Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements
NAR Genomics and Bioinformatics, vol. 5, pp. lqad091
Abstract
Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.
Authors 7
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Leiden University · Erasmus MC
Affiliation as printed
Department of Viroscience, Erasmus Medical Center , PO Box 2040, 3000 CA Rotterdam , The Netherlands
Leiden Institute of Advanced Computer Science, Leiden University , PO Box 9512, 2300 RA Leiden , The Netherlands
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Céline Koster Aachen
Leiden University · Amsterdam UMC Location University of Amsterdam · Amsterdam University Medical Centers
Affiliation as printed
Amsterdam University Medical Center, Department of Human Genetics, section Ophthalmogenetics , Location AMC, Meibergdreef 9, Amsterdam , The Netherlands
Life Science & Technology Honours College, Leiden University , PO Box 9502, 2300 RA Leiden , The Netherlands
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Affiliation as printed
CareRate , Unit E1.165, Stationsplein 45, 3013 AK Rotterdam , The Netherlands
Leiden Institute of Advanced Computer Science, Leiden University , PO Box 9512, 2300 RA Leiden , The Netherlands
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Leiden University · Johannes Gutenberg University Mainz
Affiliation as printed
Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz , 55128 Mainz , Germany
Leiden Institute of Advanced Computer Science, Leiden University , PO Box 9512, 2300 RA Leiden , The Netherlands
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Affiliation as printed
Leiden Institute of Advanced Computer Science, Leiden University , PO Box 9512, 2300 RA Leiden , The Netherlands
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Affiliation as printed
Leiden Institute of Advanced Computer Science, Leiden University , PO Box 9512, 2300 RA Leiden , The Netherlands
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Andreas Roussis corresponding
National and Kapodistrian University of Athens
Affiliation as printed
National & Kapodistrian University of Athens, Faculty of Biology, Section of Botany, Group Molecular Plant Physiology, Panepistimiopolis - Zografou - Athens , 15784, Greece
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