Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications

Molecular Cell - Tập 68 - Trang 926-939.e4 - 2017
Jennifer L. Stamos1, Alfred M. Lentzsch1, Alan M. Lambowitz1
1Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA

Tài liệu tham khảo

Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 Appleby, 2015, Viral replication. Structural basis for RNA replication by the hepatitis C virus polymerase, Science, 347, 771, 10.1126/science.1259210 Arnold, 2005, Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase, J. Biol. Chem., 280, 25706, 10.1074/jbc.M503444200 Blocker, 2005, Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase, RNA, 11, 14, 10.1261/rna.7181105 Bricogne, 2016 Carignani, 1983, An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae, Cell, 35, 733, 10.1016/0092-8674(83)90106-X Cavalier-Smith, 1991, Intron phylogeny: a new hypothesis, Trends Genet., 7, 145, 10.1016/0168-9525(91)90102-V Clark, 2016, tRNA base methylation identification and quantification via high-throughput sequencing, RNA, 22, 1771, 10.1261/rna.056531.116 Costa, 2016, Crystal structures of a group II intron lariat primed for reverse splicing, Science, 354, aaf9258, 10.1126/science.aaf9258 Das, 2014, Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage, Nucleic Acids Res., 42, 8125, 10.1093/nar/gku487 Emsley, 2010, Features and development of Coot, Acta Crystallogr. D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 Evans, 2013, How good are my data and what is the resolution?, Acta Crystallogr. D Biol. Crystallogr., 69, 1204, 10.1107/S0907444913000061 Fica, 2013, RNA catalyses nuclear pre-mRNA splicing, Nature, 503, 229, 10.1038/nature12734 Fisher, 2003, Substitutions at Phe61 in the beta3-beta4 hairpin of HIV-1 reverse transcriptase reveal a role for the Fingers subdomain in strand displacement DNA synthesis, J. Mol. Biol., 325, 443, 10.1016/S0022-2836(02)01225-1 Galej, 2013, Crystal structure of Prp8 reveals active site cavity of the spliceosome, Nature, 493, 638, 10.1038/nature11843 Galej, 2014, Structural studies of the spliceosome: zooming into the heart of the machine, Curr. Opin. Struct. Biol., 25, 57, 10.1016/j.sbi.2013.12.002 Gao, 1997, Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection, Proc. Natl. Acad. Sci. USA, 94, 407, 10.1073/pnas.94.2.407 Gillis, 2008, Structure of the Tribolium castaneum telomerase catalytic subunit TERT, Nature, 455, 633, 10.1038/nature07283 Kabsch, 2010, Xds, Acta Crystallogr. D Biol. Crystallogr., 66, 125, 10.1107/S0907444909047337 Kennell, 1993, Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria, Cell, 73, 133, 10.1016/0092-8674(93)90166-N Kissinger, 1999, Rapid automated molecular replacement by evolutionary search, Acta Crystallogr. D Biol. Crystallogr., 55, 484, 10.1107/S0907444998012517 Koonin, 2015, Origins and evolution of viruses of eukaryotes: the ultimate modularity, Virology, 479-480, 2, 10.1016/j.virol.2015.02.039 Lambowitz, 2015, Mobile bacterial group II introns at the crux of eukaryotic evolution, Microbiol. Spectr., 3, 10.1128/microbiolspec.MDNA3-0050-2014 Lambowitz, 2011, Group II introns: mobile ribozymes that invade DNA, Cold Spring Harb. Perspect. Biol., 3, a003616, 10.1101/cshperspect.a003616 Lansdon, 2010, Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex, J. Mol. Biol., 397, 967, 10.1016/j.jmb.2010.02.019 Martin, 2006, Introns and the origin of nucleus-cytosol compartmentalization, Nature, 440, 41, 10.1038/nature04531 Mitchell, 2010, Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA, Nat. Struct. Mol. Biol., 17, 513, 10.1038/nsmb.1777 Mohr, 2013, Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing, RNA, 19, 958, 10.1261/rna.039743.113 Murshudov, 2011, REFMAC5 for the refinement of macromolecular crystal structures, Acta Crystallogr. D Biol. Crystallogr., 67, 355, 10.1107/S0907444911001314 Nguyen, 2016, CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast, Curr. Opin. Struct. Biol., 36, 48, 10.1016/j.sbi.2015.12.005 Noah, 2006, Atomic force microscopy reveals DNA bending during group II intron ribonucleoprotein particle integration into double-stranded DNA, Biochemistry, 45, 12424, 10.1021/bi060612h Nottingham, 2016, RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase, RNA, 22, 597, 10.1261/rna.055558.115 Paukstelis, 2008, Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA, Nature, 451, 94, 10.1038/nature06413 Peebles, 1986, A self-splicing RNA excises an intron lariat, Cell, 44, 213, 10.1016/0092-8674(86)90755-5 Rambo, 2004, Assembly of an active group II intron-maturase complex by protein dimerization, Biochemistry, 43, 6486, 10.1021/bi049912u Qu, 2016, Structure of a group II intron in complex with its reverse transcriptase, Nat. Struct. Mol. Biol., 23, 549, 10.1038/nsmb.3220 Saldanha, 1999, RNA and protein catalysis in group II intron splicing and mobility reactions using purified components, Biochemistry, 38, 9069, 10.1021/bi982799l San Filippo, 2002, Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein, J. Mol. Biol., 324, 933, 10.1016/S0022-2836(02)01147-6 Sawaya, 1997, Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism, Biochemistry, 36, 11205, 10.1021/bi9703812 Sharp, 1985, On the origin of RNA splicing and introns, Cell, 42, 397, 10.1016/0092-8674(85)90092-3 Sontheimer, 1999, Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome, Genes Dev., 13, 1729, 10.1101/gad.13.13.1729 Wang, 1993, The Mauriceville plasmid reverse transcriptase can initiate cDNA synthesis de novo and may be related to reverse transcriptase and DNA polymerase progenitor, Cell, 75, 1071, 10.1016/0092-8674(93)90317-J Zhao, 2016, Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution, Nat. Struct. Mol. Biol., 23, 558, 10.1038/nsmb.3224 Zheng, 2015, Efficient and quantitative high-throughput tRNA sequencing, Nat. Methods, 12, 835, 10.1038/nmeth.3478 Zubradt, 2017, DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo, Nat. Methods, 14, 75, 10.1038/nmeth.4057