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Di Giacomo M, Vega TA, Cambiaso V, Picardi LA, Rodríguez GR, Pereira da Costa JH. An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life. PLANTS (BASEL, SWITZERLAND) 2023; 12:2812. [PMID: 37570966 PMCID: PMC10421356 DOI: 10.3390/plants12152812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.
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Affiliation(s)
- Melisa Di Giacomo
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Tatiana Alejandra Vega
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Liliana Amelia Picardi
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Javier Hernán Pereira da Costa
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
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Ibrahim MI, Ramadan AM, Amer M, Khan TK, Mohamed NG, Said OA. Deciphering the enigma of RNA editing in the ATP1_alpha subunit of ATP synthase in Triticum aestivum. Saudi J Biol Sci 2023; 30:103703. [PMID: 37389198 PMCID: PMC10300253 DOI: 10.1016/j.sjbs.2023.103703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023] Open
Abstract
There is evidence that RNA editing is related to plant cellular stress as well as electron transport organelles, such as mitochondria. The mitochondrial atp1 gene encodes the alpha-subunit of Atp synthase. Control as well as two periods of drought stress treatments were analyzed in the cDNAs generated from the mitochondrial atp1 gene of two cultivars of Triticum aestivum [Giza 168 (G168) and Gemmiza 10 (GM10)]. Following RNA-seq data assembly, atp1 cDNAs from the control (acc. no. OQ129415), 2-hour (acc. no. OQ129416), and 12-hour (acc. no. OQ129417) time points of the T. aestivum cultivar G168 were obtained. Control (acc. no. OQ129419), 2-hour (acc. no. OQ129420), and 12-hour (acc. no. OQ129421) samples all included reconstructed atp1 transcripts from Gemmiza 10. Atp1 transcripts were assembled using the wheat atp1 gene (acc. no. NC_036024). RNA-seq raw data was utilized to identify 11 RNA editing sites in atp1 in the tolerant cultivar Giza168 and 6 in the sensitive cultivar Gemmiza10. The significant difference in RNA editing observed between control and drought stress conditions in sites led to synonymous amino acids. This led to no change in tertiary structure between tolerant and sensitive cultivars. But the change was focused between produced protein and its correspondence sequence on DNA.
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Affiliation(s)
- Mona I.M. Ibrahim
- College of Biotechnology, Misr University for Science and Technology (MUST), Egypt
| | - Ahmed M. Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marwa Amer
- College of Biotechnology, Misr University for Science and Technology (MUST), Egypt
| | - Thana K. Khan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nermin G. Mohamed
- College of Biotechnology, Misr University for Science and Technology (MUST), Egypt
| | - Osama A. Said
- College of Biotechnology, Misr University for Science and Technology (MUST), Egypt
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Shoaib N, Liu L, Ali A, Mughal N, Yu G, Huang Y. Molecular Functions and Pathways of Plastidial Starch Phosphorylase (PHO1) in Starch Metabolism: Current and Future Perspectives. Int J Mol Sci 2021; 22:ijms221910450. [PMID: 34638789 PMCID: PMC8509025 DOI: 10.3390/ijms221910450] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
Starch phosphorylase is a member of the GT35-glycogen-phosphorylase superfamily. Glycogen phosphorylases have been researched in animals thoroughly when compared to plants. Genetic evidence signifies the integral role of plastidial starch phosphorylase (PHO1) in starch biosynthesis in model plants. The counterpart of PHO1 is PHO2, which specifically resides in cytosol and is reported to lack L80 peptide in the middle region of proteins as seen in animal and maltodextrin forms of phosphorylases. The function of this extra peptide varies among species and ranges from the substrate of proteasomes to modulate the degradation of PHO1 in Solanum tuberosum to a non-significant effect on biochemical activity in Oryza sativa and Hordeum vulgare. Various regulatory functions, e.g., phosphorylation, protein–protein interactions, and redox modulation, have been reported to affect the starch phosphorylase functions in higher plants. This review outlines the current findings on the regulation of starch phosphorylase genes and proteins with their possible role in the starch biosynthesis pathway. We highlight the gaps in present studies and elaborate on the molecular mechanisms of phosphorylase in starch metabolism. Moreover, we explore the possible role of PHO1 in crop improvement.
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Affiliation(s)
- Noman Shoaib
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
| | - Lun Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Nishbah Mughal
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
- Correspondence: (G.Y.); (Y.H.); Tel.: +86-180-0803-9351 (G.Y.); +86-028-8629-0868 (Y.H.)
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (G.Y.); (Y.H.); Tel.: +86-180-0803-9351 (G.Y.); +86-028-8629-0868 (Y.H.)
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