scholarly journals Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

2020 ◽  
Author(s):  
Ricardo Nilo-Poyanco ◽  
Carol Moraga ◽  
Gianfranco Benedetto ◽  
Ariel Orellana ◽  
Andréa Miyasaka Almeida
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Protein Localization ◽  
Gene Expression Pattern ◽  
Shotgun Proteomics ◽  
Protein Accumulation ◽  
Ripe Fruit ◽  
Ripening Process ◽  
Transcriptional Activator Protein

Abstract BackgroundFruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.ResultsTo accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2,740 proteins, using the peach genome reference v1. After data pre-treatment, 1,663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase and an ACC oxidase. These genes would be regulated by transcription factors enriched in zinc finger and GAGA-binding transcriptional activator protein domains.ConclusionsShotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from firm to soft fruit.

scholarly journals Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

2020 ◽  
Author(s):  
Ricardo Nilo-Poyanco ◽  
Carol Moraga ◽  
Gianfranco Benedetto ◽  
Ariel Orellana ◽  
Andréa Miyasaka Almeida
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Protein Localization ◽  
Gene Expression Pattern ◽  
Acc Oxidase ◽  
Shotgun Proteomics ◽  
Protein Accumulation ◽  
Ripe Fruit ◽  
Ripening Process

Abstract BackgroundFruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.ResultsTo accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2,740 proteins, using the peach genome reference v1. After data pre-treatment, 1,663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.ConclusionsShotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

scholarly journals Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ricardo Nilo-Poyanco ◽  
Carol Moraga ◽  
Gianfranco Benedetto ◽  
Ariel Orellana ◽  
Andrea Miyasaka Almeida
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Protein Localization ◽  
Gene Expression Pattern ◽  
Acc Oxidase ◽  
Shotgun Proteomics ◽  
Protein Accumulation ◽  
Ripe Fruit ◽  
Ripening Process

Abstract Background Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening. Results To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively. Conclusions Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

scholarly journals Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

2020 ◽  
Author(s):  
Ricardo Nilo-Poyanco ◽  
Carol Moraga ◽  
Gianfranco Benedetto ◽  
Ariel Orellana ◽  
Andréa Miyasaka Almeida
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Protein Localization ◽  
Gene Expression Pattern ◽  
Acc Oxidase ◽  
Shotgun Proteomics ◽  
Protein Accumulation ◽  
Ripe Fruit ◽  
Ripening Process

Abstract Background Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.Results To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2,740 proteins, using the peach genome reference v1. After data pre-treatment, 1,663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.Conclusions Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

Cell Wall Physicochemical Properties as Indicators of Peach Quality During Fruit Ripening after Cold Storage

2008 ◽  
Vol 14 (4) ◽  
pp. 385-391 ◽  
Author(s):  
G.A. Manganaris ◽  
M. Vasilakakis ◽  
I. Mignani ◽  
A. Manganaris
Keyword(s):  
Cell Wall ◽  
Physicochemical Properties ◽  
Shelf Life ◽  
Cold Storage ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Chilling Injury ◽  
Eating Quality ◽  
Peach Fruit ◽  
Cell Rupture

A comparative study between melting flesh peach fruit (Prunus persica L. Batsch cvs. Royal Glory and Morettini No 2) with contrasting tissue firmness during their on-tree ripening was conducted. Such fruit were cold stored (0 °C) for 4 and 6 weeks, and subsequently transferred at 25 °C (shelf life) for up to 5 days and evaluated for quality attributes and cell wall physicochemical properties. Data were partly unexpected, since fruit of the soft cultivar (Morettini No 2) were characterized by lower exo- and endo-PG activity, lower amounts of ethylene evolution, as well as higher amounts of endogenous calcium bound in the cell wall compared to fruit of the firmer cultivar (Royal Glory). These differences may be attributed to the incidence of chilling injury symptoms, evident as loss of juiciness in Morettini No 2 fruit, while Royal Glory fruit were characterized by acceptable appearance and eating quality even after 6 weeks cold storage plus 5 days shelf life, as the fruit softened gradually without cell rupture. Overall results showed that no direct relationship between cell wall physicochemical properties and sensory attributes can be established, indicating the complexity of peach fruit ripening. Since fruit of both cultivars presented similar tissue firmness after 5 days shelf life an attempt to distinguish normal peach fruit softening from cell rupture-chilling injury also has been made in the current study.

scholarly journals Reconstruction ofmreBExpression in Staphylococcus aureus via a Collection of New Integrative Plasmids

2014 ◽  
Vol 80 (13) ◽  
pp. 3868-3878 ◽  
Author(s):  
Ana Yepes ◽  
Gudrun Koch ◽  
Andrea Waldvogel ◽  
Juan-Carlos Garcia-Betancur ◽  
Daniel Lopez
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Cell Biology ◽  
Genetic Manipulation ◽  
Protein Localization ◽  
Antibiotic Resistance Genes ◽  
Wall Material ◽  
Content Type ◽  
Genetic Manipulations ◽  
Discrete Structures

ABSTRACTProtein localization has been traditionally explored in unicellular organisms, whose ease of genetic manipulation facilitates molecular characterization. The two rod-shaped bacterial modelsEscherichia coliandBacillus subtilishave been prominently used for this purpose and have displaced other bacteria whose challenges for genetic manipulation have complicated any study of cell biology. Among these bacteria is the spherical pathogenic bacteriumStaphylococcus aureus. In this report, we present a new molecular toolbox that facilitates gene deletion in staphylococci in a 1-step recombination process and additional vectors that facilitate the insertion of diverse reporter fusions into newly identified neutral loci of theS. aureuschromosome. Insertion of the reporters does not add any antibiotic resistance genes to the chromosomes of the resultant strains, thereby making them amenable for further genetic manipulations. We used this toolbox to reconstitute the expression ofmreBinS. aureus, a gene that encodes an actin-like cytoskeletal protein which is absent in coccal cells and is presumably lost during the course of speciation. We observed that inS. aureus, MreB is organized in discrete structures in association with the membrane, leading to an unusual redistribution of the cell wall material. The production of MreB also caused cell enlargement, but it did not revert staphylococcal shape. We present interactions of MreB with key staphylococcal cell wall-related proteins. This work facilitates the useS. aureusas a model system in exploring diverse aspects of cellular microbiology.

scholarly journals A Banana PHD-Type Transcription Factor MaPHD1 Represses a Cell Wall-Degradation Gene MaXTH6 during Fruit Ripening

2017 ◽  
Vol 3 (5) ◽  
pp. 190-198 ◽  
Author(s):  
Wei WEI ◽  
Zhongqi FAN ◽  
Jianye CHEN ◽  
Jianfei KUANG ◽  
Wangjin LU ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factor ◽  
Fruit Ripening ◽  
Cell Wall Degradation ◽  
A Cell

scholarly journals Characterization and Transcript Profiling of PME and PMEI Gene Families during Peach Fruit Maturation

2017 ◽  
Vol 142 (4) ◽  
pp. 246-259 ◽  
Author(s):  
Yunqing Zhu ◽  
Wenfang Zeng ◽  
Xiaobei Wang ◽  
Lei Pan ◽  
Liang Niu ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
Prunus Persica ◽  
Expression Patterns ◽  
Pectin Methylesterase ◽  
Gene Families ◽  
Naphthaleneacetic Acid ◽  
Regulation Mechanism ◽  
Fruit Softening ◽  
Peach Fruit

Pectins are synthesized and secreted to the cell wall as highly methyl-esterified polymers and demethyl-esterified by pectin methylesterases (PMEs), which are regulated by pectin methylesterase inhibitors (PMEIs). PMEs and PMEIs are involved in pectin degradation during fruit softening; however, the roles of the PME and PMEI gene families during fruit softening remain unclear. Here, 71 PME and 30 PMEI genes were identified in the peach (Prunus persica) genome and shown to be unevenly distributed on all eight chromosomes. The 71 PME genes comprised 36 Type-1 PMEs and 35 Type-2 PMEs. Transcriptome analysis showed that 11 PME and 15 PMEI genes were expressed during fruit ripening in melting flesh (MF) and stony-hard (SH) peaches. Three PME and five PMEI genes were expressed at higher levels in MF than in SH fruit and exhibited softening-associated expression patterns. Upstream regulatory cis elements of these genes related to hormone response, especially naphthaleneacetic acid and ethylene, were investigated. One PME (Prupe.7G192800) and two PMEIs (Prupe.1G114500 and Prupe.2G279800), and their promoters were identified as potential targets for future studies on the biochemical metabolism and regulation of fruit ripening. The comprehensive data generated in this study will improve our understanding of the PME and PMEI gene families in peach. However, further detailed investigation is necessary to elucidate the biochemical function and regulation mechanism of the PME and PMEI genes during peach fruit ripening.

scholarly journals Chitosan-based Edible Coating Prolongs Musa troglodytarum L. (‘Pisang Tongkat Langit’) Fruit Shelf-life and Changes the ACS1 and ACO1 Gene Expression Profile

2020 ◽  
Vol 43 (4) ◽  
Author(s):  
Cindy Novianti ◽  
Fenny Martha Dwivany
Keyword(s):  
Gene Expression ◽  
Shelf Life ◽  
Expression Pattern ◽  
Expression Analysis ◽  
Fruit Ripening ◽  
Gene Expression Analysis ◽  
Gene Expression Pattern ◽  
Edible Coating ◽  
Chitosan Coating ◽  
Fruit Shelf Life

Musa troglodytarum L. (‘Pisang Tongkat Langit’), a banana cultivar which originated from Eastern Indonesia, has an economic potential due to the high β-carotene content on its pulp. Being a climacteric fruit, M. troglodytarum has a short shelf-life that can reduce fruit quality. In this study, the effect of 1.25% (w/v) chitosan coating on M. troglodytarum fruit shelf-life and ACS1 and ACO1 gene expression analysis using quantitative PCR were evaluated. Results showed that the application of chitosan coating delayed the fruit ripening process for two days by delaying several fruit physical and chemical changes. ACS1 and ACO1 gene expression analysis showed a different expression pattern, the expression level was lower on chitosan-coated fruits on the first day compared to control. In conclusion, chitosan-based edible coating delayed M. troglodytarum fruit ripening and changed the ACS1 and ACO1 gene expression pattern, compared with the chitosan coating effect on Cavendish banana which also prolonged fruit ripening and suppressed ACS1 and ACO1 expression in a previous research.

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