Nucleic Acids Research, 2001, Vol. 29, No. 5 1238-1250
© 2001 Oxford University Press
Phylogenetic relationships among group II intron ORFs
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
Group II introns are widely believed to have been ancestors of spliceosomal introns, yet little is known about their own evolutionary history. In order to address the evolution of mobile group II introns, we have compiled 71 open reading frames (ORFs) related to group II intron reverse transcriptases and subjected their derived amino acid sequences to phylogenetic analysis. The phylogenetic tree was rooted with reverse transcriptases (RTs) of non-long terminal repeat retroelements, and the inferred phylogeny reveals two major clusters which we term the mitochondrial and chloroplast-like lineages. Bacterial ORFs are mainly positioned at the bases of the two lineages but with weak bootstrap support. The data give an overview of an apparently high degree of horizontal transfer of group II intron ORFs, mostly among related organisms but also between organelles and bacteria. The Zn domain (nuclease) and YADD motif (RT active site) were lost multiple times during evolution. Differences in domain structures suggest that the oldest ORFs were concise, while the ORF in the mitochondrial lineage subsequently expanded in three locations. The data are consistent with a bacterial origin for mobile group II introns.
* To whom correspondence should be addressed. Tel: +1 403 220 7933; Fax: +1 403 289 9311; Email: zimmerly{at}ucalgary.ca Present addresses: Georg Hausner, Department of Botany, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada Xu-chu Wu, Department of Cell Biology and Anatomy, University of Calgary School of Medicine, Calgary, Alberta T2N 4N1, Canada
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  F. B. Stabell, N. J. Tourasse, and A.-B. Kolsto A conserved 3' extension in unusual group II introns is important for efficient second-step splicing Nucleic Acids Res., June 1, 2009; 37(10): 3202 - 3214. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Zhuang, M. Karberg, J. Perutka, and A. M. Lambowitz EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting RNA, March 1, 2009; 15(3): 432 - 449. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Simon and S. Zimmerly A diversity of uncharacterized reverse transcriptases in bacteria Nucleic Acids Res., December 1, 2008; 36(22): 7219 - 7229. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Simon, N. A.C. Clarke, B. A. McNeil, I. Johnson, D. Pantuso, L. Dai, D. Chai, and S. Zimmerly Group II introns in Eubacteria and Archaea: ORF-less introns and new varieties RNA, September 1, 2008; 14(9): 1704 - 1713. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. K. Kojima and M. Kanehisa Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture Mol. Biol. Evol., July 1, 2008; 25(7): 1395 - 1404. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Quiroga, P. H. Roy, and D. Centron The S.ma.I2 class C group II intron inserts at integron attC sites Microbiology, May 1, 2008; 154(5): 1341 - 1353. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Khan and J. M. Archibald Lateral transfer of introns in the cryptophyte plastid genome Nucleic Acids Res., May 1, 2008; 36(9): 3043 - 3053. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. K. Basu, I. B. Rogozin, O. Deusch, T. Dagan, W. Martin, and E. V. Koonin Evolutionary Dynamics of Introns in Plastid-Derived Genes in Plants: Saturation Nearly Reached but Slow Intron Gain Continues Mol. Biol. Evol., January 1, 2008; 25(1): 111 - 119. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. R. Robart, W. Seo, and S. Zimmerly Insertion of group II intron retroelements after intrinsic transcriptional terminators PNAS, April 17, 2007; 104(16): 6620 - 6625. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Nisa-Martinez, J. I. Jimenez-Zurdo, F. Martinez-Abarca, E. Munoz-Adelantado, and N. Toro Dispersion of the RmInt1 group II intron in the Sinorhizobium meliloti genome upon acquisition by conjugative transfer Nucleic Acids Res., January 12, 2007; 35(1): 214 - 222. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. D. Molina-Sanchez, F. Martinez-Abarca, and N. Toro Excision of the Sinorhizobium meliloti Group II Intron RmInt1 as Circles in Vivo J. Biol. Chem., September 29, 2006; 281(39): 28737 - 28744. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. COSTA, F. MICHEL, and N. TORO Potential for alternative intron-exon pairings in group II intron RmInt1 from Sinorhizobium meliloti and its relatives RNA, March 1, 2006; 12(3): 338 - 341. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Hausner, R. Olson, D. Simon, I. Johnson, E. R. Sanders, K. G. Karol, R. M. McCourt, and S. Zimmerly Origin and Evolution of the Chloroplast trnK (matK) Intron: A Model for Evolution of Group II Intron RNA Structures Mol. Biol. Evol., February 1, 2006; 23(2): 380 - 391. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Meng, Y. Wang, and X.-Q. Liu An Intron-encoded Protein Assists RNA Splicing of Multiple Similar Introns of Different Bacterial Genes J. Biol. Chem., October 21, 2005; 280(42): 35085 - 35088. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Hauth, U. G. Maier, B. F. Lang, and G. Burger The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region Nucleic Acids Res., August 5, 2005; 33(14): 4433 - 4442. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. J. Tourasse, F. B. Stabell, L. Reiter, and A.-B. Kolsto Unusual Group II Introns in Bacteria of the Bacillus cereus Group J. Bacteriol., August 1, 2005; 187(15): 5437 - 5451. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Yao, J. Zhong, and A. M. Lambowitz Gene targeting using randomly inserted group II introns (targetrons) recovered from an Escherichia coli gene disruption library Nucleic Acids Res., June 9, 2005; 33(10): 3351 - 3362. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Fernandez-Lopez, E. Munoz-Adelantado, M. Gillis, A. Willems, and N. Toro Dispersal and Evolution of the Sinorhizobium meliloti Group II RmInt1 Intron in Bacteria that Interact with Plants Mol. Biol. Evol., June 1, 2005; 22(6): 1518 - 1528. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Belhocine, K. K. Yam, and B. Cousineau Conjugative Transfer of the Lactococcus lactis Chromosomal Sex Factor Promotes Dissemination of the Ll.LtrB Group II Intron J. Bacteriol., February 1, 2005; 187(3): 930 - 939. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. J.H. BLOCKER, G. MOHR, L. H. CONLAN, L. QI, M. BELFORT, and A. M. LAMBOWITZ Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase RNA, January 1, 2005; 11(1): 14 - 28. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Vellore, S. E. Moretz, and B. C. Lampson A Group II Intron-Type Open Reading Frame from the Thermophile Bacillus (Geobacillus) stearothermophilus Encodes a Heat-Stable Reverse Transcriptase Appl. Envir. Microbiol., December 1, 2004; 70(12): 7140 - 7147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ueda, A. Yamashita, J. Ishikawa, M. Shimada, T.-o Watsuji, K. Morimura, H. Ikeda, M. Hattori, and T. Beppu Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism Nucleic Acids Res., September 21, 2004; 32(16): 4937 - 4944. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X.-Q. Liu and J. Yang Bacterial Thymidylate Synthase with Intein, Group II Intron, and Distinctive ThyX Motifs J. Bacteriol., September 15, 2004; 186(18): 6316 - 6319. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Martinez-Abarca, A. Barrientos-Duran, M. Fernandez-Lopez, and N. Toro The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming Nucleic Acids Res., May 20, 2004; 32(9): 2880 - 2888. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. H. Staddon, E. M. Bryan, D. A. Manias, and G. M. Dunny Conserved Target for Group II Intron Insertion in Relaxase Genes of Conjugative Elements of Gram-Positive Bacteria J. Bacteriol., April 15, 2004; 186(8): 2393 - 2401. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. V. Sheveleva and R. B. Hallick Recent horizontal intron transfer to a chloroplast genome Nucleic Acids Res., February 3, 2004; 32(2): 803 - 810. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H.-R. Huang, M. Y. Chao, B. Armstrong, Y. Wang, A. M. Lambowitz, and P. S. Perlman 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., December 1, 2003; 23(23): 8809 - 8819. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X.-Q. Liu, J. Yang, and Q. Meng Four Inteins and Three Group II Introns Encoded in a Bacterial Ribonucleotide Reductase Gene J. Biol. Chem., November 21, 2003; 278(47): 46826 - 46831. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Turmel, C. Otis, and C. Lemieux The Mitochondrial Genome of Chara vulgaris: Insights into the Mitochondrial DNA Architecture of the Last Common Ancestor of Green Algae and Land Plants PLANT CELL, August 1, 2003; 15(8): 1888 - 1903. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Rest and D. P. Mindell Retroids in Archaea: Phylogeny and Lateral Origins Mol. Biol. Evol., July 1, 2003; 20(7): 1134 - 1142. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Mohr and A. M. Lambowitz Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants Nucleic Acids Res., January 15, 2003; 31(2): 647 - 652. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. DAI and S. ZIMMERLY ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs RNA, January 1, 2003; 9(1): 14 - 19. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Dai, N. Toor, R. Olson, A. Keeping, and S. Zimmerly Database for mobile group II introns Nucleic Acids Res., January 1, 2003; 31(1): 424 - 426. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Podar, L. Mullineaux, H.-R. Huang, P. S. Perlman, and M. L. Sogin Bacterial Group II Introns in a Deep-Sea Hydrothermal Vent Environment Appl. Envir. Microbiol., December 1, 2002; 68(12): 6392 - 6398. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Dai and S. Zimmerly Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior Nucleic Acids Res., March 1, 2002; 30(5): 1091 - 1102. [Abstract] [Full Text] [PDF]
|
|