A role for small RNA in regulation of innate immunity during plant growth

Authors: DENG, YINGTIAN - Huazhong Agricultural University; WANG, JUBIN - Huazhong Agricultural University; TUNG, JEFFREY - University Of California; LIU, DAN - Huazhong Agricultural University; ZHOU, YINGJIA - Huazhong Agricultural University; SHAUNG, HE - Huazhong Agricultural University; YUNLIAN, DU - Huazhong Agricultural University; Baker, Barbara; LI, FENG - Huazhong Agricultural University

Submitted to: Public Library of Science for Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2017
Publication Date: 1/2/2018
Citation: Deng, Y., Wang, J., Tung, J., Liu, D., Zhou, Y., Shuang, H., Yunlian, D., Baker, B.J., Li, F. 2018. A role for small RNA in regulation of innate immunity during plant growth. Public Library of Science for Pathogens. 14(1):e1006756. https://doi.org/10.1371/journal.ppat.1006756.
DOI: https://doi.org/10.1371/journal.ppat.1006756

Interpretive Summary: Biotic stress responses protect plants from disease, but can compromise growth and crop yields. Plant immune systems monitor for presence of pathogens, detecting specific molecular patterns and then mounting defenses upon recognizing an infection. Induction of defenses in the absence of a pathogen is deleterious, and can cause autoimmune syndromes that disrupt development, impair growth, and limit crop yields. Using the Solanaceae family of agronomically important crops as model systems, we discovered that we discovered a new class of DCL4-dependent miRNAs that epigenetically control expression of an antiviral RNAi gene and R genes. We found that antiviral RNAi DICER-LIKE (DCL) enzymes, DCL4/DCL2, generate miRNAs that target R genes, rather than the canonical DCL1-dependent miRNA biogenesis mechanism. Moreover, one of these miRNAs, miR6026, also targets DCL2 for repression. We propose that this mechanism forms a homeostatic regulatory network, monitoring DCL4 activity to balance antiviral defenses without triggering autoimmunity. This work will help to understand how fine-tuning expression of RNAi components and R genes can contribute to deploying a robust array of R genes and breeding efficient antiviral immunity.

Technical Abstract: Plant genomes encode large numbers of nucleotide-binding (NB) leucine-rich repeat (LRR) immune receptors (NLR) that mediate effector triggered immunity (ETI) and play key roles in protecting crops from diseases caused by devastating pathogens. Fitness costs are associated with plant NLR genes and regulation of NLR genes by micro(mi)RNAs and phased small interfering RNAs (phasiRNA) is proposed as a mechanism for reducing these fitness costs. However, whether NLR expression and NLR-mediated immunity are regulated during plant growth is unclear. We conducted genome-wide transcriptome analysis and showed that NLR expression gradually increased while expression of their regulatory small RNAs (sRNA) gradually decreased as plants matured, indicating that sRNAs could play a role in regulating NLR expression during plant growth. We further tested the role of miRNA in the growth regulation of NLRs using the tobacco mosaic virus (TMV) resistance gene Necrosis (N), which was targeted by miR6019 and miR6020. We showed that N-mediated resistance to TMV effectively restricted this virus to the infected leaves of 6-week old plants, whereas TMV infection was lethal in 1- and 3-week old seedlings due to virus-induced systemic necrosis. We further found that N transcript levels gradually increased while miR6019 levels gradually decreased during seedling maturation that occurs in the weeks after germination. Analyses of reporter genes in transgenic plants showed that growth regulation of N expression was post-transcriptionally mediated by MIR6019/6020 whereas MIR6019/6020 was regulated at the transcriptional level during plant growth. TMV infection of MIR6019/6020 transgenic plants indicated a key role for miR6019-triggered phasiRNA production for regulation of N-mediated immunity. Together our results demonstrate a mechanistic role for miRNAs in regulating innate immunity during plant growth.