Genome-wide identification and expression profiling reveal the regulatory role of U-box E3 ubiquitin ligase genes in strawberry fruit ripening and abiotic stresses resistance

The plant U-box (PUB) proteins are a type of E3 ubiquitin ligases well known for their functions in response to various stresses. They are also related to fruit development and ripening. However, PUB members possess such roles that remain unclear in strawberry. In this study, 155 PUB genes were identified in octoploid strawberry and classified into four groups. Their promoters possessed a variety of cis-acting elements, most of which are associated with abiotic stresses, followed by phytohormones response and development. Protein-protein interaction analysis suggested that FaU-box members could interact with each other as well as other proteins involved in hormone signaling and stress resistance. Transcriptome-based and RT-qPCR expression analysis revealed the potential involvement of FaU-box genes in resistance to stresses and fruit ripening. Of these, FaU-box98 and FaU-box136 were positively while FaU-box52 was negatively related to strawberry ripening. FaU-box98 comprehensively participated in resistance of ABA, cold, and salt, while FaU-box83 and FaU-box136 were broadly associated with drought and salt stresses. FaU-box18 and FaU-box52 were ABA-specific; FaU-box3 was specific to salt stress. In addition, the functional analysis of a randomly selected FaU-box (FaU-box127) showed that the transient overexpression of FaU-box127 promoted the ripening of strawberry fruit, along with significant changes in the expression levels of some ripening-related genes and the content of organic acid and soluble sugar. Overall, these findings provided comprehensive information about the FaU-box gene family and identified the potential FaU-box members participating in stress resistance and strawberry fruit ripening regulation.

[1]  Jian-Ping An,et al.  Apple U-box-type E3 ubiquitin ligase MdPUB23 reduces cold-stress tolerance by degrading the cold-stress regulatory protein MdICE1 , 2022, Horticulture research.

[2]  Haoru Tang,et al.  Alterations of Phenylpropanoid Biosynthesis Lead to the Natural Formation of Pinkish-Skinned and White-Fleshed Strawberry (Fragaria × ananassa) , 2022, International journal of molecular sciences.

[3]  H. Hellmann,et al.  Plant E3 Ligases and Their Role in Abiotic Stress Response , 2022, Cells.

[4]  M. Quint,et al.  Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling. , 2022, Annual review of plant biology.

[5]  M. Zeinalabedini,et al.  Genome-wide identification of StU-box gene family and assessment of their expression in developmental stages of Solanum tuberosum , 2022, Journal of Genetic Engineering and Biotechnology.

[6]  Chaonan Li,et al.  How Many Faces Does the Plant U-Box E3 Ligase Have? , 2022, International journal of molecular sciences.

[7]  Ya Luo,et al.  Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening , 2022, BMC plant biology.

[8]  K. Kang,et al.  Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice (Oryza sativa) , 2021, International journal of molecular sciences.

[9]  Jianquan Liu,et al.  The U‐box E3 ubiquitin ligase PalPUB79 positively regulates ABA‐dependent drought tolerance via ubiquitination of PalWRKY77 in Populus , 2021, Plant biotechnology journal.

[10]  Aide Wang,et al.  Ethylene-activated MdPUB24 mediates ubiquitination of MdBEL7 to promote chlorophyll degradation in apple fruit. , 2021, The Plant journal : for cell and molecular biology.

[11]  Xiaosan Huang,et al.  Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri) , 2021, BMC Plant Biology.

[12]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[13]  Baoshan Wang,et al.  Arabidopsis U-box E3 ubiquitin ligase PUB11 negatively regulates drought tolerance by degrading the receptor-like protein kinases LRR1 and KIN7. , 2020, Journal of integrative plant biology.

[14]  Maohui Luo,et al.  Identification of the Cytosolic Glucose-6-Phosphate Dehydrogenase Gene from Strawberry Involved in Cold Stress Response , 2020, International journal of molecular sciences.

[15]  Zhenchang Liang,et al.  Grapevine U-box E3 ubiquitin ligase VlPUB38 negatively regulates fruit ripening by facilitating abscisic-aldehyde oxidase degradation. , 2020, Plant & cell physiology.

[16]  Tengbo Huang,et al.  Plant U-box E3 ligases PUB25 and PUB26 control organ growth in Arabidopsis. , 2020, The New phytologist.

[17]  Hetong Lin,et al.  Genome-wide investigation and analysis of U-box Ubiquitin–Protein ligase gene family in apple: Expression profiles during Penicillium expansum infection process , 2020 .

[18]  Bhaskar Sharma,et al.  Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato , 2020, Scientific Reports.

[19]  Ya Luo,et al.  ABA and sucrose co-regulate strawberry fruit ripening and show inhibition of glycolysis , 2019, Molecular Genetics and Genomics.

[20]  W. Wang,et al.  Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruits of melting flesh and stony hard peach varieties , 2019, BMC Genomics.

[21]  Jian-Min Zhou,et al.  PUB25 and PUB26 Promote Plant Freezing Tolerance by Degrading the Cold Signaling Negative Regulator MYB15. , 2019, Developmental cell.

[22]  Xian-bo Zheng,et al.  Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruits of melting flesh and stony hard peach varieties , 2019, BMC Genomics.

[23]  Jeffrey P. Mower,et al.  Origin and evolution of the octoploid strawberry genome , 2019, Nature Genetics.

[24]  Ping Zheng,et al.  15 years of GDR: New data and functionality in the Genome Database for Rosaceae , 2018, Nucleic Acids Res..

[25]  Cheng-qiang He,et al.  Abiotic Stresses: General Defenses of Land Plants and Chances for Engineering Multistress Tolerance , 2018, Front. Plant Sci..

[26]  Huigang Hu,et al.  Genome-Wide Identification and Analysis of U-Box E3 Ubiquitin-Protein Ligase Gene Family in Banana , 2018, International journal of molecular sciences.

[27]  Xiaomei Liu,et al.  Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry , 2018, PloS one.

[28]  Jelle Van Leene,et al.  Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs , 2018, Front. Plant Sci..

[29]  M. Trujillo.  News from the PUB: plant U-box type E3 ubiquitin ligases. , 2018, Journal of experimental botany.

[30]  Qingzhen Zhao,et al.  The E3 Ligase DROUGHT HYPERSENSITIVE Negatively Regulates Cuticular Wax Biosynthesis by Promoting the Degradation of Transcription Factor ROC4 in Rice , 2017, Plant Cell.

[31]  Wenyu Yang,et al.  E3 Ubiquitin Ligases: Ubiquitous Actors in Plant Development and Abiotic Stress Responses. , 2017, Plant & cell physiology.

[32]  Wei Wei,et al.  The WRKY transcription factors in the diploid woodland strawberry Fragaria vesca: Identification and expression analysis under biotic and abiotic stresses. , 2016, Plant physiology and biochemistry : PPB.

[33]  D. Joshi,et al.  Role of Ubiquitin-Mediated Degradation System in Plant Biology , 2016, Front. Plant Sci..

[34]  J. Gai,et al.  Genome-Wide Identification of Soybean U-Box E3 Ubiquitin Ligases and Roles of GmPUB8 in Negative Regulation of Drought Stress Response in Arabidopsis. , 2016, Plant & cell physiology.

[35]  K. R. Reddy,et al.  Abscisic Acid and Abiotic Stress Tolerance in Crop Plants , 2016, Front. Plant Sci..

[36]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[37]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[38]  Yanxia Zhao,et al.  Sucrose functions as a signal involved in the regulation of strawberry fruit development and ripening. , 2013, The New phytologist.

[39]  R. Ewan,et al.  The ubiquitin-proteasome system: central modifier of plant signalling. , 2012, The New phytologist.

[40]  W. Kim,et al.  Roles of Four Arabidopsis U-Box E3 Ubiquitin Ligases in Negative Regulation of Abscisic Acid-Mediated Drought Stress Responses1[C][W][OA] , 2012, Plant Physiology.

[41]  Stephen P. Ficklin,et al.  Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms , 2011, PloS one.

[42]  Yuanyue Shen,et al.  Abscisic acid perception and signaling transduction in strawberry: A model for non-climacteric fruit ripening , 2011, Plant signaling & behavior.

[43]  Yuan-Yue Shen,et al.  Abscisic Acid Plays an Important Role in the Regulation of Strawberry Fruit Ripening1[W][OA] , 2011, Plant Physiology.

[44]  D. Goring,et al.  Altered Germination and Subcellular Localization Patterns for PUB44/SAUL1 in Response to Stress and Phytohormone Treatments , 2011, PloS one.

[45]  Narmada Thanki,et al.  CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..

[46]  M. Estelle,et al.  The ubiquitin-proteasome system regulates plant hormone signaling. , 2010, The Plant journal : for cell and molecular biology.

[47]  Zhen Su,et al.  plantsUPS: a database of plants' Ubiquitin Proteasome System , 2009, BMC Genomics.

[48]  D. Goring,et al.  The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates. , 2009, Journal of experimental botany.

[49]  J. Gough,et al.  Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins. , 2008, Molecular plant.

[50]  C. O'Shea,et al.  Biochemical function of typical and variant Arabidopsis thaliana U-box E3 ubiquitin-protein ligases. , 2008, The Biochemical journal.

[51]  Howard Riezman,et al.  Proteasome-Independent Functions of Ubiquitin in Endocytosis and Signaling , 2007, Science.

[52]  Jun Li,et al.  KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging , 2007, Genom. Proteom. Bioinform..

[53]  B. Mezzetti,et al.  The defH9-iaaM auxin-synthesizing gene increases plant fecundity and fruit production in strawberry and raspberry , 2004, BMC biotechnology.

[54]  L. Hurst.  The Ka/Ks ratio: diagnosing the form of sequence evolution. , 2002, Trends in genetics : TIG.

[55]  Cam Patterson,et al.  A New Gun in Town: The U Box Is a Ubiquitin Ligase Domain , 2002, Science's STKE.

[56]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[57]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[58]  Thomas D. Schmittgen,et al.  Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 2 DD C T Method , 2022 .