Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants

Abstract

enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the molecular mechanisms of its activity are unclear; they may be determined though, by short peptides and/or RNA structures encoded in the enod40 genes. We utilized conserved RNA structures in enod40 sequences to search nucleotide sequence databases and identified a number of new enod40 homologues in plant species that belong to known, but also, to yet unknown enod40-containing plant families. RNA secondary structure predictions and comparative sequence analysis of enod40 RNAs allowed us to determine the most conserved structural features, present in all known enod40 genes. Remarkably, the topology and evolution of one of the conserved structural domains are similar to those of the expansion segments found in structural RNAs such as rRNAs, RNase P and SRP RNAs. Surprisingly, the enod40 RNA structural elements are much more stronger conserved than the encoded peptides. This finding suggests that some general functions of enod40 gene could be determined by the encoded RNA structure, whereas short peptides may be responsible for more diverse functions found only in certain plant families.

Figure 1.

Conserved structures and sequence motifs in enod40 RNAs. Domains 1–6 are shown schematically and not in scale, domain numbering is from (29). The locations of sORF1 and regions I and II (dashed double arrows) are also shown. Double arrows indicate the extent of conservation of particular structures. Some deviations from the shown consensus sequences are possible.

Figure 2.

The hairpins of the enod40 domain 3 [nomenclature from (29)] from various enod40 homologues. Nucleotide positions are given in Table 1. The sequences correponding to the CUC/GAG motif are boxed. For A. thaliana, a genomic sequence is given—it differs from GenBank entry AK220907 by one substitution in the loop of hairpin 3. Species names are abbreviated by the first two characters, for complete names see Table 1.

Figure 3.

Examples of enod40 domain 2 evolution in families Asterales (A), Brassicales (B) and Solanales (C). Nucleotide positions are given in Table 1. The conserved closing stem is boxed. The insertion locations are indicated by small arrows, inserted nucleotides are in different letter font. Large arrows indicate the transitions between structures of various species determined by insertions (but they should not always correspond to real evolutionary events that may occur in reverse order or include branching). Species names are abbreviated by first two characters, for complete names see Table 1.