Structure-Function Studies of Two Yeast Homing Endonucleases that Evolved to Cleave Identical Target

Nawimanage, Rasika R.; Yuan, Ziyan; Casares, Mackenzie; Joshi, Rakesh; Lohman, Jeremy R.; Gimble, Frederick S.

doi:10.1016/j.jmb.2022.167550

Structure-Function Studies of Two Yeast Homing Endonucleases that Evolved to Cleave Identical Target

Journal Article · 01 May 2022 · J. Mol. Biol.

DOI:https://doi.org/10.1016/j.jmb.2022.167550· OSTI ID:1871736

Nawimanage, Rasika R.; Yuan, Ziyan; Casares, Mackenzie; Joshi, Rakesh; Lohman, Jeremy R.; Gimble, Frederick S.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; UNIVERSITY

OSTI ID:: 1871736

Journal Information:: J. Mol. Biol., Journal Name: J. Mol. Biol. Journal Issue: (9) Vol. 434

Country of Publication:: United States

Language:: ENGLISH

References (71)

Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions. Perrin, A.; Buckle, M.; Dujon, B. The EMBO Journal, Vol. 12, Issue 7 https://doi.org/10.1002/j.1460-2075.1993.tb05956.x	journal	July 1993
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
How to measure and predict the molar absorption coefficient of a protein Pace, C. Nick; Vajdos, Felix; Fee, Lanette Protein Science, Vol. 4, Issue 11 https://doi.org/10.1002/pro.5560041120	journal	November 1995
I- Ppo I and I- Cre I homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment 1 1Edited by G. Smith Argast, Gretchen M.; Stephens, Kathryn M.; Emond, Mary J. Journal of Molecular Biology, Vol. 280, Issue 3 https://doi.org/10.1006/jmbi.1998.1886	journal	July 1998
Homing Endonucleases: From Genetic Anomalies to Programmable Genomic Clippers Belfort, Marlene; Bonocora, Richard P. Methods in Molecular Biology, p. 1-26 https://doi.org/10.1007/978-1-62703-968-0_1	book	January 2014
A group I intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intron Gauthier, Antonin; Turmel, Monique; Lemieux, Claude Current Genetics, Vol. 19, Issue 1 https://doi.org/10.1007/BF00362086	journal	January 1991
Homing endonucleases: structure, function and evolution Jurica, M. S.; Stoddard, B. L. Cellular and Molecular Life Sciences (CMLS), Vol. 55, Issue 10 https://doi.org/10.1007/s000180050372	journal	August 1999
Group I introns as mobile genetic elements: Facts and mechanistic speculations — a review Dujon, Bernard Gene, Vol. 82, Issue 1 https://doi.org/10.1016/0378-1119(89)90034-6	journal	October 1989
Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI Chevalier, Brett; Turmel, Monique; Lemieux, Claude Journal of Molecular Biology, Vol. 329, Issue 2 https://doi.org/10.1016/S0022-2836(03)00447-9	journal	May 2003
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene Jacquier, A.; Dujon, B. Cell, Vol. 41, Issue 2 https://doi.org/10.1016/S0092-8674(85)80011-8	journal	June 1985
Design, Activity, and Structure of a Highly Specific Artificial Endonuclease Chevalier, Brett S.; Kortemme, Tanja; Chadsey, Meggen S. Molecular Cell, Vol. 10, Issue 4 https://doi.org/10.1016/S1097-2765(02)00690-1	journal	October 2002
The Crystal Structure of the Gene Targeting Homing Endonuclease I-SceI Reveals the Origins of its Target Site Specificity Moure, Carmen M.; Gimble, Frederick S.; Quiocho, Florante A. Journal of Molecular Biology, Vol. 334, Issue 4 https://doi.org/10.1016/j.jmb.2003.09.068	journal	December 2003
Engineered I-CreI Derivatives Cleaving Sequences from the Human XPC Gene can Induce Highly Efficient Gene Correction in Mammalian Cells Arnould, Sylvain; Perez, Christophe; Cabaniols, Jean-Pierre Journal of Molecular Biology, Vol. 371, Issue 1 https://doi.org/10.1016/j.jmb.2007.04.079	journal	August 2007
Engineering Variants of the I-SceI Homing Endonuclease with Strand-specific and Site-specific DNA-nicking Activity Niu, Yan; Tenney, Kristen; Li, Hongye Journal of Molecular Biology, Vol. 382, Issue 1 https://doi.org/10.1016/j.jmb.2008.07.010	journal	September 2008
Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity Joshi, Rakesh; Ho, Kwok Ki; Tenney, Kristen Journal of Molecular Biology, Vol. 405, Issue 1 https://doi.org/10.1016/j.jmb.2010.10.029	journal	January 2011
The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease Shen, Betty W.; Lambert, Abigail; Walker, Bradley C. Journal of Molecular Biology, Vol. 428, Issue 1 https://doi.org/10.1016/j.jmb.2015.12.005	journal	January 2016
Homing Endonucleases: From Microbial Genetic Invaders to Reagents for Targeted DNA Modification Stoddard, Barry L. Structure, Vol. 19, Issue 1 https://doi.org/10.1016/j.str.2010.12.003	journal	January 2011
Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity Lambert, Abigail R.; Hallinan, Jazmine P.; Shen, Betty W. Structure, Vol. 24, Issue 6 https://doi.org/10.1016/j.str.2016.03.024	journal	June 2016
Mitochondrial Proteins Moonlighting in the Nucleus Monaghan, Richard M.; Whitmarsh, Alan J. Trends in Biochemical Sciences, Vol. 40, Issue 12 https://doi.org/10.1016/j.tibs.2015.10.003	journal	December 2015
Homing endonuclease structure and function Stoddard, Barry L. Quarterly Reviews of Biophysics, Vol. 38, Issue 01 https://doi.org/10.1017/S0033583505004063	journal	February 2005
Metal-Dependent DNA Cleavage Mechanism of the I -Cre I LAGLIDADG Homing Endonuclease ^, Chevalier, Brett; Sussman, Django; Otis, Christian Biochemistry, Vol. 43, Issue 44 https://doi.org/10.1021/bi048970c	journal	October 2004
Directed Evolution and Substrate Specificity Profile of Homing Endonuclease I-SceI Doyon, Jeffrey B.; Pattanayak, Vikram; Meyer, Carissa B. Journal of the American Chemical Society, Vol. 128, Issue 7 https://doi.org/10.1021/ja057519l	journal	February 2006
Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae Gimble, Frederick S.; Thorner, Jeremy Nature, Vol. 357, Issue 6376 https://doi.org/10.1038/357301a0	journal	May 1992
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases Redondo, Pilar; Prieto, Jesús; Muñoz, Inés G. Nature, Vol. 456, Issue 7218 https://doi.org/10.1038/nature07343	journal	November 2008
Exploitation of binding energy for catalysis and design Thyme, Summer B.; Jarjour, Jordan; Takeuchi, Ryo Nature, Vol. 461, Issue 7268 https://doi.org/10.1038/nature08508	journal	October 2009
Meganuclease targeting of PCSK9 in macaque liver leads to stable reduction in serum cholesterol Wang, Lili; Smith, Jeff; Breton, Camilo Nature Biotechnology, Vol. 36, Issue 8 https://doi.org/10.1038/nbt.4182	journal	July 2018
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases Szczepek, Michal; Brondani, Vincent; Büchel, Janine Nature Biotechnology, Vol. 25, Issue 7 https://doi.org/10.1038/nbt1317	journal	July 2007
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Langer, Gerrit; Cohen, Serge X.; Lamzin, Victor S. Nature Protocols, Vol. 3, Issue 7 https://doi.org/10.1038/nprot.2008.91	journal	June 2008
Visualizing phosphodiester-bond hydrolysis by an endonuclease Molina, Rafael; Stella, Stefano; Redondo, Pilar Nature Structural & Molecular Biology, Vol. 22, Issue 1 https://doi.org/10.1038/nsmb.2932	journal	December 2014
Understanding the indirect DNA read-out specificity of I-CreI Meganuclease Prieto, Jesús; Redondo, Pilar; López-Méndez, Blanca Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-28599-0	journal	July 2018
Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization Takeuchi, R.; Choi, M.; Stoddard, B. L. Proceedings of the National Academy of Sciences, Vol. 111, Issue 11 https://doi.org/10.1073/pnas.1321030111	journal	March 2014
Recognition and cleavage site of the intron-encoded omega transposase. Colleaux, L.; D'Auriol, L.; Galibert, F. Proceedings of the National Academy of Sciences, Vol. 85, Issue 16 https://doi.org/10.1073/pnas.85.16.6022	journal	August 1988
Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Rouet, P.; Smih, F.; Jasin, M. Proceedings of the National Academy of Sciences, Vol. 91, Issue 13 https://doi.org/10.1073/pnas.91.13.6064	journal	June 1994
Recurrent invasion and extinction of a selfish gene Goddard, M. R.; Burt, A. Proceedings of the National Academy of Sciences, Vol. 96, Issue 24 https://doi.org/10.1073/pnas.96.24.13880	journal	November 1999
Mining Endonuclease Cleavage Determinants in Genomic Sequence Data Szeto, Mindy D.; Boissel, Sandrine J. S.; Baker, David Journal of Biological Chemistry, Vol. 286, Issue 37 https://doi.org/10.1074/jbc.M111.259572	journal	July 2011
Protein footprinting approach to mapping DNA binding sites of two archaeal homing enzymes: evidence for a two-domain protein structure Lykke-Andersen, J. Nucleic Acids Research, Vol. 24, Issue 20 https://doi.org/10.1093/nar/24.20.3982	journal	October 1996
Evolutionarily conserved and functionally important residues in the I- CeuI homing endonuclease Turmel, M. Nucleic Acids Research, Vol. 25, Issue 13 https://doi.org/10.1093/nar/25.13.2610	journal	July 1997
Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases Lucas, P. Nucleic Acids Research, Vol. 29, Issue 4 https://doi.org/10.1093/nar/29.4.960	journal	February 2001
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes Roberts, R. J. Nucleic Acids Research, Vol. 31, Issue 7 https://doi.org/10.1093/nar/gkg274	journal	April 2003
A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells Epinat, J. -C. Nucleic Acids Research, Vol. 31, Issue 11 https://doi.org/10.1093/nar/gkg375	journal	June 2003
Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI Silva, G. H. Nucleic Acids Research, Vol. 32, Issue 10 https://doi.org/10.1093/nar/gkh618	journal	June 2004
enoLOGOS: a versatile web tool for energy normalized sequence logos Workman, C. T.; Yin, Y.; Corcoran, D. L. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki439	journal	July 2005
Thermodynamics of DNA target site recognition by homing endonucleases Eastberg, J. H.; Smith, A. M.; Zhao, L. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm867	journal	November 2007
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway Moure, C. M.; Gimble, F. S.; Quiocho, F. A. Nucleic Acids Research, Vol. 36, Issue 10 https://doi.org/10.1093/nar/gkn178	journal	April 2008
Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins Li, Hui; Pellenz, Stefan; Ulge, Umut Nucleic Acids Research, Vol. 37, Issue 5 https://doi.org/10.1093/nar/gkp004	journal	January 2009
Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds Grizot, Sylvestre; Epinat, Jean-Charles; Thomas, Séverine Nucleic Acids Research, Vol. 38, Issue 6 https://doi.org/10.1093/nar/gkp1171	journal	December 2009
Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease Grizot, Sylvestre; Smith, Julianne; Daboussi, Fayza Nucleic Acids Research, Vol. 37, Issue 16 https://doi.org/10.1093/nar/gkp548	journal	July 2009
High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display Jarjour, Jordan; West-Foyle, Hoku; Certo, Michael T. Nucleic Acids Research, Vol. 37, Issue 20 https://doi.org/10.1093/nar/gkp726	journal	September 2009
Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering Ulge, Umut Y.; Baker, David A.; Monnat, Raymond J. Nucleic Acids Research, Vol. 39, Issue 10 https://doi.org/10.1093/nar/gkr022	journal	February 2011
Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications Li, Hui; Ulge, Umut Y.; Hovde, Blake T. Nucleic Acids Research, Vol. 40, Issue 6 https://doi.org/10.1093/nar/gkr1072	journal	November 2011
Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space Jacoby, Kyle; Metzger, Michael; Shen, Betty W. Nucleic Acids Research, Vol. 40, Issue 11 https://doi.org/10.1093/nar/gkr1303	journal	February 2012
Non-specific protein–DNA interactions control I-CreI target binding and cleavage Molina, Rafael; Redondo, Pilar; Stella, Stefano Nucleic Acids Research, Vol. 40, Issue 14 https://doi.org/10.1093/nar/gks320	journal	April 2012
Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases Baxter, Sarah; Lambert, Abigail R.; Kuhar, Ryan Nucleic Acids Research, Vol. 40, Issue 16 https://doi.org/10.1093/nar/gks502	journal	June 2012
Massively parallel determination and modeling of endonuclease substrate specificity Thyme, Summer B.; Song, Yifan; Brunette, T. J. Nucleic Acids Research, Vol. 42, Issue 22 https://doi.org/10.1093/nar/gku1096	journal	November 2014
Creating a monomeric endonuclease TALE-I-SceI with high specificity and low genotoxicity in human cells Lin, Jianfei; Chen, He; Luo, Ling Nucleic Acids Research, Vol. 43, Issue 2 https://doi.org/10.1093/nar/gku1339	journal	December 2014
Engineering altered protein–DNA recognition specificity Bogdanove, Adam J.; Bohm, Andrew; Miller, Jeffrey C. Nucleic Acids Research, Vol. 46, Issue 10 https://doi.org/10.1093/nar/gky289	journal	April 2018
Up-to-dating of complete sequenced DNA data of Hansenula wingei yeast mitochondria Sekito, T. Nucleic Acids Symposium Series, Vol. 48, Issue 1 https://doi.org/10.1093/nass/48.1.179	journal	November 2004
Adaptation for Horizontal Transfer in a Homing Endonuclease Koufopanou, Vassiliki; Goddard, Matthew R.; Burt, Austin Molecular Biology and Evolution, Vol. 19, Issue 3 https://doi.org/10.1093/oxfordjournals.molbev.a004077	journal	March 2002
Directed evolution of homing endonuclease I-SceI with altered sequence specificity Chen, Z.; Wen, F.; Sun, N. Protein Engineering Design and Selection, Vol. 22, Issue 4 https://doi.org/10.1093/protein/gzp001	journal	January 2009
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Geometry of metal–ligand interactions in proteins Harding, Marjorie M. Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 3 https://doi.org/10.1107/S0907444900019168	journal	March 2001
Metal–ligand geometry relevant to proteins and in proteins: sodium and potassium Harding, Marjorie M. Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 5 https://doi.org/10.1107/S0907444902003712	journal	April 2002
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions Prieto, Jesús; Redondo, Pilar; Merino, Nekane Acta Crystallographica Section F Structural Biology Communications, Vol. 72, Issue 6 https://doi.org/10.1107/S2053230X16007512	journal	May 2016
Invasion of a multitude of genetic niches by mobile endonuclease genes Gimble, Frederick S. FEMS Microbiology Letters, Vol. 185, Issue 2 https://doi.org/10.1111/j.1574-6968.2000.tb09046.x	journal	April 2000
Homing endonucleases from mobile group I introns: discovery to genome engineering Stoddard, Barry L. Mobile DNA, Vol. 5, Issue 1 https://doi.org/10.1186/1759-8753-5-7	journal	January 2014
The Phylogenetic Relationships of the Hat-shaped Ascospore-forming, Nitrate-assimilating Pichia Species, Formerly Classified in the Genus Hansenula S ydow et S ydow , Based on the Partial Sequences of 18S and 26S Ribosomal RNAs (Saccharomycetaceae): The Proposals of Three New Genera, Ogataea , Kuraishia , and Nakazawaea Yamada, Yuzo; Maeda, Kojiro; Mikata, Kozaburo Bioscience, Biotechnology, and Biochemistry, Vol. 58, Issue 7 https://doi.org/10.1271/bbb.58.1245	journal	January 1994
Molecular scissors for in situ cellular repair Prieto, Jesús; Molina, Rafael; Montoya, Guillermo Critical Reviews in Biochemistry and Molecular Biology, Vol. 47, Issue 3 https://doi.org/10.3109/10409238.2011.652358	journal	January 2012

Similar Records

Structure-Function Studies of Two Yeast Homing Endonucleases that Evolved to Cleave Identical Target

Journal Article · 2022 · J. Mol. Biol. · OSTI ID:1869976

Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases

Journal Article · 2018 · Nucleic Acids Research · OSTI ID:1544824

Structure and specificity of an antibody targeting a proteolytically cleaved IgG hinge

Journal Article · 2015 · Proteins · OSTI ID:1194202

Structure-Function Studies of Two Yeast Homing Endonucleases that Evolved to Cleave Identical Target

Citation Formats

References (71)

Similar Records

Related Subjects