The dispersal of five group II introns among natural populations of Escherichia coli

Abstract

Group II introns are self-splicing RNAs that also act as retroelements in bacteria, mitochondria, and chloroplasts. Group II introns were identified in Escherichia coli in 1994, but have not been characterized since, and, instead, other bacterial group II introns have been studied for splicing and mobility properties. Despite their apparent intractability, at least five distinct group II introns exist naturally in E. coli strains. To illuminate their function and learn how the introns have dispersed in their natural host, we have investigated their distribution in the ECOR reference collection. Two introns were cloned and sequenced to complete their partial sequences. Unexpectedly, southern blots showed all ECOR strains to contain fragments and/or full-length copies of group II introns, with some strains containing up to 15 intron copies. One intron, E.c.I4, has two natural homing sites in IS629 and IS911 elements, and the intron can be present in one, both, or neither homing site in a given strain. Nearly all strains that contain full-length introns also contain unfilled homing sites, suggesting either that mobility is highly inefficient or that most full-length copies are nonfunctional. The data indicate independent mobility of the introns, as well as mobility via the host DNA elements, and overall, the pattern of intron distribution resembles that of IS elements.

EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting

“…EcI5 is a CL/IIB1 intron, whose IEP contains an En domain ( Fig. 1; Burland et al 1998;Dai and Zimmerly 2002b). We found that EcI5 is highly active in retrohoming.…”

“…The intron is inserted within a noncoding region of the plasmid, but in the same orientation as most other plasmid genes. Southern hybridizations and PCR analysis showed that EcI5 is also inserted at the same site in DNAs isolated from 19 of 72 ECOR strains, although always in fragmented form (Dai and Zimmerly 2002b). By using the computer algorithm developed here for identifying EcI5 target sites, we found no efficient target sites for the wildtype intron (log-odds score > 8.2 and Watson-Crick or wobble base pairs at all EBS/IBS positions) in sequenced E. coli O157 genomes (EC4115, EDL933, and Sakai), and only one such target site in the nonessential gene cusS in the genome of E. coli K12 MG1655, which does not carry the plasmid.…”

“…EcI5 was found in virulence plasmid pO157 in E. coli strain O157:H7 (Burland et al 1998;Dai and Zimmerly 2002b). The intron is inserted within a noncoding region of the plasmid, but in the same orientation as most other plasmid genes.…”

“…Group II intron EcI5 and its IEP. (A) Predicted secondary structure of EcI5 RNA; data adapted from Dai and Zimmerly (2002b). The structure consists of six double-helical domains (DI-DVI).…”

An Unexplored Diversity of Reverse Transcriptases in Bacteria

“…Third, the distribution of group II introns across bacterial species and strains is sporadic (44,54,57,58). For example, related strains of Escherichia coli can harbor from one to 15 copies of group II introns (59), and some genomes contain over 20 identical copies of an intron (60).…”