Nucleotide sequences of the self-splicing group-II intron of rps16 have first been determined in nine species of the Solanum genus. It was found that the observed variations in the intron length (855-864 bp) was associated with indels of 1 to 9 b. Altogether, five indels and 50 nucleotide substitutions were detected, which were used to identify six Solanum haplotypes. Although the intron sequence was in general fairly well conserved, the distribution of the described mutations among its structural elements corresponding to six preRNA domains was qualitatively and quantitatively nonuniform. The highest polymorphism levels were observed in domains I, II, and IV. The sequence of domain V was absolutely invariable, which is in agreement with its functional significance.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.7868/s0016675813070126 | DOI Listing |
A previous study found that a domesticated bacterial group II intron-like reverse transcriptase (G2L4 RT) functions in double-strand break repair (DSBR) via microhomology-mediated end joining (MMEJ) and that a mobile group II intron-encoded RT has a basal DSBR activity that uses conserved structural features of non-LTR-retroelement RTs. Here, we determined G2L4 RT apoenzyme and snap-back DNA synthesis structures revealing novel structural adaptations that optimized its cellular function in DSBR. These included a unique RT3a structure that stabilizes the apoenzyme in an inactive conformation until encountering an appropriate substrate; a longer N-terminal extension/RT0-loop with conserved residues that together with a modified active site favors strand annealing; and a conserved dimer interface that localizes G2L4 RT homodimers to DSBR sites with both monomers positioned for MMEJ.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro-a new group-II intron-encoded RT-to map and quantify genome-wide tRNA modifications in Induro-tRNAseq.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail. These difficulties are compounded for small RNAs as cryo-EM is inherently more difficult for lower molecular weight macromolecules. Here we present a strategy for fusing small RNAs to a group II intron that yields high resolution structures of the appended RNA.
View Article and Find Full Text PDFACS Chem Biol
January 2025
Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States.
We report the discovery of small molecules that target the RNA tertiary structure of self-splicing group II introns and display potent antifungal activity against yeasts, including the major public health threat . High-throughput screening efforts against a yeast group II intron resulted in an inhibitor class which was then synthetically optimized for enhanced inhibitory activity and antifungal efficacy. The most highly refined compounds in this series display strong, gene-specific antifungal activity against .
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Biomimetic Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, Dortmund 44227, Germany.
Group II introns are ancient self-splicing ribozymes and retrotransposons. Though long speculated to have originated before translation, their dependence on intron-encoded proteins for splicing and mobility has cast doubt on this hypothesis. While some group II introns are known to retain part of their catalytic repertoire in the absence of protein cofactors, protein-free complete reverse splicing of a group II intron into a DNA target has never been demonstrated.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!