The Natural Antisense Transcript DONE40 Derived from the lncRNA ENOD40 Locus Interacts with SET Domain Protein ASHR3 During Inception of Symbiosis in Arachis hypogaea

Abstract

The lncRNA ENOD40 is required for cortical cell division during root nodule symbiosis (RNS) of legumes, though it is not essential for actinorhizal RNS. Our objective was to understand whether ENOD40 was required for aeschynomenoid nodule formation in Arachis hypogaea. AhENOD40 express from chr5 (AhENOD40-1) and chr15 (AhENOD40-2) during symbiosis, and RNA interference of these transcripts drastically affected nodulation indicating the importance of ENOD40 in A.hypogaea. Furthermore, we demonstrated several distinct characteristics of ENOD40: (i) Natural antisense transcript of ENOD40 was detected from the AhENOD40-1 locus (designated as NAT-AhDONE40). (ii) Both AhENOD40-1 and AhENOD40-2 had two exons, whereas NAT-AhDONE40 was monoexonic. RT-qPCR analysis indicated both sense and antisense transcripts to be present in both cytoplasm and nucleus, and their expression increased with the progress of symbiosis. (iii) RNA Pulldown from whole cell extracts of infected roots at 4DPI indicated NAT-AhDONE40 to interact with the SET (Su(var)3-9, Enhancer-of-zeste and Trithorax) domain containing Ash (Absent Small homeotic disc) family protein AhASHR3 and this interaction was further validated using RNA immunoprecipitation and EMSA. (iv) ChIP assays indicate deposition of ASHR3 specific histone marks H3K36me3 and H3K4me3 in both the ENOD40 loci during the progress of symbiosis. ASHR3 is known for its role in optimizing cell proliferation and reprogramming. Since both ASHR3 and ENOD40 from legumes cluster away from those in actinorhizal plants and other nonlegumes in phylogenetic distance trees, we hypothesize that the interaction of DONE40 with ASHR3 could have evolved for adapting the nodule organogenesis program for legumes.

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

“…Similar to previous identification of more than one enod40 gene in some species ( 9 , 10 , 38 , 39 ), we identified duplicated enod40 homologues in a number of genomes ( Supplementary Table S1 ). In particular, the majority of legumes have two enod40 genes, with some species comprising three or four copies.…”

The plant noncoding transcriptome: a versatile environmental sensor

“…Upon infection by the symbiotic bacteria, AhDONE40 recruits the SET domain‐containing protein AhASHR3 to activate ENOD40 through H3K36me3 and H3K4me3 deposition. Considering that ASHR3 and ENOD40 from legumes cluster away from those in actinorhizal plants and other nonlegumes in phylogenetic distance trees, it was proposed that the interaction of DONE40 with ASHR3 could have evolved for adapting the nodule organogenesis program in legumes (Ganguly et al , 2021).…”

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

“…NNC1 encodes a protein that targets the promoter of the early nodulin gene, ENOD40 ( Wang et al., 2014 ). The ENOD40 RNA is a special class of RNAs in plants, known as bifunctional RNAs, with both coding and non-coding functions ( Röhrig et al., 2002 ; Ganguly et al., 2021 ). ENOD40 initiates the proliferation of root cortical cells and increases nodule numbers ( Crespi et al., 1994 ; Charon et al., 1997 ; Campalans et al., 2004 ).…”