Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development

2019 ◽  
Vol 18 (3) ◽  
pp. 982-994 ◽  
Author(s):  
Zhoubin Liu ◽  
Junheng Lv ◽  
Zhuqing Zhang ◽  
Heng Li ◽  
Bozhi Yang ◽  
...  
Keyword(s):  
Fruit Development ◽  
Metabolic Pathways ◽  
Proteome Analysis ◽  
Pepper Fruit

scholarly journals Identification of Optimal Reference Genes for Normalization of qPCR Analysis during Pepper Fruit Development

2017 ◽  
Vol 8 ◽  
Author(s):  
Yuan Cheng ◽  
Xin Pang ◽  
Hongjian Wan ◽  
Golam J. Ahammed ◽  
Jiahong Yu ◽  
...  
Keyword(s):  
Fruit Development ◽  
Reference Genes ◽  
Qpcr Analysis ◽  
Pepper Fruit

Anthocyanin accumulation and expression analysis of biosynthesis-related genes during chili pepper fruit development

2013 ◽  
Vol 57 (1) ◽  
pp. 49-55 ◽  
Author(s):  
C. Aza-Gonzalez ◽  
L. Herrera-Isidron ◽  
H. G. Nunez-Palenius ◽  
O. Martinez De La Vega ◽  
N. Ochoa-Alejo
Keyword(s):  
Expression Analysis ◽  
Fruit Development ◽  
Chili Pepper ◽  
Anthocyanin Accumulation ◽  
Pepper Fruit

Proteome Analysis of Drosophila Mutants Identifies a Regulatory Role for 14–3–3ε in Metabolic Pathways

2017 ◽  
Vol 16 (5) ◽  
pp. 1976-1987
Author(s):  
Yeap S. Ng ◽  
Alexandra Sorvina ◽  
Christie A. Bader ◽  
Florian Weiland ◽  
Angel F. Lopez ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Proteome Analysis ◽  
Regulatory Role ◽  
Drosophila Mutants

scholarly journals Analysis of Quantitative Traits in Pepper Using Molecular Markers

2000 ◽  
Author(s):  
Ilan Paran ◽  
Molly Jahn
Keyword(s):  
Ssr Markers ◽  
Fruit Quality ◽  
Fruit Development ◽  
Simple Sequence Repeat ◽  
Quantitative Traits ◽  
Fruit Shape ◽  
Sequence Repeat ◽  
Molecular Tools ◽  
Pepper Fruit ◽  
Simple Sequence

Original objectives: The overall goal of the proposal was to determine the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoids content (3) Determine possible association between capsaicinoids and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoids in pepper fruit and identify candidate genes for C. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was only little known prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous simple sequence repeat (SSR) markers and the integration of several independent maps into a single resource map that consists of over 2000 markers. Unlike previous maps that consisted mostly of tomato-originated RFLP markers, the SSR-based map consists of largely pepper markers. Therefore, the SSR and integrated maps provide ample of tools for use in marker-assisted selection for diverse targets throughout the Capsicum genome. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, the most unique characteristics of pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master key for capsaicinoids accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTLs that control capsaicinoids content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTLs that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTLs controlling fruit shape, fs3.1 and fs10.1, that differentiate between elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advancement of our understanding at the genetic and molecular levels of important processes of pepper fruit development. Concomitantly to gaining biological knowledge, we were able to develop molecular tools that can be implemented for pepper improvement. 

scholarly journals Proteome Analysis of Hypoxic Glioblastoma Cells Reveals Sequential Metabolic Adaptation of One-Carbon Metabolic Pathways

2017 ◽  
Vol 16 (11) ◽  
pp. 1906-1921 ◽  
Author(s):  
Kangling Zhang ◽  
Pei Xu ◽  
James L. Sowers ◽  
Daniel F. Machuca ◽  
Barsam Mirfattah ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Proteome Analysis ◽  
Metabolic Adaptation ◽  
Glioblastoma Cells

Proteome analysis on systemic and portal vein plasma reveals differences in metabolic pathways in patients eligible for bariatric surgery

2021 ◽  
Vol 331 ◽  
pp. e171
Author(s):  
V. Moons ◽  
A.S. Meijnikman ◽  
A. Mak ◽  
D. Mendes Bastos ◽  
M. De Brauw ◽  
...  
Keyword(s):  
Bariatric Surgery ◽  
Portal Vein ◽  
Metabolic Pathways ◽  
Proteome Analysis

A differentially expressed proteomic analysis in placental tissues in relation to pungency during the pepper fruit development

PROTEOMICS ◽  
2006 ◽  
Vol 6 (19) ◽  
pp. 5248-5259 ◽  
Author(s):  
Je Min Lee ◽  
Seyoon Kim ◽  
Ji Young Lee ◽  
Eun Young Yoo ◽  
Myeong Cheoul Cho ◽  
...  
Keyword(s):  
Fruit Development ◽  
Proteomic Analysis ◽  
Differentially Expressed ◽  
Pepper Fruit

scholarly journals An R Package for Data Mining Chili Pepper Fruit Transcriptomes

2020 ◽  
Author(s):  
Christian Escoto-Sandoval ◽  
Alan Flores-Díaz ◽  
M. Humberto Reyes-Valdés ◽  
Neftalí Ochoa-Alejo ◽  
Octavio Martinez
Keyword(s):  
Gene Expression ◽  
Data Mining ◽  
Fruit Development ◽  
Expression Profiles ◽  
Open Data ◽  
Enrichment Analysis ◽  
R Package ◽  
Chili Pepper ◽  
Rna Seq ◽  
Pepper Fruit

Abstract Background: Open data sharing is instrumental for the advance of biological sciences. Gene expression is the primary molecular phenotype, usually estimated through RNA-Seq experiments. Large scope interpretation of RNA-Seq results is complicated by the extensive gene expression range, as well as by the diversity of biological sources and experimental treatments. Here we present “Salsa”, an auto-contained R package for extracting useful knowledge about gene expression during the development of chili pepper fruit. Methods and Results: Data from 168 RNA-Seq libraries, comprising more than 3.4 billion reads, were analyzed and curated to represent standardized expression profiles (SEPs) for all genes expressed during fruit development in 12 chili pepper accessions. Accessions have representatives of domesticated varieties, wild ancestors and crosses, covering a broad spectrum of genotypes. Data are organized in a relational way, and functions allow data mining from the level of single genes up to whole genomes, grouping profiles by different criteria. Those include any combination of expression model, accession, protein description and gene ontology (GO) term, among others. Also, GO enrichment analysis can be performed over any set of genes. Conclusions: “Salsa” opens endless possibilities for mining the transcriptome of chili pepper during fruit development.

scholarly journals Comprehensive Phosphoproteomic Analysis of Pepper Fruit Development Provides Insight into Plant Signaling Transduction

2020 ◽  
Vol 21 (6) ◽  
pp. 1962 ◽  
Author(s):  
Zhoubin Liu ◽  
Junheng Lv ◽  
Yuhua Liu ◽  
Jing Wang ◽  
Zhuqing Zhang ◽  
...  
Keyword(s):  
Protein Kinases ◽  
Fruit Development ◽  
Development Stage ◽  
Receptor Protein ◽  
Plant Signaling ◽  
Signaling Transduction ◽  
Calcium Dependent ◽  
Pepper Fruit ◽  
Mitogen Activated Protein ◽  
Dependent Protein

Limited knowledge is available for phosphorylation modifications in pepper (Capsicum annuum L.), especially in pepper fruit development. In this study, we conducted the first comprehensive phosphoproteomic analysis of pepper fruit at four development stage by Tandem Mass Tag proteomic approaches. A total of 2639 unique phosphopeptides spanning 1566 proteins with 4150 nonredundant sites of phosphorylation were identified, among which 2327 peptides in 1413 proteins were accurately quantified at four different stages. Mature Green (MG) to breaker stage showed the largest number of differentially expressed phosphoproteins and the number of downregulated phosphoproteins was significantly higher than that of upregulated after MG stage. Twenty seven phosphorylation motifs, including 22 pSer motifs and five pThr motifs and 85 kinase including 28 serine/threonine kinases, 14 receptor protein kinases, six mitogen-activated protein kinases, seven calcium-dependent protein kinases, two casein kinases, and some other kinases were quantified. Then the dynamic changes of phosphorylated proteins in ethylene and abscisic acid signaling transduction pathways during fruit development were analyzed. Our results provide a cascade of phosphoproteins and a regulatory network of phosphorylation signals, which help to further understand the mechanism of phosphorylation in pepper fruit development.

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