Article

Mobile group II introns. Annu Rev Genet

Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Texas 78712, USA.
Annual Review of Genetics (Impact Factor: 15.72). 02/2004; 38(1):1-35. DOI: 10.1146/annurev.genet.38.072902.091600
Source: PubMed

ABSTRACT

Mobile group II introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility mechanism in which the excised intron RNA reverse splices directly into a DNA target site and is then reverse transcribed by the intron-encoded protein. After DNA insertion, the introns remove themselves by protein-assisted, autocatalytic RNA splicing, thereby minimizing host damage. Here we discuss the experimental basis for our current understanding of group II intron mobility mechanisms, beginning with genetic observations in yeast mitochondria, and culminating with a detailed understanding of molecular mechanisms shared by organellar and bacterial group II introns. We also discuss recently discovered links between group II intron mobility and DNA replication, new insights into group II intron evolution arising from bacterial genome sequencing, and the evolutionary relationship between group II introns and both eukaryotic spliceosomal introns and non-LTR-retrotransposons. Finally, we describe the development of mobile group II introns into gene-targeting vectors, "targetrons," which have programmable target specificity.

Download full-text

Full-text

Available from: Steven Zimmerly
    • "Self-splicing Group II introns are not present in eukaryotic nuclear genome (Edgell et al. 2011), spliceosomal introns only in eukaryotes (see (Dumesic et al. 2013; Martin and Koonin 2006; Pyle 2012; Roy and Gilbert 2006) for reviews on the origin of splicesomal introns). While RNA-catalyzed self-splicing is the distinctive hallmark of these introns, their splicing in vivo requires protein maturases that accelerate splicing chemistry and act as RNA chaperone proteins [reviewed in (Lambowitz and Zimmerly 2004; Meng et al. 2005)]. Fourteen nuclear-encoded proteins are required for splicing Chlamydomonas chloroplast Type II 'self-splicing' introns, most of which share no similarity with the components of the nuclear spliceosome (Rivier et al. 2001). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The evolution of life from the simplest, original form to complex, intelligent animal life occurred through a number of key innovations. Here we present a new tool to analyze these key innovations by proposing that the process of evolutionary innovation may follow one of three underlying processes, namely a Random Walk, a Critical Path, or a Many Paths process, and in some instances may also constitute a "Pull-up the Ladder" event. Our analysis is based on the occurrence of function in modern biology, rather than specific structure or mechanism. A function in modern biology may be classified in this way either on the basis of its evolution or the basis of its modern mechanism. Characterizing key innovations in this way helps identify the likelihood that an innovation could arise. In this paper, we describe the classification, and methods to classify functional features of modern organisms into these three classes based on the analysis of how a function is implemented in modern biology. We present the application of our categorization to the evolution of eukaryotic gene control. We use this approach to support the argument that there are few, and possibly no basic chemical differences between the functional constituents of the machinery of gene control between eukaryotes, bacteria and archaea. This suggests that the difference between eukaryotes and prokaryotes that allows the former to develop the complex genetic architecture seen in animals and plants is something other than their chemistry. We tentatively identify the difference as a difference in control logic, that prokaryotic genes are by default 'on' and eukaryotic genes are by default 'off.' The Many Paths evolutionary process suggests that, from a 'default off' starting point, the evolution of the genetic complexity of higher eukaryotes is a high probability event.
    No preview · Article · Jul 2015 · Journal of Molecular Evolution
  • Source
    • "1A), which were predicted as group II introns based on the putative secondary structure (supplementary fig. S3, Supplementary Material online; Note that no obvious ORF was found in any of the three introns, although typical group II introns carry an intronic ORF coding reverse transcriptase, maturase, and endonuclease domains [e.g., Lambowitz and Zimmerly 2004; Kamikawa et al. 2009]). We suspect that a gene-duplication has created a tandem array of ycf3-like regions (cycf3; colored in light blue and dark blue in fig. "

    Full-text · Dataset · Apr 2015
  • Source
    • "1A), which were predicted as group II introns based on the putative secondary structure (supplementary fig. S3, Supplementary Material online; Note that no obvious ORF was found in any of the three introns, although typical group II introns carry an intronic ORF coding reverse transcriptase, maturase, and endonuclease domains [e.g., Lambowitz and Zimmerly 2004; Kamikawa et al. 2009]). We suspect that a gene-duplication has created a tandem array of ycf3-like regions (cycf3; colored in light blue and dark blue in fig. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Unlike many other photosynthetic dinoflagellates, whose plastids contain a characteristic carotenoid peridinin, members of the genus Lepidodinium are the only known dinoflagellate species possessing green alga-derived plastids. However, the precise origin of Lepidodinium plastids has hitherto remained uncertain. In this study, we completely sequenced the plastid genome of Lepidodinium chlorophorum NIES-1868. Our phylogenetic analyses of 52 plastid-encoded proteins unite L. chlorophorum exclusively with a pedinophyte, Pedinomonas minor, indicating that the green-colored plastids in Lepidodinium spp. were derived from an endosymbiotic pedinophyte or a green alga closely related to pedinophytes. Our genome comparison incorporating the origin of the Lepidodinium plastids strongly suggests that the endosymbiont plastid genome acquired by the ancestral Lepidodinium species has lost genes encoding proteins involved in metabolism and biosynthesis, protein/metabolite transport, and plastid division during the endosymbiosis. We further discuss the commonalities and idiosyncrasies in genome evolution between the L. chlorophorum plastid and other plastids acquired through endosymbiosis of eukaryotic photoautotrophs. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Full-text · Article · Apr 2015 · Genome Biology and Evolution
Show more