Group I Introns and Inteins: Disparate Origins but Convergent Parasitic Strategies

Abstract

Genomes of most organisms harbor DNA of foreign origin that has no known function. Since these elements may not contribute to a host's fitness but utilize host resources for their perpetuation, it is appropriate to consider them genetic parasites (4). With the advent of sequencing technologies, a wide variety of parasitic elements have been discovered in bacteria from all environments, including obligate intracellular pathogens (100), which were thought to be shielded from horizontal gene transfer (HGT). Detection of a parasitic genetic element in a genome represents only a snapshot of the continuing and dynamic interplay between the host's attempts to purge the element and the element's ability to persist. These adaptable genetic parasites have evolved mechanisms to overcome defenses (75) of the cellular machinery to ultimately invade, colonize, and replicate within the host. Their success is very evident in the human genome, which consists mostly of such apparently superfluous DNA (65). Even compact bacterial genomes packed with functional genes contain mobile genetic elements (100), underscoring their universality in nature.A number of parasitic genetic elements are found in bacterial genomes, including transposons, insertion sequences, prophages, introns, inteins, and intervening sequences. While bacteria, especially pathogenic bacteria, are well studied, their parasitic genetic elements have not received as much attention. In the past few years, while studying the obligate intracellular pathogen Coxiella burnetii, we came to appreciate the intimate relationship between bacterial hosts and parasitic elements (92,93). In addition, interesting new studies have shed light on the evolutionary histories of group I introns, inteins, and homing endonucleases (HEs) (9, 109) and infused excitement into the field. This minireview, which focuses on the biology and evolution of group I introns and inteins found in bacteria, is an attempt to catalyze interest among bacteriologists in these fascinating genetic parasites. GROUP I INTRONSIntrons are noncoding, intragenic regions that are removed from precursor RNA to form the mature RNA by splicing the exons (coding regions that flank introns) together. They are much more common in eukaryotes than in bacteria (50). Introns are classified into four groups based on splicing mechanisms (47): group I, group II/group III, spliceosomal, and tRNA/archaeal introns. Spliceosomal introns are found in eukaryotes and utilize spliceosomes (large protein-RNA complexes) for splicing (70), whereas tRNA introns splice with the help of specialized enzymes (74). Group I and group II introns are able to self-splice-using different mechanisms-without the aid of any proteins and are thus referred to as ribozymes (104). A self-splicing group I intron from Tetrahymena thermophila was one of the first ribozymes to be described, in the early 1980s (61). Ribozymes are considered legacies of a primordial RNA world, where RNA possessed both informationencoding and catalytic properties, before the adven...

An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease

“…Why multiple IISs are found is unclear. The best strategy for group I introns to proliferate is to locate into highly conserved DNA sequences that have an essential biological role, which are often encountered in the gene pool, and that are conserved across the biological spectrum (Raghavan and Minnick, 2009). psbA fulfils these criteria and therefore provides an ideal 'home' for an intron.…”

“…Presumably, for the gene encoding F-CphI to become integrated into the intron, it has to be removed from its current position. As HEs are normally found within intergenic regions, their inexact removal is unlikely to cause a detrimental effect (Raghavan and Minnick, 2009). However, in S-PM2, the 3 0 end of psbA and the 5 0 end of the gene encoding F-CphI are directly linked by the asRNA CfrI.…”

Bacterial Genome Instability

“…Inteins are widespread in bacteria (124)(125)(126)(127)(128)(129)(130)(131)(132)(133)(134)(135)(136). They are peptides of 134 to 608 amino acids encoded in frame within host proteins.…”

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

“…These are found in many different genomes including chloroplast and mitochondrial genomes of lower eukaryotes and higher plants, as well as in archaebacterial and eubacterial genomes (Hasselmayer et al, 2004;Haugen et al, 2005;Vicens and Cech, 2006;Raghavan and Minnick, 2009;Ton-Hoang et al, 2010;McManus et al, 2012). Furthermore, they are also found in certain nuclear genes of unicellular eukaryotes such as diatoms, euglenoids, green and red algae, and in some viral genomes.…”