Accurate, comprehensive database of group I introns and their homing endonucleases

Figures

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  Figure 1.. A comprehensive database of group I introns. (a) Workflow followed to generate the database of group I intron with reliable boundaries and identify putative homing endonucleases in them. The workflow was applied to the entire NT database. (b) Bar plot showing the distribution of identified group I introns across organism types. The majority of group I introns were found in plants, followed by fungi. (c) As in (b), but excluding plants and fungi. (d) Comparison of the length distribution of all introns and only of introns with homing endonucleases. As expected, the latter are larger.

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  Figure 2.. Validation of multiple homing endonucleases found in a single intron. (a) BLAST hits obtained with each of the five homing endonucleases (HEGs) identified in intron NC_062883.1_4. BLAST was performed only against sequences with an experimental structure deposited in the PDB. Only the top 10 hits are shown for each sequence. In all cases, significant hits against homing endonucleases were found. (b) Comparison of the structure of a HEG of the double-motif LAGLIDADG family (chain A of PDB ID 6UVW; grey) with the structures predicted by AlphaFold 3 for the 5 HEGs identified in intron NC_062883.1_4. In all cases except HEG4, the predicted structures contain all the standard fold of a double-motif LAGLIDADG HEG, and differ in the insertions present in flexible loops. The structure predicted for HEG4 corresponds instead to that of a single-motif LAGLIDADG HEG. (c), Overimposition of the predicted structures for the five HEGs of intron NC_062883.1_4.

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  Figure 3.. Distribution of introns in each organism type. (a) Distribution of intron subtypes. (b) Distribution of subcellular locations.

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  Figure 4.. Presence of consensus structural elements across intron subtypes. Each bar plot corresponds to a subtype. Each bar represents the frequency of occurrence of a consensus structural elements across all of the introns of a given subtype.

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  Figure 5.. Distribution of intron sizes by subtype. Considerable differences in intron size distribution were observed among the different subtypes.

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  Figure 6.. Graphical user interface for the group 1 intron database. The GUI is divided in two areas. The left panel allows to input selection criteria (intron subtype, organism name, and organism type), while the right panel displays the information for the group 1 introns fulfilling the selection criteria in a tabular format. The selected introns and all associated information can be downloaded into a single file with the Download results button. The contents of fields too large to be displayed in a single cell of reasonable size can be fully visualized by clicking on the corresponding cell.