“serine-type peptidase activity” were probably the most enriched MF terms; and “chloroplast”, “thylakoid”, andInt. J. Mol. Sci. 2022, 23,10 of”plastid” have been probably the most enriched CC terms. Further KEGG enrichment evaluation revealed that “ribosome biogenesis in eukaryotes”, “plant hormone signal transduction”, “benzoxazinoid biosynthesis”, “alanine, aspartate and glutamate metabolism”, and “limonene and pinene degradation” had been essentially the most overrepresented pathways in the up-regulated DEGs (Figure 12A), and “photosynthesis”, “photosynthesis-antenna proteins”, “carbon fixation in photosynthetic organisms”, “phenylalanine metabolism”, “flavonoid biosynthesis”, “CCR2 Inhibitor manufacturer porphyrin and chlorophyll metabolism”, “ubiquinone along with other terpenoid-quinone biosynthesis”, “starch and sucrose metabolism”, and “carbon metabolism” were by far the most overrepresented pathways inside the down-regulated DEGs (Figure 12B). These BRPF3 Inhibitor Storage & Stability outcomes indicated that the expression level of genes associated to protein metabolic and hormone signaling, which had been elevated within the dnl2 mutant, along with the expression degree of genes associated to photosynthesis and cell wall biosynthesis were suppressed.Figure 11. The significantly enriched GO terms with the up-regulated and down-regulated DEGs involving dnl2 and the wild-type. (A) The enriched BP, MF, and CC terms on the up-regulated DEGs. (B) The enriched BP, MF, and CC terms of the down-regulated DEGs.Int. J. Mol. Sci. 2022, 23,11 ofFigure 12. Enriched Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment of DEGs amongst dnl2 and the wild-type. Enriched KEGG pathways of up-regulated DEGs (A) and down-regulated DEGs (B) in dnl2 compared using the wild-type. The point size represents the amount of genes within the pathway; the color depth indicates the q-value.2.eight. Altered Expression of Hormone Pathway-Related Genes within the dnl2 Mutant Phytohormones play an important part in cell elongation and plant development. In our RNA-seq results, extra than 100 DEGs associated to IAA, GA, ABA, ETH, BR, and jasmonic acid (JA) synthesis and signal transduction had been identified. Notably, 35 genes involved in auxin biosynthesis and signaling have been differentially expressed involving dnl2 and the wildtype plants (Figure 13A and Table S3). For IAA biosynthesis, a flavin monooxygenase-like protein (Zm00001d018652, YUC), which catalyzes the final step of conversion from indole3-pyruvate (IPyA) to IAA [44], was down-regulated by 2.75-fold in dnl2, when indole-3acetaldehyde oxidase (Zm00001d013098, AOX2), which converts indole-3-acetaldehyde (IAD) into IAA [45], was up-regulated by 2.35-fold in dnl2. Auxin response gene households, mostly including seven Aux/IAA (auxin/indole acetic acid), three GH3 (Gretchen Hagen 3), seven SAUR (smaller auxin up RNA), 3 ARF (auxin response element), and 3 PIN (polar auxin transport), exhibited altered expression levels in dnl2 [46,47]. Zm00001d010697 (GH3.six), Zm00001d039345 (GH3), and Zm00001d043244 (GH3.1) belong towards the GH3 gene family members, which participates in auxin homeostasis by catalyzing auxin conjugation and binding free of charge IAA to amino acids [48], and their expression levels were improved by 2.8to 28.6-fold in dnl2. Zm00001d053004 (AIC2) is definitely an auxin transporter-like protein, and its expression level in dnl2 was decreased by 9.3-fold in comparison with the wild-type. The altered expression amount of these genes may possibly disturb IAA homeostasis in the dnl2 mutant. Gibberellins are vital regulators of internode elongation and plant height. The DWARF1 (Zm00001d039634) encod