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

Abstract

Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

“…This intricate regulation protects the genome from both external and internal factors [18]. For example, miRNAs act as negative regulators of target gene expression at the post-transcriptional level, while lncRNAs may compete with miRNAs to build a regulatory network that coordinates the expression of target genes [19,20].…”

The plant noncoding transcriptome: a versatile environmental sensor

“…Long noncoding RNA interactome in plant nutrient signaling Although a growing number of lncRNAs have been implicated in nutrient perception and uptake, the molecular bases behind their action remain unknown (Bakirbas & Walker, 2022;Fan et al, 2022). In rice, an lncRNA-mediated mechanism regulating phosphate homeostasis was uncovered.…”

MicroRNA 4407 modulates nodulation in soybean by repressing a root‐specific ISOPENTENYLTRANSFERASE (GmIPT3)

“…SNF is an energy‐intensive process and depends highly on the energy supply from the host plant (Streeter, 1980; Alok et al ., 2020). The autoregulation of nodulation (AON) pathway is important for controlling nodule formation in order to prevent uncontrolled supernodulation, a process that could lead to excessive energy dissipation of the host (Searle et al ., 2003; Fan et al ., 2022). In the AON pathway in soybean, the microRNA, miR172c, is activated by the induction of GmNINa caused by rhizobial infection (Wang et al ., 2019) and, in turn, inhibits the expression of its target gene, Nodule Number Control 1 ( GmNNC1 ; Wang et al ., 2014).…”