Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides

Abstract

The 2′,3′-cycling ribonuclease (RNase) genes are catalysts of RNA cleavage and include the RNase T2 gene family. RNase T2 genes perform important roles in plants and have been conserved in the genome of eukaryotic organisms. In this study we identified 21 EURNS genes in Eucommia ulmoides Oliver (E. ulmoides) and analyzed their structure, chromosomal location, phylogenetic tree, gene duplication, stress-related cis-elements, and expression patterns in different tissues. The length of 21 predicted EURNS proteins ranged from 143 to 374 amino acids (aa), their molecular weight (MW) ranged from 16.21 to 42.38 kDa, and their isoelectric point (PI) value ranged from 5.08 to 9.09. Two classifications (class I and class III) were obtained from the conserved domains analysis and phylogenetic tree. EURNS proteins contained a total of 15 motifs. Motif 1, motif 2, motif 3, and motif 7 were distributed in multiple sequences and were similar to the conserved domain of RNase T2. EURNS genes with similar structure and the predicted EURNS proteins with conserved motif compositions are in the same group in the phylogenetic tree. The results of RT-PCR and transcription data showed that EURNS genes have tissue-specific expression and exhibited obvious trends in different developmental stages. Gene duplication analysis results indicated that segment duplication may be the dominant duplication mode in this gene family. This study provides a theoretical basis for research on the RNase T2 gene family and lays a foundation for the further study of EURNS genes.

High Ribonuclease Activity in the Testa of Common Bean Seedlings during Germination: Implication and Characterization of the Ribonuclease T2 PvRNS3

“…However, in plants, the T2 ribonuclease family is composed of many different members, and there is evidence of frequent duplications/gene losses that resulted in different numbers of genes in different species [7]. For instance, the RNase T2 family is composed of five members in Arabidopsis [8], eight in rice [9], thirteen in common bean [5] and soybean [10], and twenty-one in Eucommia ulmoides [11]. This suggests that besides the ancestral function of RNases, these proteins have acquired a variety of biological functions in plants.…”

“…The S-ribonucleases have been postulated to be involved in self-incompatibility, whereas the S-like ribonucleases participate in a wide range of physiological processes, such as biotic and abiotic stress responses, the maintenance of phosphate homeostasis, or production of small RNAs [7]. Phylogenetic analyses of these members identified three different clades defining three different classes; Classes I and II are the S-like ribonucleases, whereas the Class III corresponds to S-ribonucleases [5,11,13,14].…”