[ James A. Shapiro ] James A. Shapiro

Group II introns

(Morl and Schmelzer 1990; Ferat and Michel 1993; Lazowska, Meunier et al. 1994; Zimmerly, Guo et al. 1995; Dunny and McKay 1999; Saldanha, Chen et al. 1999; Zimmerly, Moran et al. 1999; Cousineau, Lawrence et al. 2000; Eskes, Liu et al. 2000; Guo, Karberg et al. 2000; Hiller, Hetzer et al. 2000; Martinez-Abarca and Toro 2000; Mohr, Smith et al. 2000; Bonen and Vogel 2001; Dickson, Huang et al. 2001; Karberg, Guo et al. 2001; Centron and Roy 2002; Dai and Zimmerly 2002; Klein and Dunny 2002; Podar, Mullineaux et al. 2002; Dai and Zimmerly 2003; Huang, Chao et al. 2003; Lehmann and Schmidt 2003; Mohr and Lambowitz 2003; Munoz-Adelantado, San Filippo et al. 2003; Zhong, Karberg et al. 2003; Zhong and Lambowitz 2003; Cui, Matsuura et al. 2004; Lambowitz and Zimmerly 2004; Odom, Shenkenberg et al. 2004; Watanabe and Lambowitz 2004; Conlan, Stanger et al. 2005; Jones, Kierlin et al. 2005; Ostersetzer, Cooke et al. 2005; Smith, Zhong et al. 2005; Zhao and Lambowitz 2005; Asakura and Barkan 2006; Costa, Michel et al. 2006; Mohr, Matsuura et al. 2006; Noah, Park et al. 2006; Poole 2006; Rawsthorne, Turner et al. 2006; Toor, Robart et al. 2006; Belhocine, Mak et al. 2007; Cui and Davis 2007; Fedorova and Zingler 2007; Nisa-Martinez, Jimenez-Zurdo et al. 2007; Robart, Seo et al. 2007; Stabell, Tourasse et al. 2007; Toro, Jimenez-Zurdo et al. 2007; Yao and Lambowitz 2007; Belhocine, Mak et al. 2008; Coros, Piazza et al. 2008; Mastroianni, Watanabe et al. 2008; Simon, Clarke et al. 2008; Toor, Rajashankar et al. 2008; Tourasse and Kolsto 2008; Valles, Halanych et al. 2008; Zhao, Niu et al. 2008; Kroeger, Watkins et al. 2009; Roitzsch and Pyle 2009; Zhuang, Mastroianni et al. 2009; Mohr, Ghanem et al. 2010; Molina-Sanchez, Martinez-Abarca et al. 2010; Mullineux, Costa et al. 2010; Pyle 2010; Tourasse, Stabell et al. 2010; Zoschke, Nakamura et al. 2010; Chillon, Martinez-Abarca et al. 2011; Huang, Shaikh et al. 2011; Leclercq, Giraud et al. 2011)




Asakura, Y. and A. Barkan (2006). "Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns." Plant Physiol 142(4): 1656-1663. http://www.ncbi.nlm.nih.gov/pubmed/17071648.

Belhocine, K., A. B. Mak, et al. (2007). "Trans-splicing of the Ll.LtrB group II intron in Lactococcus lactis." Nucleic Acids Res\ 35\(7\): 2257-2268\. http://www.ncbi.nlm.nih.gov/pubmed/17389638\.

Belhocine, K., A. B. Mak, et al. (2008). "Trans-splicing versatility of the Ll.LtrB group II intron." Rna\ 14\(9\): 1782-1790\. http://www.ncbi.nlm.nih.gov/pubmed/18648072\.

Bonen, L. and J. Vogel (2001). "The ins and outs of group II introns." Trends Genet\ 17\(6\): 322-331\. http://www.ncbi.nlm.nih.gov/pubmed/11377794\.

Centron, D. and P. H. Roy (2002). "Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion." Antimicrob Agents Chemother 46(5): 1402-1409. http://www.ncbi.nlm.nih.gov/pubmed/11959575.

Chillon, I., F. Martinez-Abarca, et al. (2011). "Splicing of the Sinorhizobium meliloti RmInt1 group II intron provides evidence of retroelement behavior." Nucleic Acids Res 39(3): 1095-1104. http://www.ncbi.nlm.nih.gov/pubmed/20876688.

Conlan, L. H., M. J. Stanger, et al. (2005). "Localization, mobility and fidelity of retrotransposed Group II introns in rRNA\ genes." Nucleic Acids Res\ 33\(16\): 5262-5270\. http://www.ncbi.nlm.nih.gov/pubmed/16170154\.

Coros, C. J., C. L. Piazza, et al. (2008). "A mutant screen reveals RNase E as a silencer of group II intron retromobility in\ Escherichia coli." Rna\ 14\(12\): 2634-2644\. http://www.ncbi.nlm.nih.gov/pubmed/18945808\.

Costa, M., F. Michel, et al. (2006). "Potential for alternative intron-exon pairings in group II intron RmInt1 from Sinorhizobium meliloti and its relatives." RNA 12(3): 338-341. http://www.ncbi.nlm.nih.gov/pubmed/16431983.

Cousineau, B., S. Lawrence, et al. (2000). "Retrotransposition of a bacterial group II intron." Nature 404: 1018-1021. .

Cui, X. and G. Davis (2007). "Mobile group II intron targeting: applications in prokaryotes and perspectives in\ eukaryotes." Front Biosci\ 12\: 4972-4985\. http://www.ncbi.nlm.nih.gov/pubmed/17569624\.

Cui, X., M. Matsuura, et al. (2004). "A group II intron-encoded maturase functions preferentially in cis and requires both the reverse transcriptase and X domains to promote RNA splicing." J Mol Biol 340(2): 211-231. http://www.ncbi.nlm.nih.gov/pubmed/15201048.

Dai, L. and S. Zimmerly (2002). "Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior." Nucleic Acids Res 30(5): 1091-1102. http://www.ncbi.nlm.nih.gov/pubmed/11861899.

Dai, L. and S. Zimmerly (2003). "ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs." RNA 9(1): 14-19. http://www.ncbi.nlm.nih.gov/pubmed/12554871.

Dickson, L., H. R. Huang, et al. (2001). "Retrotransposition of a yeast group II intron occurs by reverse splicing directly into ectopic DNA sites." Proc Natl Acad Sci U S A 98(23): 13207-13212. http://www.ncbi.nlm.nih.gov/pubmed/11687644.

Dunny, G. M. and L. L. McKay (1999). "Group II introns and expression of conjugative transfer functions in lactic acid bacteria." Antonie Van Leeuwenhoek 76(1-4): 77-88. http://www.ncbi.nlm.nih.gov/pubmed/10532373.

Eskes, R., L. Liu, et al. (2000). "Multiple homing pathways used by yeast mitochondrial group II introns." Mol Cell Biol 20(22): 8432-8446. http://www.ncbi.nlm.nih.gov/pubmed/11046140.

Fedorova, O. and N. Zingler (2007). "Group II introns: structure, folding and splicing mechanism." Biol Chem 388(7): 665-678. http://www.ncbi.nlm.nih.gov/pubmed/17570818.

Ferat, J. L. and F. Michel (1993). "Group II self splicing introns in bacteria." Nature 364: 358-361. .

Guo, H., M. Karberg, et al. (2000). "Group II introns designed to insert into therapeutically relevant DNA target sites in human cells." Science 289(5478): 452-457. http://www.ncbi.nlm.nih.gov/pubmed/10903206.

Hiller, R., M. Hetzer, et al. (2000). "Transposition and exon shuffling by group II intron RNA molecules in pieces." J Mol Biol 297(2): 301-308. http://www.ncbi.nlm.nih.gov/pubmed/10715202.

Huang, H. R., M. Y. Chao, et al. (2003). "The DIVa maturase binding site in the yeast group II intron aI2 is essential for \ intron homing but not for in vivo splicing." Mol Cell Biol\ 23\(23\): 8809-8819\. http://www.ncbi.nlm.nih.gov/pubmed/14612420\.

Huang, T., T. R. Shaikh, et al. (2011). "The group II intron ribonucleoprotein precursor is a large, loosely packed structure." Nucleic Acids Res 39(7): 2845-2854. http://www.ncbi.nlm.nih.gov/pubmed/21131279.

Jones, J. P., 3rd, M. N. Kierlin, et al. (2005). "Retargeting mobile group II introns to repair mutant genes." Mol Ther 11(5): 687-694. http://www.ncbi.nlm.nih.gov/pubmed/15851007.

Karberg, M., H. Guo, et al. (2001). "Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria." Nat Biotechnol 19(12): 1162-1167. http://www.ncbi.nlm.nih.gov/pubmed/11731786.

Klein, J. R. and G. M. Dunny (2002). "Bacterial group II introns and their association with mobile genetic elements." Front Biosci\ 7\: d1843-1856\. http://www.ncbi.nlm.nih.gov/pubmed/12133822\.

Kroeger, T. S., K. P. Watkins, et al. (2009). "A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing." Proc Natl Acad Sci U S A 106(11): 4537-4542. http://www.ncbi.nlm.nih.gov/pubmed/19251672.

Lambowitz, A. M. and S. Zimmerly (2004). "Mobile group II introns." Annu. Rev. Genet. 38: 1-35. http://www.ncbi.nlm.nih.gov/pubmed/15568970.

Lazowska, J., B. Meunier, et al. (1994). "Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers." Embo J 13(20): 4963-4972. http://www.ncbi.nlm.nih.gov/pubmed/7525273.

Leclercq, S., I. Giraud, et al. (2011). "Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbionts." Mol Biol Evol 28(1): 685-697. http://www.ncbi.nlm.nih.gov/pubmed/20819906.

Lehmann, K. and U. Schmidt (2003). "Group II introns: structure and catalytic versatility of large natural ribozymes." Crit Rev Biochem Mol Biol 38(3): 249-303. http://www.ncbi.nlm.nih.gov/pubmed/12870716.

Martinez-Abarca, F. and N. Toro (2000). "Group II introns in the bacterial world." Mol Microbiol 38(5): 917-926. http://www.ncbi.nlm.nih.gov/pubmed/11123668.

Mastroianni, M., K. Watanabe, et al. (2008). "Group II intron-based gene targeting reactions in eukaryotes." PLoS One 3(9): e3121. http://www.ncbi.nlm.nih.gov/pubmed/18769669.

Mohr, G., E. Ghanem, et al. (2010). "Mechanisms used for genomic proliferation by thermophilic group II introns." PLoS Biol 8(6): e1000391. http://www.ncbi.nlm.nih.gov/pubmed/20543989.

Mohr, G. and A. M. Lambowitz (2003). "Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants." Nucleic Acids Res 31(2): 647-652. http://www.ncbi.nlm.nih.gov/pubmed/12527773.

Mohr, G., D. Smith, et al. (2000). "Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences." Genes Dev 14(5): 559-573. http://www.ncbi.nlm.nih.gov/pubmed/10716944.

Mohr, S., M. Matsuura, et al. (2006). "A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone." Proc Natl Acad Sci U S A 103(10): 3569-3574. http://www.ncbi.nlm.nih.gov/pubmed/16505350.

Molina-Sanchez, M. D., F. Martinez-Abarca, et al. (2010). "Structural features in the C-terminal region of the Sinorhizobium meliloti RmInt1 group II intron-encoded protein contribute to its maturase and intron DNA-insertion function." Febs J 277(1): 244-254. http://www.ncbi.nlm.nih.gov/pubmed/19951359.

Morl, M. and C. Schmelzer (1990). "Integration of group II intron bI1 into a foreign RNA by reversal of the self-splicing reaction in vitro." Cell 60(4): 629-636. http://www.ncbi.nlm.nih.gov/pubmed/2406027.

Mullineux, S. T., M. Costa, et al. (2010). "A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions." Rna 16(9): 1818-1831. http://www.ncbi.nlm.nih.gov/pubmed/20656798.

Munoz-Adelantado, E., J. San Filippo, et al. (2003). "Mobility of the Sinorhizobium meliloti group II intron RmInt1 occurs by reverse splicing into DNA, but requires an unknown reverse transcriptase priming mechanism." J Mol Biol 327(5): 931-943. http://www.ncbi.nlm.nih.gov/pubmed/12662921.

Nisa-Martinez, R., J. I. Jimenez-Zurdo, et al. (2007). "Dispersion of the RmInt1 group II intron in the Sinorhizobium meliloti genome upon acquisition by conjugative transfer." Nucleic Acids Res 35(1): 214-222. http://www.ncbi.nlm.nih.gov/pubmed/17158161.

Noah, J. W., S. Park, et al. (2006). "Atomic force microscopy reveals DNA bending during group II intron ribonucleoprotein particle integration into double-stranded DNA." Biochemistry 45(41): 12424-12435. http://www.ncbi.nlm.nih.gov/pubmed/17029398.

Odom, O. W., D. L. Shenkenberg, et al. (2004). "A horizontally acquired group II intron in the chloroplast psbA gene of a psychrophilic Chlamydomonas: in vitro self-splicing and genetic evidence for maturase activity." RNA 10(7): 1097-1107. http://www.ncbi.nlm.nih.gov/pubmed/15208445.

Ostersetzer, O., A. M. Cooke, et al. (2005). "CRS1, a chloroplast group II intron splicing factor, promotes intron folding\ through specific interactions with two intron domains." Plant Cell\ 17\(1\): 241-255\. http://www.ncbi.nlm.nih.gov/pubmed/15598799\.

Podar, M., L. Mullineaux, et al. (2002). "Bacterial group II introns in a deep-sea hydrothermal vent environment." Appl Environ Microbiol 68(12): 6392-6398. http://www.ncbi.nlm.nih.gov/pubmed/12450865.

Poole, A. M. (2006). "Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes?" Biol Direct 1: 36. http://www.ncbi.nlm.nih.gov/pubmed/17156426.

Pyle, A. M. (2010). "The tertiary structure of group II introns: implications for biological function and evolution." Crit Rev Biochem Mol Biol 45(3): 215-232. http://www.ncbi.nlm.nih.gov/pubmed/20446804.

Rawsthorne, H., K. N. Turner, et al. (2006). "Multicopy integration of heterologous genes, using the lactococcal group II intron targeted to bacterial insertion sequences." Appl Environ Microbiol 72(9): 6088-6093. http://www.ncbi.nlm.nih.gov/pubmed/16957233.

Robart, A. R., W. Seo, et al. (2007). "Insertion of group II intron retroelements after intrinsic transcriptional terminators." Proc Natl Acad Sci U S A 104(16): 6620-6625. http://www.ncbi.nlm.nih.gov/pubmed/17420455.

Roitzsch, M. and A. M. Pyle (2009). "The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility." RNA 15(3): 473-482. http://www.ncbi.nlm.nih.gov/pubmed/19168748.

Saldanha, R., B. Chen, et al. (1999). "RNA and protein catalysis in group II intron splicing and mobility reactions\ using purified components." Biochemistry\ 38\(28\): 9069-9083\. http://www.ncbi.nlm.nih.gov/pubmed/10413481\.

Simon, D. M., N. A. Clarke, et al. (2008). "Group II introns in eubacteria and archaea: ORF-less introns and new varieties." RNA 14(9): 1704-1713. http://www.ncbi.nlm.nih.gov/pubmed/18676618.

Smith, D., J. Zhong, et al. (2005). "Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming." Genes Dev 19(20): 2477-2487. http://www.ncbi.nlm.nih.gov/pubmed/16230535.

Stabell, F. B., N. J. Tourasse, et al. (2007). "Group II intron in Bacillus cereus has an unusual 3' extension and splices 56 nucleotides downstream of the predicted site." Nucleic Acids Res 35(5): 1612-1623. http://www.ncbi.nlm.nih.gov/pubmed/17301069.

Toor, N., K. Rajashankar, et al. (2008). "Structural basis for exon recognition by a group II intron." Nat Struct Mol Biol 15(11): 1221-1222. http://www.ncbi.nlm.nih.gov/pubmed/18953333.

Toor, N., A. R. Robart, et al. (2006). "Self-splicing of a group IIC intron: 5' exon recognition and alternative 5'\ splicing events implicate the stem-loop motif of a transcriptional terminator." Nucleic Acids Res\ 34\(22\): 6461-6471\. http://www.ncbi.nlm.nih.gov/pubmed/17130159\.

Toro, N., J. I. Jimenez-Zurdo, et al. (2007). "Bacterial group II introns: not just splicing." FEMS Microbiol Rev\ 31\(3\): 342-358\. http://www.ncbi.nlm.nih.gov/pubmed/17374133\.

Tourasse, N. J. and A. B. Kolsto (2008). "Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution." Nucleic Acids Res 36(14): 4529-4548. http://www.ncbi.nlm.nih.gov/pubmed/18587153.

Tourasse, N. J., F. B. Stabell, et al. (2010). "Structural and functional evolution of group II intron ribozymes: insights from unusual elements carrying a 3' extension." N Biotechnol 27(3): 204-211. http://www.ncbi.nlm.nih.gov/pubmed/20219707.

Valles, Y., K. M. Halanych, et al. (2008). "Group II introns break new boundaries: presence in a bilaterian's genome." PLoS One 3(1): e1488. http://www.ncbi.nlm.nih.gov/pubmed/18213396.

Watanabe, K. and A. M. Lambowitz (2004). "High-affinity binding site for a group II intron-encoded reverse transcriptase/maturase within a stem-loop structure in the intron RNA." RNA 10(9): 1433-1443. http://www.ncbi.nlm.nih.gov/pubmed/15273321.

Yao, J. and A. M. Lambowitz (2007). "Gene targeting in gram-negative bacteria by use of a mobile group II intron ("Targetron") expressed from a broad-host-range vector." Appl Environ Microbiol 73(8): 2735-2743. http://www.ncbi.nlm.nih.gov/pubmed/17322321.

Zhao, J. and A. M. Lambowitz (2005). "Inaugural Article: A bacterial group II intron-encoded reverse transcriptase\ localizes to cellular poles." Proc Natl Acad Sci U S A\ 102\(45\): 16133-16140\. http://www.ncbi.nlm.nih.gov/pubmed/16186487\.

Zhao, J., W. Niu, et al. (2008). "Group II intron protein localization and insertion sites are affected by\ polyphosphate." PLoS Biol\ 6\(6\): e150\. http://www.ncbi.nlm.nih.gov/pubmed/18593213\.

Zhong, J., M. Karberg, et al. (2003). "Targeted and random bacterial gene disruption using a group II intron (targetron) vector containing a retrotransposition-activated selectable marker." Nucleic Acids Res 31(6): 1656-1664. http://www.ncbi.nlm.nih.gov/pubmed/12626707.

Zhong, J. and A. M. Lambowitz (2003). "Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription." Embo J 22(17): 4555-4565. http://www.ncbi.nlm.nih.gov/pubmed/12941706.

Zhuang, F., M. Mastroianni, et al. (2009). "Linear group II intron RNAs can retrohome in eukaryotes and may use nonhomologous end-joining for cDNA ligation." Proc Natl Acad Sci U S A 106(43): 18189-18194. http://www.ncbi.nlm.nih.gov/pubmed/19833873.

Zimmerly, S., H. Guo, et al. (1995). "Group II intron mobility occurs by target DNA-primed reverse transcription." Cell 82(4): 545-554. http://www.ncbi.nlm.nih.gov/pubmed/7664334.

Zimmerly, S., J. V. Moran, et al. (1999). "Group II intron reverse transcriptase in yeast mitochondria. Stabilization and regulation of reverse transcriptase activity by the intron RNA." J Mol Biol 289(3): 473-490. http://www.ncbi.nlm.nih.gov/pubmed/10356323.

Zoschke, R., M. Nakamura, et al. (2010). "An organellar maturase associates with multiple group II introns." Proc Natl Acad Sci U S A 107(7): 3245-3250. http://www.ncbi.nlm.nih.gov/pubmed/20133623.