Nucleic Acids Research, 2002, Vol. 30, No. 5 1091-1102
© 2002 Oxford University Press
Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
Group II introns are novel genetic elements that have properties of both catalytic RNAs and retroelements. Initially identified in organellar genomes of plants and lower eukaryotes, group II introns are now being discovered in increasing numbers in bacterial genomes. Few of the newly sequenced bacterial introns are correctly identified or annotated by those who sequenced them. Here we have compiled and thoroughly analyzed group II introns and their fragments in bacterial DNA sequences reported to GenBank. Intron distribution in bacterial genomes differs markedly from the distribution in organellar genomes. Bacterial introns are not inserted into conserved genes, are often inserted outside of genes altogether and are frequently fragmented, suggesting a high rate of intron gain and loss. Some introns have multiple natural homing sites while others insert after transcriptional terminators. All bacterial group II introns identified to date encode reverse transcriptase open reading frames and are either active retroelements or derivatives of retroelements. Together, these observations suggest that group II introns in bacteria behave primarily as retroelements rather than as introns, and that the strategy for group II intron survival in bacteria is fundamentally different from intron survival in organelles.
* To whom correspondence should be addressed. Tel: +1 403 220 7933; Fax: +1 403 289 9311; Email: zimmerly{at}ucalgary.ca
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. P. Craig, S. Bekal, M. Hudson, L. Domier, T. Niblack, and K. N. Lambert Analysis of a Horizontally Transferred Pathway Involved in Vitamin B6 Biosynthesis from the Soybean Cyst Nematode Heterodera glycines Mol. Biol. Evol., October 1, 2008; 25(10): 2085 - 2098. [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]
|
|
|
|
 |
|
 W. Wei, R. E. Davis, R. Jomantiene, and Y. Zhao Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution PNAS, August 19, 2008; 105(33): 11827 - 11832. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. J. Tourasse and A.-B. Kolsto 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., August 1, 2008; 36(14): 4529 - 4548. [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]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 J. Yao and A. M. Lambowitz Gene Targeting in Gram-Negative Bacteria by Use of a Mobile Group II Intron ("Targetron") Expressed from a Broad-Host-Range Vector Appl. Envir. Microbiol., April 15, 2007; 73(8): 2735 - 2743. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. B. Stabell, N. J. Tourasse, S. Ravnum, and A.-B. Kolsto Group II intron in Bacillus cereus has an unusual 3' extension and splices 56 nucleotides downstream of the predicted site Nucleic Acids Res., March 12, 2007; 35(5): 1612 - 1623. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Toor, A. R. Robart, J. Christianson, and S. Zimmerly 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., December 2, 2006; 34(22): 6461 - 6471. [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. J. Ostheimer, M. Rojas, H. Hadjivassiliou, and A. Barkan Formation of the CRS2-CAF2 Group II Intron Splicing Complex Is Mediated by a 22-Amino Acid Motif in the COOH-terminal Region of CAF2 J. Biol. Chem., February 24, 2006; 281(8): 4732 - 4738. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Lynch The Origins of Eukaryotic Gene Structure Mol. Biol. Evol., February 1, 2006; 23(2): 450 - 468. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Smith, J. Zhong, M. Matsuura, A. M. Lambowitz, and M. Belfort Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming Genes & Dev., October 15, 2005; 19(20): 2477 - 2487. [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]
|
|
|
|
 |
|
 M. Sunde Class I Integron with a Group II Intron Detected in an Escherichia coli Strain from a Free-Range Reindeer Antimicrob. Agents Chemother., June 1, 2005; 49(6): 2512 - 2514. [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]
|
|
|
|
|
|
Y. Chen, J. R. Klein, L. L. McKay, and G. M. Dunny Quantitative Analysis of Group II Intron Expression and Splicing in Lactococcus lactis Appl. Envir. Microbiol., May 1, 2005; 71(5): 2576 - 2586. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Bacic, A. C. Parker, J. Stagg, H. P. Whitley, W. G. Wells, L. A. Jacob, and C. J. Smith Genetic and Structural Analysis of the Bacteroides Conjugative Transposon CTn341 J. Bacteriol., April 15, 2005; 187(8): 2858 - 2869. [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]
|
|
|
|
 |
|
 O. Ostersetzer, A. M. Cooke, K. P. Watkins, and A. Barkan CRS1, a Chloroplast Group II Intron Splicing Factor, Promotes Intron Folding through Specific Interactions with Two Intron Domains PLANT CELL, January 1, 2005; 17(1): 241 - 255. [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]
|
|
|
|
 |
|
 L. Dickson, S. Connell, H.-R. Huang, R. M. Henke, L. Liu, and P. S. Perlman Abortive Transposition by a Group II Intron in Yeast Mitochondria Genetics, September 1, 2004; 168(1): 77 - 87. [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]
|
|
|
|
|
|
A. R. ROBART, N. K. MONTGOMERY, K. L. SMITH, and S. ZIMMERLY Principles of 3' splice site selection and alternative splicing for an unusual group II intron from Bacillus anthracis RNA, May 1, 2004; 10(5): 854 - 862. [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]
|
|
|
|
|
|
G. Kholodii, S. Mindlin, Z. Gorlenko, M. Petrova, J. Hobman, and V. Nikiforov Translocation of transposition-deficient (TndPKLH2-like) transposons in the natural environment: mechanistic insights from the study of adjacent DNA sequences Microbiology, April 1, 2004; 150(4): 979 - 992. [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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
G. Kholodii, Zh. Gorlenko, S. Mindlin, J. Hobman, and V. Nikiforov Tn5041-like transposons: molecular diversity, evolutionary relationships and distribution of distinct variants in environmental bacteria Microbiology, November 1, 2002; 148(11): 3569 - 3582. [Abstract] [Full Text] [PDF]
|
|