Genome-Wide Identification and Analysis of Polygalacturonase Genes in Solanum lycopersicum

Ke, Xubo; Wang, Huasen; Li, Yang; Bao-cheng, Zhu; Zang, Yunxiang; He, Yehua; Cao, Jiashu; Zhu, Zhujun; Yu, Youjian

doi:10.3390/ijms19082290

Cited by 35 publications

(47 citation statements)

References 56 publications

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“…The Physicochemical characteristic of SlWAK-RLKs, including protein length, isoelectric point (pI) and molecular weight (MW) were predicted by ExPASy ProtParam ( ) [ 29 , 30 ]. SlWAK-RLKs protein structure prediction information were obtained from the SMART website ( ) [ 21 , 27 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.)

Sun

Song

Chen

et al. 2020

Genes

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The wall-associated kinase (WAK) and wall-associated kinase like (WAKL) is a subfamily of receptor-like kinases associated with the cell wall, which have been suggested as sensors of the extracellular environment and triggers of intracellular signals. However, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum L.). In this study, 11 SlWAK and 18 SlWAKL genes were identified in an uneven distribution in 9 of 12 chromosomes. GUB-WAK-bind (wall-associated receptor kinase galacturonan-binding) and epidermal growth factor (EGF) domains appear more often in SlWAK proteins. However, more SlWAKLs (wall-associated kinase like) have a WAK-assoc (wall-associated receptor kinase C-terminal) domain. Based on their phylogenetic relationships, 29 SlWAK-RLKs (wall associated kinase-receptor like kinases) were clustered into three distinct categories analogous to those in Arabidopsis thaliana. High similarities were found in conserved motifs of the genes within each group. Cis-elements in the promoter region of these 29 genes were found mainly in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), anaerobic, light, wound, and MYB transcription factors. Public tomato genome RNA-seq data indicates that multiple SlWAK-RLKs showed different expression patterns under developmental and ripening stages of fruits, such as SlWAK4, SlWAKL11, SlWAKL9, SlWAKL15, SlWAKL14, and SlWAKL1, their RPKM (Reads Per Kilo bases per Million reads) value constantly increases during the fruit expansion period, and decreases as the fruit matures. In tomato leaves, our RNA-seq data showed that nine SlWAK-RLKs transcripts (SlWAK3, SlWAK4, SlWAK10,SlWAKL1, SlWAKL2, SlWAKL3, SlWAKL5, SlWAKL14, and SlWAKL18) were significantly induced (p < 0.001), and three transcripts (SlWAK2, SlWAK5, and SlWAKL15) were significantly inhibited (p < 0.001) under mechanical wounding. The qRT-PCR (Quantitative reverse transcription polymerase chain reaction) of SlWAKL1 and SlWAKL6 verify these results.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.)

Sun

Song

Chen

et al. 2020

Genes

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“…Our proteomics profiling of sweet cherry abscising carpopodium showed bidirectional changes in the expression of the cell wall-related proteins, probably associated not only with the ongoing process of abscission but also with the progressive development of the organs that are not dropped (Table S4). However, it is worth noting that most of the enzymes involved in cell wall degradation showed a trend of up-regulation, including cellulose [3], pectinase [47], polygalacturonase [48], β-galactosidase [49], which play a major role in cell wall degradation. Moreover, the enzymatic activity of cellulose, pectinase and polygalacturonase were significantly higher than non-abscising carpopodium (Figure 2a).…”

Section: Cell Wall Metabolism and Abscissionmentioning

confidence: 99%

Comparative Proteomics Profiling Illuminates the Fruitlet Abscission Mechanism of Sweet Cherry as Induced by Embryo Abortion

Qiu

Zhuang

Yang

et al. 2020

IJMS

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Sweet cherry (Prunus avium L.) is a delicious nutrient-rich fruit widely cultivated in countries such as China, America, Chile, and Italy. However, the yield often drops severely due to the frequently-abnormal fruitlet abscission, and few studies on the metabolism during its ripening process at the proteomic level have been executed so far. To get a better understanding regarding the sweet cherry abscission mechanism, proteomic analysis between the abscising carpopodium and non-abscising carpopodium of sweet cherry was accomplished using a newly developed Liquid chromatography-mass spectrometry/mass spectrometry with Tandem Mass Tag (TMT-LC-MS/MS) methodology. The embryo viability experiments showed that the vigor of the abscission embryos was significantly lower than that of retention embryo. The activity of cell wall degrading enzymes in abscising carpopodium was significantly higher than that in non-abscising carpopodium. The anatomy results suggested that cells in the abscission zone were small and separated. In total, 6280 proteins were identified, among which 5681 were quantified. It has been observed that differentially accumulated proteins (DAPs) influenced several biological functions and various subcellular localizations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that plenty of metabolic pathways were notably enriched, particularly those involved in phytohormone biosynthesis, cell wall metabolism, and cytoskeletal metabolism, including 1-aminocyclopropane-1-carboxylate oxidase proteins which promote ethylene synthesis, and proteins promoting cell wall degradation, such as endoglucanases, pectinase, and polygalacturonase. Differential expression of proteins concerning phytohormone biosynthesis might activate the shedding regulation signals. Up-regulation of several cell wall degradation-related proteins possibly regulated the shedding of plant organs. Variations of the phytohormone biosynthesis and cell wall degradation-related proteins were explored during the abscission process. Furthermore, changes in cytoskeleton-associated proteins might contribute to the abscission of carpopodium. The current work represented the first study using comparative proteomics between abscising carpopodium and non-abscising carpopodium. These results indicated that embryo abortion might lead to phytohormone synthesis disorder, which effected signal transduction pathways, and hereby controlled genes involved in cell wall degradation and then caused the abscission of fruitlet. Overall, our data may give an intrinsic explanation of the variations in metabolism during the abscission of carpopodium.

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“…Cell‐wall degradation is associated with cell‐wall hydrolases, including pectinesterase (PME), polygalacturonase (PG), β ‐gal, α ‐arabinofuranosidase ( α ‐L‐af), xyloglucan endotransglycosylase / hydrolase (XTH), and cellulase . Pectinesterase catalyzes the demethylesterification of cell‐wall polygalacturonans, which promotes the hydrolysis of polygalacturonic acid by PG . β ‐Gal is hydrolyzed to pectin and hemicellulose, as a pectin‐debranching enzyme .…”

Section: Introductionmentioning

confidence: 99%

“…15 Pectinesterase catalyzes the demethylesterification of cell-wall polygalacturonans, 16 which promotes the hydrolysis of polygalacturonic acid by PG. 17 ⊎-Gal is hydrolyzed to pectin and hemicellulose, as a pectin-debranching enzyme. 10 ⊍-L-af can remove arabinose units from fruit cell wall polysaccharides residues.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals delaying of the ripening and cell‐wall degradation of kiwifruit by hydrogen sulfide

et al. 2020

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BACKGROUND Hydrogen sulfide (H2S) is a known signaling molecule in plants, which has the ability to delay fruit ripening. Our previous studies have shown that H2S treatment could delay the maturation of kiwifruits by inhibiting ethylene production, improving protective enzyme activities, and decreasing the accumulation of reactive oxygen species to protect the cell membrane during storage. The mechanism related to the way in which H2S affected kiwifruit maturation was still unclear. We performed transcriptome sequencing to explore the influences of H2S on the softening of kiwifruit. RESULTS The firmness and the soluble solids content (SSC) of the kiwifruit were significantly better maintained with H2S treatment compared to the control during the storage period (P < 0.05). Transmission electron microscopy (TEM) showed that degradation of the cell wall was inhibited after H2S treatment. Based on transcriptome data analysis and quantitative real‐time polymerase chain reaction (qRT‐PCR), expression levels of endo‐1,4‐β‐glucanase (β‐glu), β‐galactosidase (β‐gal) and pectinesterase (PME) decreased whereas pectinesterase inhibitor (PMEI) significantly increased in response to H2S. The members of the signal transduction pathway involved in ethylene were also identified. Hydrogen sulfide inhibited the expression of ethylene receptor 2 (ETR2), ERF003, ERF5, and ERF016, and increased the expression of ethylene‐responsive transcription factor 4 (ERF4) and ERF113. CONCLUSION Hydrogen sulfide could delay the ripening and senescence of kiwifruit by regulating the cell‐wall degrading enzyme genes and affecting ethylene signal transduction pathway genes. Our results revealed the effect of H2S treatment on the softening of kiwifruit at the transcription level, laying a foundation for further research. © 2020 Society of Chemical Industry

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Genome-Wide Identification and Analysis of Polygalacturonase Genes in Solanum lycopersicum

Cited by 35 publications

References 56 publications

Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.)

Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.)

Comparative Proteomics Profiling Illuminates the Fruitlet Abscission Mechanism of Sweet Cherry as Induced by Embryo Abortion

Transcriptome analysis reveals delaying of the ripening and cell‐wall degradation of kiwifruit by hydrogen sulfide

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