4.2 m6A methylation regulated the expression
of genes
m6A primarily occurs in highly expressed genes during
BPH infestation (Figure 2a,b). In
contrast, m6A mainly occurs in rice genes with low
expression levels during viral infection (Zhang et al., 2021a).
Responsive m6A modification is sensitive and complex
during biological stress, and different stressors may induce
m6A methylation in genes with varying expression
levels. Through KEGG analyses, we identified differentially expressed
transcripts in many pathways containing m6A
modifications (Supporting Information: Figure S11). Four component genes
in the principal constituents of rice m6A modification
machinery can undergo m6A modification. Their relative
expression levels showed considerable variations (Figure 3a–d). Thus,
m6A machinery can govern the expression of key
component genes via m6A methylation, resulting in
significant alterations in overall cellular m6A levels
in rice when confronted with BPH infestation. This suggest a potential
role for m6A in modulating plant defense against
insects.
We found differential regulatory patterns of m6A
modifications in gene expression across different plant specific BPH
response pathways. The m6A modification direction of
genes related to the four methylation components, and major phytohormone
pathways (which including JA, SA, auxin, GA), Bph , and cellulose
synthesis, showed a positive correlation with the target transcript
expression (Figure 3-6; Supporting Information: Table S9, S11, S15,
S20). No apparent regulatory
patterns were found for the hemicellulose synthesis-related genes
(Figure 4C; Supporting Information: Table S14). Thus, the levels of
m6A modification display specific enrichment patterns
depends on the type of metabolic pathways. Based on studies on
regulation of m6A modifications in rice by various
viruses and fungi (Shi et al., 2019; Zhang et al., 2021a), our findings
suggest a potential role for m6A in modulating plant
defense against insects.
4.3 m6A
methylation regulated plant defense and growth upon insect infestation
Growth reduction is commonly associated with herbivore attack and
defense activation, which is known as the growth-defense trade-off (He
et al., 2022). Therefore, plants decide when to grow or defend
themselves to optimize their fitness in a changing environment. Research
into the molecular mechanisms underlying these growth-defense trade-offs
has shown that phytohormones signaling and crosstalk between
phytohormones play central roles (Huot et al., 2014; He et al., 2022).
Auxin, GA and JA are important growth-and defense-related phytohormones,
respectively (Yang et al., 2012). As one of the earliest phytohormones
identified, auxin plays an essential role in most aspects of plant
growth and development, and also play a vital role in plant defense
against diverse pathogens (Spaepen & Vanderleyden, 2011). InArabidopsis , the core JA-responsive basic helix-loop-helix
transcription factor MYC2-mediated repression expression of the growth
regulator PLT integrates JA action into the auxin pathway in regulating
root meristem activity and stem cell niche maintenance (Chen et al.,
2011). BPH attack activates GA catabolism in rice plants via two GA
catabolism genes, that is, GA2ox3 and GA2ox7 , contribute
to BPH-induced growth restriction and are upregulated by JA signaling.
The JA-responsive transcription
factor MYC2 binds to the promoters of GA2ox3 and GA2ox7 to
regulate their expression. Therefore, the MYC2-GA2ox module regulates
the growth-defense trade-off when BPH attacks rice, which provides a
mechanism for phytohormone crosstalk (Jin et al., 2023).
Although the overall m6A methylation of rice was
constrained by BPH damage (Figure 1f,g), JA signaling pathway-related
genes were altered and accompanied by a predominance of upregulated
transcripts and up-directed m6A methylation sites
(Figure 5, Supporting Information: Table S15). Some key genes
responsible for rice growth pathways have shown distinct
m6A-modification directions from JA pathway. This was
reflected in attenuated m6A-modification levels of
auxin and GA biosynthesis-related genes under BPH attack, which
contributed to the downregulated expression of these transcripts. The
rice GA catabolism process was activated after BPH infection, and the
significantly upregulated OsGA2ox3 , OsWRKY71 , andOsCRY1b genes displayed a positive correlation between
m6A modifications and gene expression (Figure 6,
Supporting Information: Table
S20-S22). This indicated that
plant defense was activated but growth was suppressed during BPH attack,
this growth–defense trade-off was likely regulated by
m6A
methylation-mediated Auxin, GA, and
JA pathways in BPH-infested rice.
Overall, m6A modification levels were repressed under
BPH infestation, with m6A primarily modifying highly
expressed genes. Here, we proposed a simplified model for rice
m6A RNA methylation modulation in key defense and
growth pathways induced by BPH infestation (Figure 7).
m6A modification was positively correlated with the
expression of key genes, mainly in insect–stress response and
growth pathways in rice, and may
have contributed to plants prioritizing defense overgrowth during BPH
attack.