Browsing by Author "Wu, Li"

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    Bioinformatic and phylogenetic analyses of retroelements in bacteria
    (2018-11-29) Wu, Li; Zimmerly, Steven; Fraser, Marie Elizabeth; De Koning, A. P. Jason; DeVinney, Rebekah; Russell, Tony S.
    Retroelements are mobile elements that are capable of transposing into new loci within genomes via an RNA intermediate. Various types of retroelements have been identified from both eukaryotic and prokaryotic organisms. This dissertation includes four individual projects that focus on using bioinformatic tools to analyse retroelements in bacteria, especially group II introns and diversity-generating retroelements (DGRs). The introductory Chapter I gives an overview of several newly-identified retroelements in eukaryotes and prokaryotes. In Chapter II, a general search for bacterial RTs from the GenBank DNA sequenced database was performed using automated methods. It not only enlarged the collection of bacterial reverse transcriptases (RTs), but also revealed several new classes of RTs. In Chapter III, another automated search was performed to identify group II introns. All predicted introns were automatically folded and then manually refined. Other information, such as multiple copies and non-standard intron organisations, were also identified. Next, all introns were subjected in several analyses in order to depict common properties for each class, such as preferences in target sites and DNA strands. Using this enlarged dataset, Chapter IV aimed to resolve the phylogeny of group II introns and investigate whether the intron-encoded protein (IEP) and RNA portions coevolved. Among trees constructed from various datasets, such as using different sequence masks, smaller sampled subsets or morphological features, the hypothesis that the IEP and RNA coevolved was supported by comparisons among most trees, even though it seemed to be rejected by formal topology tests. Finally, Chapter V compiled and systematically classified the most recent set of DGRs, which can be used as a reliable reference to direct future DGR-related studies and experimental designs.
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    A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank
    (2013-12) Abebe, Michael; Candales, Manuel A; Duong, Adrian; Hood, Keyar S; Li, Tony; Neufeld, Ryan AE; Shakenov, Abat; Sun, Runda; Wu, Li; Jarding, Ashley M; Semper, Cameron; Zimmerly, Steven
    Background Accurate and complete identification of mobile elements is a challenging task in the current era of sequencing, given their large numbers and frequent truncations. Group II intron retroelements, which consist of a ribozyme and an intron-encoded protein (IEP), are usually identified in bacterial genomes through their IEP; however, the RNA component that defines the intron boundaries is often difficult to identify because of a lack of strong sequence conservation corresponding to the RNA structure. Compounding the problem of boundary definition is the fact that a majority of group II intron copies in bacteria are truncated. Results Here we present a pipeline of 11 programs that collect and analyze group II intron sequences from GenBank. The pipeline begins with a BLAST search of GenBank using a set of representative group II IEPs as queries. Subsequent steps download the corresponding genomic sequences and flanks, filter out non-group II introns, assign introns to phylogenetic subclasses, filter out incomplete and/or non-functional introns, and assign IEP sequences and RNA boundaries to the full-length introns. In the final step, the redundancy in the data set is reduced by grouping introns into sets of ≥95% identity, with one example sequence chosen to be the representative. Conclusions These programs should be useful for comprehensive identification of group II introns in sequence databases as data continue to rapidly accumulate.
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    A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank
    (BioMed Central, 2013-12-20) Abebe, Michael; Candales, Michael A; Duong, Adrian; Hood, Keyar S; Li, tony; Neufeld, Ryan A E; Shakenov, Abat; Sun, Runda; Wu, Li; Jarding, Ashley M; Semper, Cameron; Zimmerly, Steven
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    Tetraloop-Receptor Interactions in RNA Crystal Structures
    (2013-07-15) Wu, Li; Zimmerly, Steven
    This dissertation addresses two aspects of RNA tertiary structure. The first section is a computational analysis of tetraloop-receptor interactions in RNA crystal structures. A total of 78 loop-receptor interactions were collected from the Protein Data Bank and grouped into four structural classes. The majority have the standard conformation discovered by earlier studies, indicating that these are the most favoured conformations. However, much structural diversity was found in the rest of this set, and several potential motifs were identified that can be studied in the future. In the second section, a FRET-based analysis was designed to obtain distance information between two selected sites in a group II intron. This project is at an initial stage, and will be extended in future. Together, the results advance our understanding of a specific type of RNA structural motif, and lay groundwork for further modelling a group II intron RNA in the future.
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    An unexplored diversity of reverse transcriptases in bacteria
    (ASMscience, 2015) Zimmerly, Steven; Wu, Li
    Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.