Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in Petunias.
Petal senescence is a complex programmed process. It has been demonstrated previously that treatment with ethylene, a plant hormone involved in senescence, can extensively alter transcriptome and proteome profiles in plants. However, little is known regarding the impact of ethylene on posttranslational modification (PTM) or the association between PTM and the proteome. Protein degradation is one of the hallmarks of senescence, and ubiquitination, a major PTM in eukaryotes, plays important roles in protein degradation. In this study, we first obtained reference petunia (Petunia hybrida) transcriptome data via RNA sequencing. Next, we quantitatively investigated the petunia proteome and ubiquitylome and the association between them in petunia corollas following ethylene treatment. In total, 51,799 unigenes, 3,606 proteins, and 2,270 ubiquitination sites were quantified 16 h after ethylene treatment. Treatment with ethylene resulted in 14,448 down-regulated and 6,303 up-regulated unigenes (absolute log2fold change > 1 and false discovery rate < 0.001), 284 down-regulated and 233 up-regulated proteins, and 320 up-regulated and 127 down-regulated ubiquitination sites using a 1.5-fold threshold (P < 0.05), indicating that global ubiquitination levels increase during ethylene-mediated corolla senescence in petunia. Several putative ubiquitin ligases were up-regulated at the protein and transcription levels. Our results showed that the global proteome and ubiquitylome were negatively correlated and that ubiquitination could be involved in the degradation of proteins during ethylene-mediated corolla senescence in petunia. Ethylene regulates hormone signaling transduction pathways at both the protein and ubiquitination levels in petunia corollas. In addition, our results revealed that ethylene increases the ubiquitination levels of proteins involved in endoplasmic reticulum-associated degradation.
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China.
Jianhang
0000-0001-8977-8596
J
Guo
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China.
Juanxu
J
Liu
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China.
Qian
Q
Wei
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China.
Rongmin
R
Wang
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China.
Weiyuan
W
Yang
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China.
Yueyue
Y
Ma
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China.
Guoju
G
Chen
Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture (J.G., J.L., Q.W., R.W., W.Y., Y.M., Y.Y.), and College of Horticulture (J.G., G.C., Y.Y.), South China Agricultural University, Guangzhou 510642, China yuyixun@scau.edu.cn.
Yixun
0000-0001-5538-8661
Y
Yu
D000596:Amino Acids / Q000096:biosynthesis; D060746:Endoplasmic Reticulum-Associated Degradation; D005030:Ethylenes / Q000378:metabolism / Q000494:pharmacology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D032306:Petunia / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D010937:Plant Growth Regulators / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D025801:Ubiquitin / Q000378:metabolism; D054875:Ubiquitination / Q000187:drug effects; D055549:Volatile Organic Compounds / Q000378:metabolism
D000596:Amino Acids; D005030:Ethylenes; D010937:Plant Growth Regulators; D010940:Plant Proteins; D020543:Proteome; D025801:Ubiquitin; D055549:Volatile Organic Compounds; C036216:ethylene