Multilayer regulatory landscape during pattern‐triggered immunity in rice

Abstract

Upon fungal and bacterial pathogen attack, plants launch pattern-triggered immunity (PTI) by recognizing pathogen-associated molecular patterns (PAMPs) to defend against pathogens. Although PTI-mediated response has been widely studied, a systematic understanding of the reprogrammed cellular processes during PTI by multi-omics analysis is lacking. In this study, we generated metabolome, transcriptome, proteome, ubiquitome and acetylome data to investigate rice (Oryza sativa) PTI responses to two PAMPs, the fungi-derived chitin and the bacteriaderived flg22. Integrative multi-omics analysis uncovered convergence and divergence of rice responses to these PAMPs at multiple regulatory layers. Rice responded to chitin and flg22 in a similar manner at the transcriptome and proteome levels, but distinct at the metabolome level. We found that this was probably due to post-translational regulation including ubiquitination and acetylation, which reshaped gene expression by modulating enzymatic activities, and possibly led to distinct metabolite profiles. We constructed regulatory atlas of metabolic pathways, including the defence-related phenylpropanoid and flavonoid biosynthesis and linoleic acid derivative metabolism. The multi-level regulatory network generated in this study sets the foundation for in-depth mechanistic dissection of PTI in rice and potentially in other related poaceous crop species.

Multi-Omics Analysis Reveals a Regulatory Network of ZmCCT During Maize Resistance to Gibberella Stalk Rot at the Early Stage

“…For instance, plant hormone signal transduction, pentose phosphate pathway, alpha-linolenic acid metabolism, and fructose and mannose metabolism were specifically enriched at 1 hpi ( Figure 2C ). DEGs at 3 hpi were specifically enriched in plant-pathogen infection, MAPK signaling pathways, beta-alanine metabolism, biotin metabolism, flavonoid biosynthesis, galactose metabolism, terpenoids biosynthesis, and linoleic acid metabolism ( Tang et al, 2021 ). By connecting multiple metabolic pathways enriched in DEGs, we observed glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, diterpenoid biosynthesis, benzoxazinoid biosynthesis, and alanine, aspartate, and glutamate metabolisms were co-regulated by DEGs at 1 and 3 hpi, indicating that these pathways were probably important to activate defense response in maize at the early stage of infection ( Figure 2C ).…”

Metabolomic- and Molecular Networking-Based Exploration of the Chemical Responses Induced in Citrus sinensis Leaves Inoculated with Xanthomonas citri

“…citri inoculation. Such a pathway was also found to be up-regulated in rice leaves 48 h after treatment with the bacterial-derived elicitor flagellin (flg22) . The responsiveness to X.…”

“…Such a pathway was also found to be up-regulated in rice leaves 48 h after treatment with the bacterial-derived elicitor flagellin (flg22). 52 The responsiveness to X. citri-flg22 in Citrus was also correlated to resistance mechanisms against citrus canker. 53 Likewise, the overexpression of unsaturated FA biosynthesis was correlated to resistance to Colletotrichum gloeosporioides in avocado 54 and P. syringae pv.…”

Genome-wide analysis of epigenetic and transcriptional changes in the pathogenesis of RGSV in rice

“…An integrated multi-omics approach has been used to identify and decipher stress resistance and disease immune responses in economically important crops, including wheat, soybean and rice, and to build on this to investigate genes that control important agronomic traits ( Deshmukh et al., 2014 ; Talukdar and Sinjushin, 2015 ; Shah et al., 2018 ; Wang et al., 2019a ; Tang et al., 2021 ). In the field of viruses, integrated multi-omics analysis to reveal the mechanisms of viral perturbation to the host has been extensively and intensively studied in the animal and medical fields.…”