The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic

Long noncoding RNAs (lncRNAs) are emerging as important regulators in plant development, but few of them have been functionally characterized in fruit ripening. Here, we have identified 25,613 lncRNAs from strawberry ripening fruits based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries, most of which exhibited distinct temporal expression patterns. A novel lncRNA, FRILAIR harbours the miR397 binding site that is highly conserved in diverse strawberry species. FRILAIR overexpression promoted fruit maturation in the Falandi strawberry, which was consistent with the finding from knocking down miR397, which can guide the mRNA cleavage of both FRILAIR and LAC11a (encoding a putative laccase-11-like protein). Moreover, LAC11a mRNA levels were increased in both FRILAIR overexpressing and miR397 knockdown fruits, and accelerated fruit maturation was also found in LAC11a overexpressing fruits. Overall, our study demonstrates that FRILAIR can act as a noncanonical target mimic of miR397 to modulate the expression of LAC11a in the strawberry fruit ripening process.

Download Full-text

PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs

Nucleic Acids Research ◽

10.1093/nar/gkaa910 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D1489-D1495 ◽

Cited By ~ 1

Author(s):

Jingjing Jin ◽

Peng Lu ◽

Yalong Xu ◽

Zefeng Li ◽

Shizhou Yu ◽

...

Keyword(s):

Noncoding Rna ◽

Regulatory Networks ◽

Expression Patterns ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Data Driven ◽

Rna Seq ◽

Protein Coding ◽

User Friendly ◽

Coding Potential

Abstract Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http://plncdb.tobaccodb.org/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five built-in search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.

Download Full-text

Cytosolic/Plastid Glyceraldehyde-3-Phosphate Dehydrogenase Is a Negative Regulator of Strawberry Fruit Ripening

Genes ◽

10.3390/genes11050580 ◽

2020 ◽

Vol 11 (5) ◽

pp. 580 ◽

Cited By ~ 1

Author(s):

Ya Luo ◽

Cong Ge ◽

Min Yang ◽

Yu Long ◽

Mengyao Li ◽

...

Keyword(s):

Fruit Ripening ◽

Reduced Glutathione ◽

Expression Patterns ◽

Plant Stress ◽

Negative Regulator ◽

Strawberry Fruit ◽

Catalytic Function ◽

Strawberry Fruit Ripening ◽

Transient Overexpression ◽

H2o2 Level

Cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) and plastid glyceraldehyde-3-phosphate dehydrogenase (GAPCp) are key enzymes in glycolysis. Besides their catalytic function, GAPC/GAPCp participates in the regulation of plant stress response and growth and development. However, the involvement of GAPC/GAPCp in the regulation of fruit ripening is unclear. In this study, FaGAPC2 and FaGAPCp1 in strawberries were isolated and analyzed. FaGAPC2 and FaGAPCp1 transcripts showed high transcript levels in the fruit. Transient overexpression of FaGAPC2 and FaGAPCp1 delayed fruit ripening, whereas RNA interference promoted fruit ripening and affected fruit anthocyanins and sucrose levels. Change in the expression patterns of FaGAPC2 and FaGAPCp1 also influenced the expression of several glycolysis-related and ripening-related genes such as CEL1, CEL2, SS, ANS, MYB5, NCED1, ABI1, ALDO, PK, and G6PDH, and H2O2 level and reduced glutathione (GSH)/glutathione disulfide (GSSG) redox potential. Meanwhile, metabolomics experiments showed that transient overexpression of FaGAPCp1 resulted in a decrease in anthocyanins, flavonoids, organic acid, amino acids, and their derivatives. In addition, abscisic acid (ABA) and sucrose treatment induced the production of large amounts of H2O2 and inhibited the expression of FaGAPC2/FaGAPCp1 in strawberry fruit. These results revealed that FaGAPC2/FaGAPCp1 is a negative regulator of ABA and sucrose mediated fruit ripening which can be regulated by oxidative stress.

Download Full-text

A Method for Assaying of Protein Kinase Activity In Vivo and Its Use in Studies of Signal Transduction in Strawberry Fruit Ripening

International Journal of Molecular Sciences ◽

10.3390/ijms221910495 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10495

Author(s):

Wei Wang ◽

Zhengrong Dai ◽

Jie Li ◽

Jinyao Ouyang ◽

Tianyu Li ◽

...

Keyword(s):

Signal Transduction ◽

Protein Kinase ◽

Fruit Ripening ◽

Kinase Activity ◽

Expression Patterns ◽

Protein Kinase Activity ◽

Strawberry Fruit ◽

Simple Method ◽

Strawberry Fruit Ripening

Strawberry (Fragaria × ananassa) fruit ripening is regulated by a complex of cellular signal transduction networks, in which protein kinases are key components. Here, we report a relatively simple method for assaying protein kinase activity in vivo and specifically its application to study the kinase, FaMPK6, signaling in strawberry fruit. Green fluorescent protein (GFP)-tagged FaMPK6 was transiently expressed in strawberry fruit and after stimuli were applied to the fruit it was precipitated using an anti-GFP antibody. The precipitated kinase activity was measured in vitro using 32P-ATP and myelin basic protein (MBP) as substrates. We also report that FaMPK6 is not involved in the abscisic acid (ABA) signaling cascade, which is closely associated with FaMPK6 signaling in other plant species. However, methyl jasmonate (MeJA), low temperature, and high salt treatments were all found to activate FaMPK6. Transient manipulation of FaMPK6 expression was observed to cause significant changes in the expression patterns of 2749 genes, of which 264 were associated with MeJA signaling. The data also suggest a role for FaMPK6 in modulating cell wall metabolism during fruit ripening. Taken together, the presented method is powerful and its use will contribute to a profound exploration to the signaling mechanism of strawberry fruit ripening.

Download Full-text

Downregulation of RdDM during strawberry fruit ripening

Genome Biology ◽

10.1186/s13059-018-1587-x ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 29

Author(s):

Jingfei Cheng ◽

Qingfeng Niu ◽

Bo Zhang ◽

Kunsong Chen ◽

Ruihua Yang ◽

...

Keyword(s):

Fruit Ripening ◽

Strawberry Fruit ◽

Strawberry Fruit Ripening

Download Full-text

Melatonin accelerates strawberry fruit ripening by triggering GAMYB gene expression and promoting ABA accumulation

Scientia Horticulturae ◽

10.1016/j.scienta.2021.109919 ◽

2021 ◽

Vol 281 ◽

pp. 109919

Author(s):

Sirvan Mansouri ◽

Hassan Sarikhani ◽

Mohammad Sayyari ◽

Morteza Soleimani Aghdam

Keyword(s):

Gene Expression ◽

Fruit Ripening ◽

Strawberry Fruit ◽

Strawberry Fruit Ripening

Download Full-text

MAPK5 and MAPK10 overexpression influences strawberry fruit ripening, antioxidant capacity and resistance to Botrytis cinerea

Planta ◽

10.1007/s00425-021-03804-z ◽

2021 ◽

Vol 255 (1) ◽

Author(s):

Yunting Zhang ◽

Yu Long ◽

Yiting Liu ◽

Min Yang ◽

Liangxin Wang ◽

...

Keyword(s):

Antioxidant Capacity ◽

Botrytis Cinerea ◽

Fruit Ripening ◽

Strawberry Fruit ◽

Strawberry Fruit Ripening

Download Full-text

Ethylene is involved in strawberry fruit ripening in an organ-specific manner

Journal of Experimental Botany ◽

10.1093/jxb/ert257 ◽

2013 ◽

Vol 64 (14) ◽

pp. 4421-4439 ◽

Cited By ~ 62

Author(s):

Catharina Merchante ◽

José G. Vallarino ◽

Sonia Osorio ◽

Irene Aragüez ◽

Natalia Villarreal ◽

...

Keyword(s):

Fruit Ripening ◽

Strawberry Fruit ◽

Specific Manner ◽

Organ Specific ◽

Strawberry Fruit Ripening

Download Full-text

Cloning, Characterization, and Expression Features of Chicken CDS2 Splicing Variants

10.21203/rs.3.rs-80587/v1 ◽

2020 ◽

Author(s):

Yuanyuan Xu ◽

Shuping Zhang ◽

Yujun Guo ◽

Wen Chen ◽

Yanqun Huang

Keyword(s):

Adipose Tissue ◽

Real Time ◽

Real Time Pcr ◽

Expression Patterns ◽

Mrna Levels ◽

Exogenous Insulin ◽

Quantitative Real Time Pcr ◽

Temporal Expression ◽

Spatio Temporal ◽

The Brain

Abstract Background: The CDS gene encodes the CDP-diacylglycerol synthase enzyme that catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid. At present, there are no reports of CDS2 in birds. Here, we identified chicken CDS2 transcripts by combining conventional RT- PCR amplification, 5' RACE (Fig. 1A), and 3' RACE, explored the spatio-temporal expression profiles of total CDS2 and the longest transcript variant CDS2-4, and investigated the effect of exogenous insulin on total the mRNA level of CDS2 by quantitative real-time PCR. Results: Four transcripts of chicken CDS2 (CDS2-1, -2, -3, and -4) were identified, which were alternatively spliced at the 3′-untranslated region (UTR). CDS2 was widely expressed in all tissues examined and the longest variant CDS2-4 was the major transcript. Both total CDS2 and CDS2-4 were prominently expressed in adipose tissue and the heart, and exhibited low expression in the liver and pectoralis of 49 day-old chickens. Quantitative real-time PCR revealed that total CDS2 and CDS2-4 had different spatio-temporal expression patterns in chicken. Total CDS2 exhibited a similar temporal expression tendency with a high level in the later period of incubation (embryonic day 19 [E19] or 1-day-old) in the brain, liver, and pectoralis. While CDS2-4 presented a distinct temporal expression pattern in these tissues, CDS2-4 levels peaked at 21 days in the brain and pectoralis, while liver CDS2-4 mRNA levels were highest at the early stage of hatching (E10). Total CDS2 (P < 0.001) and CDS2-4 (P = 0.0090) mRNA levels in the liver were differentially regulated throughout development of the chicken. Exogenous insulin significantly downregulated the level of total CDS2 at 240 min in the pectoralis of Silky chickens (P < 0.01). Total CDS2 levels in the liver of Silky chickens were higher than that of the broiler in the basal state and after insulin stimulation. Conclusion: Chicken CDS2 has multiple transcripts with variation at the 3′-UTR, which was prominently expressed in adipose tissue. Total CDS2 and CDS2-4 presented distinct spatio-temporal expression patterns, and they were differentially regulated with age in liver. Insulin could regulate chicken CDS2 levels in a breed- and tissue-specific manner.

Download Full-text