Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements

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.

Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long “Non-Coding” RNAs

“…It is also involved in the stimulation of colonization of plant roots by fungi [ 44 ]. In addition to plants of the order Fagales , homologs of this RNA have been identified in monocots such as rice and maize, indicating conservation of its molecular targets between dicots and monocots [ 35 , 45 ]. In contrast to legumes, rice OsENOD40 is specifically expressed in rice stems and is involved in organ differentiation and vascular tissue development [ 46 ].…”

“…In soybeans, ENOD40 directs the synthesis of 12- and 24-amino-acid long peptides that are encoded by short ORF1 and ORF2, respectively. Alfalfa ENOD40 ORF1 and ORF2 genes encode short peptides of 13 and 27 amino acids [ 35 , 45 ]. ENOD40 region coding for a short peptide of 12–13 amino acids is also conserved in many, but not all, non-leguminous species [ 45 ].…”

“…Alfalfa ENOD40 ORF1 and ORF2 genes encode short peptides of 13 and 27 amino acids [ 35 , 45 ]. ENOD40 region coding for a short peptide of 12–13 amino acids is also conserved in many, but not all, non-leguminous species [ 45 ]. Translation in vitro of soybean ENOD40 RNA has been demonstrated to produce both ORF1 and ORF2 peptides, and these chemically synthesized peptide products have been found to bind to sucrose synthase [ 35 ].…”

“…Translation in vitro of soybean ENOD40 RNA has been demonstrated to produce both ORF1 and ORF2 peptides, and these chemically synthesized peptide products have been found to bind to sucrose synthase [ 35 ]. It seems that the mechanisms of ENOD40 gene related to nodule formation may act via its RNA transcript molecule, and its encoded peptides may be responsible for some unknown functions only required in some specific legume plants [ 45 ].…”