, RAYMOND J. MONNAT, JR., BARRY L. STODDARD
1 Introduction	33	(2)
2 Structures of LAGLIDADG Homing Endonucleases	35	(3)
3 Mechanisms of DNA Target Site Recognition and Specificity	38	(3)
4 Mechanism of DNA Cleavage	41	(4)
References	45	(4)
HNH Endonucleases	49	(18)
ANTHONY H. KEEBLE, MARIA J. MATÉ, COLIN KLEANTHOUS
1 Introduction	49	(1)
2 The HNH Family — A Tree of Three Branches	50	(4)
2.1 The HNH Consensus Sequence	50	(1)
2.2 The Cysteine-Containing HNH Motif (cysHNH)	51	(1)
2.3 The HNN Variant	52	(1)
2.4 The HNH Motif Is Part of the Wider ββαa-Me Superfamily of Endonucleases	52	(2)
3 Enzymology of HNH/ββαa-Me Motif Endonucleases	54	(4)
3.1 The HNH/ββα-Me Motif Is Functionally Adaptable	54	(2)
3.2 Biochemical Properties	56	(1)
3.3 HNH/ββα-Me Enzymes Require Single Divalent Cations for Activity	57	(1)
4 Structural Analysis of HNH Endonuclease Mediated dsDNA Cleavage	58	(4)
4.1 Relaxation of Substrate Strain is Conserved in the Cleavage Mechanisms of HNH/ββα-Me Enzymes	58	(1)
4.2 Metal Ion Coordination in the DNA-Bound Complex	59	(1)
4.3 Mechanism of Mg²+-Dependent Cleavage by HNH Endonucleases and Why Zn²+ Does Not Support Catalytic Activity	60	(2)
5 Conclusions	62	(1)
References	63	(4)
GIY-YIG Homing Endonucleases - Beads on a String	67	(18)
PATRICK VAN ROEY, VICTORIA DERBYSHIRE
1 Introduction	67	(2)
2 Occurrence and Functions of GIY-YIG Enzymes	69	(1)
3 I-TevI as the Model GIY-YIG Enzyme: Structure and Function	70	(9)
3.1 Catalytic Domain	71	(3)
3.2 DNA-Binding Domain	74	(1)
3.3 Flexible Linker and Distance Determination	75	(2)
3.4 I-TevI Endonuclease Is Bifunctional, Also Serving As a Transcriptional Autorepressor	77	(2)
4 DNA-Binding Domain Diversity and Conserved Modules	79	(2)
References	81	(4)
His-Cys Box Homing Endonucleases	85	(18)
ERIC A. GALBURT, MELISSA S. JURICA
1 The His-Cys Box Family of Homing Endonucleases	86	(3)
2 Expression of His-Cys Box Homing Endonucleases from Nuclear rDNA Transcripts	89	(2)
3 Structure, DNA Binding, and Catalytic Mechanism	91	(8)
3.1 Structure of a His-Cys Box Endonuclease: I-PpoI	91	(2)
3.2 DNA Binding and Recognition	93	(3)
3.3 Catalytic Mechanism	96	(1)
3.3.1 Catalytic Metal Coordination	96	(1)
3.3.2 Alignment and Activation of the Hydrolytic Water	97	(1)
3.3.3 Conformational Changes and Transition State Stabilization	98	(1)
4 HNH and His-Cys Box Homing Endonucleases	99	(1)
References	100	(3)
Group I Introns and Their Maturases: Uninvited, but Welcome, Guests	103	(18)
MARK G. CAPRARA, RICHARD B. WARING
1 Discovery of Self-Splicing Group I Introns	104	(2)
2 Genes Within Introns	106	(1)
3 How Many Maturases?	106	(1)
4 The Mechanism of Maturase-Assisted Splicing	107	(3)
5 Maturases Cooperate with Other Proteins for Splicing	110	(1)
6 Maturases or DNA Endonucleases?	110	(1)
7 How Intertwined Are the DNA and RNA Activities in Maturases?	111	(2)
8 Evolution of Maturase Activity	113	(1)
9 Concluding Remarks	114	(2)
References	116	(5)
Group II Intron Homing Endonucleases: Ribonucleoprotein Complexes with Programmable Target Specificity	121	(26)
ALAN M. LAMBOWITZ, GEORG MOHR, STEVEN ZIMMERLY
1 Introduction	121	(1)
2 Group II Intron Structure	122	(1)
3 Catalytic Properties of the Intron RNA	122	(3)
4 Biochemical Activities of Group II Intron-Encoded Proteins	125	(1)
5 Mobility Mechanisms	126	(2)
6 Binding of the IEP to the Intron RNA	128	(2)
7 DNA Target Site Recognition by Group II Intron Homing Endonucleases	130	(2)
8 DNA Target Site Recognition by Ll.LtrB Intron RNPs	132	(3)
9 Group II Introns as Gene-Targeting Vectors	135	(6)
References	141	(6)
Free-Standing Homing Endonucleases of T-Even Phage: Freeloaders or Functionaries?	147	(14)
DAVID R. EDGELL
1 Introduction	147	(1)
2 When Is a Free-Standing Endonuclease a Homing Endonuclease?	148	(1)
3 Intronless Homing and Marker Exclusion	149	(3)
4 The Recognition Sites of Free-Standing Endonucleases Are Distinct from the Endonuclease Insertion Site	152	(1)
5 How Do Free-Standing Endonucleases Prevent Cleavage of Their Host Genome?	153	(1)
6 The Separation of Cleavage and Insertion Sites Influences Endonuclease Mobility	154	(1)
7 The Sporadic Distribution of Free-Standing Homing Endonucleases	155	(1)
8 The "Function" of Free-Standing Endonucleases	156	(1)
9 The Diversity of Endonuclease Function	157	(1)
References	158	(3)
Function and Evolution of HO and VDE Endonucleases in Fungi	161	(16)
JAMES E. HABER, KENNETH H. WOLFE
1 Introduction	161	(1)
2 Mating-Type Genes in S. cerevisiae	162	(1)
3 HO-Induced MAT Switching in S. cerevisiae	163	(1)
4 Mechanism of MAT Switching	164	(1)
5 Donor Preference Associated with MAT Switching	164	(2)
6 Evolutionary Origins of the HO Gene and Other Components of the MAT Switching System	166	(1)
7 Linkage of an HM Cassette with the Recombination Enhancer (RE)	167	(1)
8 The HO Endonuclease Site in MATα1	168	(1)
9 Relationship of HO to VDE	169	(3)
10 Hypothesis for the Evolutionary Origin of HO	172	(1)
References	173	(4)
Engineering Homing Endonucleases for Genomic Applications	177	(16)
FREDERICK S. GIMBLE
1 Introduction	177	(1)
2 The Modular Organization of Homing Endonucleases and Their Endonucleolytic Activity	178	(2)
3 Probing the Modular Structure of Homing Endonucleases by Protein Engineering	180	(2)
4 Engineering Homing Enzymes with Novel Functions	182	(8)
4.1 Changing the Recognition Site Specificity of Homing Endonucleases	182	(1)
4.1.1 Altering Homing Endonuclease Specificity by Domain Shuffling	182	(3)
4.1.2 Altering Homing Endonuclease Specificity Using Genetic Screens and Selections	185	(4)
4.2 Introducing Molecular Switches into Homing Endonucleases	189	(1)
5 Conclusions and Future Prospects	190	(1)
References	190	(3)
Inteins - A Historical Perspective	193	(18)
FRANCINE B. PERLER
1 Introduction	194	(1)
2 Efforts To Prove That Splicing Is Post-translational	194	(1)
3 Intein Motifs and Conserved Residues	195	(2)
4 Intein Polymorphisms and Non-canonical Inteins	197	(1)
5 Criteria for Intein Designation	198	(1)
6 The Minimal Splicing Element	198	(1)
7 Splicing of Split Inteins: Trans-Splicing	199	(1)
8 The Influence of Exteins and Insertion Site Characteristics	200	(1)
9 The Challenge of Deciphering the Protein-Splicing Mechanism	201	(3)
10 Splicing of Non-canonical Inteins	204	(1)
11 Why Are Inteins So Robust?	205	(1)
12 Control, Control, Control	205	(1)
13 Perspectives for the Future	206	(1)
References	207	(4)
Origin and Evolution of Inteins and Other Hint Domains	211	(22)
BARAKET DASSA, SHMUEL PIETROKOVSKI
1 Introduction	211	(2)
2 Hint Domain Families	213	(12)
2.1 Inteins	213	(1)
2.1.1 Inteins Include Different Domains	213	(1)
2.1.2 Intein Protein Hosts and Insertion Points	214	(1)
2.1.3 Inteins Are Sporadically Distributed	215	(1)
2.1.4 A Non-selfish Intein-Derived Protein	216	(1)
2.1.5 Split Inteins	217	(1)
2.2 Hog-Hint Domains	218	(1)
2.2.1 Phylogenetic Distribution of Hog-Hint Domains	218	(2)
2.3 BIL-Hint Domains	220	(1)
2.3.1 Phylogenetic Distribution of BIL Domains	221	(1)
2.3.2 Protein Distribution of BIL Domains	222	(1)
2.3.3 Biochemical Activity and Biological Roles of BIL Domains	222	(2)
2.4 Other Hint Domains	224	(1)
3 Origin of the Hint Domains	225	(4)
3.1 Features of the Progenitor Hint Domain	225	(2)
3.2 Emergence of the Progenitor Hint Domain	227	(2)
References	229	(4)
Biochemical Mechanisms of Intein-Mediated Protein Splicing	233	(24)
KENNETH V. MILLS, HENRY PAULUS
1 Conserved Features of Intein Structure	234	(1)
2 The Canonical Protein-Splicing Mechanism	234	(9)
2.1 First Step of Protein Splicing - N/O or N/S Acyl Shift	235	(3)
2.2 Second Step of Protein Splicing - Transesterification	238	(2)
2.3 Third Step of Protein Splicing - Asparagine Cyclization	240	(1)
2.4 Finishing Reaction	241	(1)
2.5 Association of Split Inteins	242	(1)
3 Non-canonical Inteins and Their Mechanisms	243	(4)
3.1 Substitution of the N-Terminal Nucleophile	243	(2)
3.2 Substitution of the C-Terminal Asparagine	245	(1)
3.3 Hedgehog Autoprocessing Domains	245	(1)
3.4 Bacterial Intein-Like Domains	246	(1)
4 Protein Splicing as a System	247	(4)
4.1 Side Reactions	247	(2)
4.2 What Coordinates the Steps in the Protein-Splicing Pathway?	249	(2)
5 Conclusions	251	(1)
References	252	(5)
The Structure and Function of Intein-Associated Homing Endonucleases	257	(16)
CARMEN M. MOURE, FLORANTE A. QUIOCHO
1 Introduction	257	(1)
2 Architecture of Inteins: A Two-Domain Organization	258	(3)
2.1 The Splicing Domain	260	(1)
2.2 Endonuclease Domain	261	(1)
3 DNA Binding to the Splicing and Endonuclease Domains of PI-SceI	261	(5)
3.1 Protein-DNA Contacts Across the Splicing and Endonuclease Domains	263	(1)
3.2 Protein Conformational Changes	263	(1)
3.3 DNA Bending	264	(2)
3.4 DNA Recognition	266	(1)
4 DNA Cleavage	266	(3)
4.1 Active Sites	266	(1)
4.2 Divalent Metal Binding at the Active Sites	267	(2)
References	269	(4)
Harnessing Inteins for Protein Purification and Characterization	273	(20)
HAORONG CHONG, MING-QUN XU
1 Introduction	273	(1)
2 Intein Fusion Systems for Protein Purification	273	(10)
2.1 C-Terminal Fusion System	275	(2)
2.2 N-Terminal Fusion System	277	(1)
2.3 Choosing an Appropriate Intein Fusion System	278	(2)
2.4 Choosing an Appropriate Residue at the Fusion Junction	280	(1)
2.5 Conditions for Intein Cleavage	281	(2)
2.6 Intein Fusion Systems for High-Throughput and Large-Scale Applications	283	(1)
3 Protein trans-Splicing and Cleavage Systems	283	(1)
4 Intein-Mediated Protein Ligation (IPL)	284	(5)
4.1 Intein-Mediated Peptide Array (IPA)	286	(2)
4.2 Kinase Assays Using Carrier Protein-Peptide Substrates	288	(1)
4.3 Purification of Peptide-Specific Antibody	289	(1)
5 Remarks and Conclusions	289	(1)
References	290	(3)
Production of Cyclic Proteins and Peptides	293	(14)
ALI TAVASSOLI, TODD A. NAUMANN, STEPHEN J. BENKOVIC
1 Introduction	293	(2)
1.1 Naturally Occurring Cyclic Peptides	293	(2)
1.2 Intein-Mediated Cyclization	295	(1)
2 Intein-Mediated Ligation	295	(2)
3 TWIN	297	(1)
4 trans- and cis-Splicing	298	(1)
5 Cyclization with Artificially Split Inteins	299	(1)
6 SICLOPPS	300	(2)
7 Summary	302	(1)
References	302	(5)
Inteins for Split-Protein Reconstitutions and Their Applications	307	(18)
TAKEAKI OZAWA, YOSHIO UMEZAWA
1 Introduction	307	(1)
2 General Characteristics of Protein Splicing	308	(1)
3 Reporter Protein Reconstitution	309	(12)
3.1 Detection of Protein-Protein Interactions	311	(4)
3.2 Protein Splicing in Intracellular Organelles	315	(1)
3.2.1 Identification of Organelle-Localized Proteins from cDNA Libraries	315	(2)
3.2.2 Detection of Protein Nuclear Transport	317	(2)
3.2.3 trans-Splicing in the Chloroplast in Plant Cells	319	(1)
3.3 Screening of Potential Antimycobacterial Agents	320	(1)
4 Future Directions	321	(1)
References	322	(3)
Intein Reporter and Selection Systems	325	(20)
DAVID W. WOOD, GEORGIOS SKRETAS
1 Introduction	325	(2)
2 Systems for Direct Observation of Intein Function	327	(1)
3 Selection and Reporter Systems for Intein Function	328	(12)
3.1 Insertion into the LacZα Gene	331	(1)
3.2 Insertion into the Saccharomyces cerevisiae VAT2 Gene	331	(1)
3.3 Thymidylate Synthase System for Selection in vivo	332	(1)
3.4 Kanamycin Resistance: the ORFTRAP System	333	(1)
3.5 DNA gyraseA: Negative Selection for Splicing in vivo	334	(1)
3.6 Bacterial ccdB: Negative Selection for Splicing or Cleaving	335	(1)
3.7 T4 DNA Polymerase: Negative-Splicing Selection in vivo	336	(1)
3.8 Yeast Gal4 Gene: Temperature-Sensitive Splicing in vivo	337	(1)
3.9 Green Fluorescent Protein: Reporter for Splicing in vitro	338	(1)
3.10 trans-Splicing Intein Systems	339	(1)
4 Summary	340	(1)
References	341	(4)
Industrial Applications of Intein Technology	345	(20)
DAVID W. WOOD, SARAH W. HARCUM, GEORGES BELFORT
1 Introduction	346	(1)
2 Scale-Up of Intein Processes	346	(11)
2.1 Conventional Affinity Tag Processes	347	(1)
2.2 Intein-Mediated Protein Purification	347	(1)
2.2.1 Modeling Large-Scale Intein Bioseparations	348	(2)
2.2.2 Economics of the IMPACT Process Scale-Up	350	(1)
2.3 Economic Optimization of Intein-Based Bioseparations	350	(1)
2.3.1 Buffers	351	(2)
2.3.2 Resins	353	(1)
2.3.3 Alternate Intein-Cleaving Modes	354	(1)
2.4 Economics of an Optimal Large-Scale Intein Process	355	(1)
2.5 Additional Considerations for Intein Process Scale-Up	356	(1)
3 Scale-Down of Intein Processes	357	(5)
3.1 Microfluidics	358	(3)
3.2 Protein Micro-arrays	361	(1)
4 Summary	362	(1)
References	363	(2)
Subject Index	365