Alternative polyadenylation of the stacyose synthase gene mediates source-sink regulation in cucumber

Zhang, Jinji; Gu, Hao; Dai, Hua; Zhang, Zhiping; Miao, Minmin

doi:10.1016/j.jplph.2019.153111

Cited by 14 publications

(14 citation statements)

References 37 publications

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“…Alternative polyadenylation is an important posttranscriptional regulatory mechanism that increases the complexity of the transcriptome and proteome (Sadek et al, 2019). APA causes a single gene to produce more than one transcriptome by changing the length of untranslated regions (UTRs) or coding regions (Zhang et al, 2020). APA in the UTR allows genes to produce different isoforms that have distinct UTR lengths but encode the same protein.…”

Section: Introductionmentioning

confidence: 99%

“…APA in the UTR allows genes to produce different isoforms that have distinct UTR lengths but encode the same protein. Changes in the UTR length may affect mRNA stability, translation efficiency, or subcellular localization because UTRs usually harbor the target sites of microRNAs (miRNAs), RNA binding proteins, and other functional non-coding RNAs, and changes in the UTR length may lead to the gain or loss of these target sites (Chen et al, 2017b;Mayya and Duchaine, 2019;Zhang et al, 2020). These changes eventually affect the physiological and biochemical processes of plants.…”

Section: Introductionmentioning

confidence: 99%

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A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Shen

Wen

et al. 2021

Front. Plant Sci.

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Liriodendron chinense is an economically and ecologically important deciduous tree species. Although the reference genome has been revealed, alternative polyadenylation (APA), transcription factors (TFs), long non-coding RNAs (lncRNAs), and co-expression networks of tissue-specific genes remain incompletely annotated. In this study, we used the bracts, petals, sepals, stamens, pistils, leaves, and shoot apex of L. chinense as materials for hybrid sequencing. On the one hand, we improved the annotation of the genome. We detected 13,139 novel genes, 7,527 lncRNAs, 1,791 TFs, and 6,721 genes with APA sites. On the other hand, we found that tissue-specific genes play a significant role in maintaining tissue characteristics. In total, 2,040 tissue-specific genes were identified, among which 9.2% of tissue-specific genes were affected by APA, and 1,809 tissue-specific genes were represented in seven specific co-expression modules. We also found that bract-specific hub genes were associated plant defense, leaf-specific hub genes were involved in energy metabolism. Moreover, we also found that a stamen-specific hub TF Lchi25777 may be involved in the determination of stamen identity, and a shoot-apex-specific hub TF Lchi05072 may participate in maintaining meristem characteristic. Our study provides a landscape of APA, lncRNAs, TFs, and tissue-specific gene co-expression networks in L. chinense that will improve genome annotation, strengthen our understanding of transcriptome complexity, and drive further research into the regulatory mechanisms of tissue-specific genes.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Shen

Wen

et al. 2021

Front. Plant Sci.

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“…Several evidences support that alkaline a-Gals catabolize RFOs imported from the phloem in cucurbit sink leaves [14,38,39]. The expression of CsAGA1 increased from leaf 1 to leaf 3 and then declined (Fig 5), the fluctuation pattern is consistent with the sink to source transition process of cucumber leaves (leaf 1 to leaf 3 were sink leaves and leaf 4 to leaf 7 were source leaves) [37], indicating its possible role of RFOs unloading in young cucumber leaves. During leaf senescence, galactolipids and galactoproteins of tonoplast or plastid membrane would be decomposed for reutilization as a source of carbon or energy [6,40].…”

Section: Plos Onementioning

confidence: 52%

“…CsGAL2, which significantly expressed (Fig 5) and showed a cell-wall localization [9], is mostly perform this function. Besides loading into the phloem, there is a stachyose pool in cucumber leaves for temporary storage (Fig 5) [37]. CsAGA2, another high expressed α-Gal in cucumber leaves (Fig 5 ), may be responsible for the catabolism of accumulated RFOs in cucumber leaves.…”

Section: Plos Onementioning

confidence: 99%

Characteristics and expression patterns of six α-galactosidases in cucumber (Cucumis sativus L.)

et al. 2021

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Six putative α-galactosidase genes (α-Gals), three acid forms (CsGAL1, CsGAL2, CsGAL3) and three alkaline forms (CsAGA1, CsAGA2, CsAGAL3), were found in the cucumber genome. It is interesting to know the expression pattern and possible function of these α-Gals in the cucumber plant since it is a stachyose-translocating species. In this study, full-length cDNAs of six α-Gals were cloned and heterologously expressed. The result showed that all recombinant proteins revealed acid or alkaline α-Gal activities with different substrate specificities and pH or temperature responding curves, indicating their distinct roles in cucumber plants. Phylogenetic analysis of collected α-Gal amino acid sequences from different plants indicated that the ancestor of both acid and alkaline α-Gals existed before monocots and dicots separated. Generally, six α-Gal genes are universally expressed in different cucumber organs. CsGAL2 highly expressed in fasting-growing leaves, fruits and germinating seeds; CsGAL3 mainly distributes in vacuoles and significantly expressed in cucumber fruits, senescent leaves and seeds during late stage germination; The expression of CsAGA1 increased from leaf 1 to leaf 3 (sink leaves) and then declined from leaf 4 to leaf 7 (source leaves), and this isoform also highly expressed in male flowers and germinating seeds at early stage; CsAGA2 significantly expressed in cucumber leaves and female flowers; CsAGA3 is localized in plastids and also actively expressed in senescent leaves and germinating seeds; The role of CsGAL1 in cucumber plants is now unclear since its expression was relatively low in all organs. According to their expression patterns, subcellular localizations and previously reported functions of these isoforms in other plants, combining the data of soluble sugars contents in different tissues, the possible functions of these α-Gals were discussed.

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“…The primer specificity was verified using artificial RNAs as templates according to Zhang et al . [ 29 ]. Absolute quantitative RT–PCR (qRT–PCR) was performed to compare the expression abundance of different isoforms of CsSTS and CsGolS s. The generation of standard curves and the calculation of copy numbers were conducted according to Zhang et al .…”

Section: Methodsmentioning

confidence: 99%

Galactinol synthase 1 improves cucumber performance under cold stress by enhancing assimilate translocation

Dai

Zhu

Wang

et al. 2022

Horticulture Research

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Cucumber (Cucumis sativus L.) predominately translocates raffinose family oligosaccharides (RFOs) in the phloem and accumulates RFOs in leaves. Galactinol synthase (GolS) catalyzes the critical step of RFO biosynthesis, and determining the functional diversity of multiple GolS isoforms in cucumber is of scientific significance. In this study, we found that all four isoforms of CsGolS in the cucumber genome were upregulated by different abiotic stresses. β-glucuronidase staining and tissue separation experiments suggested that CsGolS1 is expressed in vascular tissues, whereas the other three CsGolSs are located in mesophyll cells. Further investigation indicates that CsGolS1 plays double roles in both assimilate loading and stress response in minor veins, which could increase the RFO concentration in the phloem sap and then improve assimilate transport under adverse conditions. Cold-induced minor vein-specific overexpression of CsGolS1 enhanced the assimilate translocation efficiency and accelerated the growth rates of sink leaves, fruits and whole plants under cold stress. Finally, our results demonstrate a previously unknown response to adverse environments and provide a potential biotechnological strategy to improve the stress resistance of cucumber.

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Alternative polyadenylation of the stacyose synthase gene mediates source-sink regulation in cucumber

Cited by 14 publications

References 37 publications

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Characteristics and expression patterns of six α-galactosidases in cucumber (Cucumis sativus L.)

Galactinol synthase 1 improves cucumber performance under cold stress by enhancing assimilate translocation

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