Transfer RNA genes in pieces

Randau, Lennart; Söll, Dieter

doi:10.1038/embor.2008.101

Cited by 80 publications

(77 citation statements)

References 49 publications

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“…Directed BLASTN searches with the uninterrupted cognate genes from Beggiatoa alba B18LD revealed that these contain inserts, with the sequence coding for the first 38 tRNA bases (up to the end of the predicted anticodon loop) separated from the remainder of the genes by spacers of 272 and 316 nucleotides (nt), respectively (see footnote to Table S2 in the supplemental material). This is a common position for self-splicing group I introns in bacterial and chloroplast tRNAs (25). The BOGUAY inserts appear to have at least some of the conserved group I intron secondary structures (not shown), but proof that they can excise would require experimentation.…”

Section: Resultsmentioning

confidence: 99%

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

MacGregor

Biddle

Teske

2013

Appl Environ Microbiol

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The draft genome sequence of a single orange Beggiatoa ("Candidatus Maribeggiatoa") filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to the fdxN excision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceae matches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

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Section: Resultsmentioning

confidence: 99%

Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

MacGregor

Biddle

Teske

2013

Appl Environ Microbiol

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“…(ii) Introns in nuclear and archaeal transfer RNA genes: present in tRNA genes of eukaryotic nuclear or archaeal genomes (Marck and Grosjean 2003;Randau and Söll 2008), and also in some coding genes in archaea (Yokobori et al 2009;Doose et al 2013). They do not share functional or structural similarities with the other types of introns, as they are typically very short and their splicing is fully catalyzed by protein enzymes (rather than ribozymes) (Randau and Söll 2008).…”

Section: Other Types Of Intronsmentioning

confidence: 99%

Origin of Spliceosomal Introns and Alternative Splicing

Irimia

Roy

2014

Cold Spring Harbor Perspectives in Biology

125

121

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In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intronrich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages. SURPRISES AND MYSTERIES OF INTRONS AND INTRON EVOLUTIONW ith mid-20th century breakthroughs, molecular cell biology finally seemed to obey a relatively simple logic. Genetic information was encoded in DNA genes (Avery et al. 1944;Watson and Crick 1953), which were transcribed into RNA and subsequently translated into functional proteins (Crick 1958). However, a most unexpected finding "interrupted" this logic. The coding information of DNA genes was sometimes broken into pieces separated by sequences whose sole apparent purpose was to generate an extra RNA sequence that then had to be removed to generate intact proteincoding messenger RNAs. The initial findings in viruses (Berget et al. 1977;Chow et al. 1977) were soon extended to many cellular genes. With the advent of large-scale sequencing projects, it became clear that one kind of intron (the spliceosomal introns), as well as the cellular machinery that removes them (the spliceosome), are ubiquitous in eukaryotic genomes. For example, the average human transcript contains 9 introns, totaling several hundred thousand introns across the genome and comprising a quarter of the DNA content of each cell (Lander et al. 2001;Venter et al. 2001). Moreover, functions for some introns began to

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“…6,8,26 Some of them are not directly observable as split reads, however. This is the case e.g., for tRNA-Lys and tRNA-Gln, which have nearly identical paralogs that attract the mature tRNA reads to the unspliced loci irrespective of their true origin.…”

Section: Mapping the Rna-seq Trash Binmentioning

confidence: 99%