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Wu F, Mai Y, Chen C, Xia R. SynGAP: a synteny-based toolkit for gene structure annotation polishing. Genome Biol 2024; 25:218. [PMID: 39138517 PMCID: PMC11323386 DOI: 10.1186/s13059-024-03359-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Genome sequencing has become a routine task for biologists, but the challenge of gene structure annotation persists, impeding accurate genomic and genetic research. Here, we present a bioinformatics toolkit, SynGAP (Synteny-based Gene structure Annotation Polisher), which uses gene synteny information to accomplish precise and automated polishing of gene structure annotation of genomes. SynGAP offers exceptional capabilities in the improvement of gene structure annotation quality and the profiling of integrative gene synteny between species. Furthermore, an expression variation index is designed for comparative transcriptomics analysis to explore candidate genes responsible for the development of distinct traits observed in phylogenetically related species.
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Affiliation(s)
- Fengqi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China
| | - Yingxiao Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
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Kato Y, Nomura T. Functional characterization of Capsicum chinense vanillin aminotransferase: Detection of vanillylamine-forming activity from vanillin. Biochem Biophys Rep 2024; 38:101692. [PMID: 38571553 PMCID: PMC10987797 DOI: 10.1016/j.bbrep.2024.101692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
In capsaicin biosynthesis, vanillin aminotransferase (VAMT; EC 2.6.1.119) catalyzes the conversion of vanillin (V) to vanillylamine (VA). In vitro analysis of the recombinant VAMT enzyme has been reported; however, this enzyme catalyzed only the V-forming reaction and not the VA-forming reaction, which is inconsistent with the postulated pathway for capsaicin biosynthesis. In this study, we expressed, purified, and characterized functional recombinant VAMT of Capsicum chinense cv. Habanero from an Escherichia coli strain. The enzyme catalyzed reversible transamination between V and VA, and its VA-forming activity was high when γ-aminobutyric acid (GABA) was used as an amino donor. The enzyme exhibited maximum activity at pH 8.0 and 55 °C, and was stable up to 60 °C over a pH range from 4.5 to 8.0. The enzyme was stable in the presence of various chemicals and metal ions. The enzyme accepted several 4-8-carbon long primary amines and ω-amino acids with carbon chains longer than 4 as amino donors despite the narrow specificity of the amino acceptor. Based on its kinetic attributes and localization, VAMT appears to have evolved from GABA-aminotransferase to catalyze reversible transamination between V and VA, and is responsible for VA biosynthesis using GABA as an amino donor in the cytosol of capsicum fruit cells.
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Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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Li Z, Jia Z, Li J, Kang D, Li M, Ma S, Cheng Q, Shen H, Sun L. Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2024; 15:1405190. [PMID: 38984163 PMCID: PMC11231373 DOI: 10.3389/fpls.2024.1405190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/13/2024] [Indexed: 07/11/2024]
Abstract
Introduction Pepper (Capsicum spp.) is a vegetable that is cultivated globally and has undergone extensive domestication, leading to a significant diversification in its agronomic traits. With the advancement of genomics in pepper and the reduction in sequencing costs, the high-throughput detection of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels) has become increasingly critical for analyzing pepper germplasms and improving breeding programs. As a result, there is a pressing need for a cost-effective, high-throughput, and versatile technique suitable for both foreground and background selection in pepper breeding. Methods In the present study, Python-based web scraping scripts were utilized to systematically extract data from published literatures and relevant sequence databases focusing on pepper genomes. Subsequent to data extraction, SNPs and indels were meticulously identified and filtered. This process culminated in the delineation of core polymorphic sites, which were instrumental in the development of specific probes. Following this, comprehensive phenotypic and genotypic analyses were conducted on a diverse collection of 420 pepper germplasms. Concurrently, a genome-wide association study (GWAS) was conducted to elucidate the genetic determinants of helical fruit shape in peppers. Results In this study, a 45K pepper Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip was developed on the GenoBaits platform. This chip is composed of 45,389 probes, of which 42,535 are derived from core polymorphic sites (CPS) in the background genetic landscape, while 2,854 are associated with foreground agronomic traits, spanning across 43 traits. The CPS probes are spaced at an average interval of 68 Kb. We have assessed the performance of this chip on 420 pepper germplasms, with successful capture of target DNA fragments by 45,387 probes. Furthermore, the probe capture ratio surpassed 70% in 410 of the 420 germplasms tested. Using this chip, we have efficiently genotyped 273 germplasms for spiciness levels and elucidated the genetic relationships among 410 pepper germplasms. Our results allowed for precise clustering of sister lines and C. chinense germplasms. In addition, through a GWAS for helical fruit shape, we identified three quantitative trait loci (QTLs): heli2.1, heli11.1, and heli11.2. Within the heli11.1 QTL, a gene encoding the tubulin alpha chain was identified, suggesting its potential role in the helical growth pattern of pepper fruits. Discussion In summary, the 45K pepper GBTS liquid-phase gene chip offers robust detection of polymorphic sites and is a promising tool for advancing research into pepper germplasm and the breeding of new pepper varieties.
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Affiliation(s)
- Zixiong Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Zhiqi Jia
- Department of Vegetable Science, College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jisuo Li
- Beijing Bona Oriental Agricultural Technology Development Co., Ltd, Beijing, China
| | - Dongmu Kang
- Beijing Bona Oriental Agricultural Technology Development Co., Ltd, Beijing, China
| | - Mingxuan Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Shijie Ma
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
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Nakaniwa R, Misawa Y, Nakasato S, Sano K, Tanaka Y, Nakatani S, Kobata K. Biochemical Aspects of Putative Aminotransferase Responsible for Converting Vanillin to Vanillylamine in the Capsaicinoid Biosynthesis Pathway in Capsicum Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:559-565. [PMID: 38134368 DOI: 10.1021/acs.jafc.3c07369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The biosynthesis pathway of capsaicinoids includes the conversion of vanillin to vanillylamine, where putative aminotransferase (pAMT) is thought to be the enzyme responsible in Capsicum plants. The objectives of this study were to prove that pAMT is the enzyme responsible for this conversion in plants and to clarify its catalytic properties using biochemical methods. Both an extract of habanero placenta and recombinant pAMT (rpAMT) constructed by using an Escherichia coli expression system were able to convert vanillin to vanillylamine in the presence of γ-aminobutyric acid as an amino donor and pyridoxal phosphate as a coenzyme. Conversion from vanillin to vanillylamine by the placenta extract was significantly attenuated by adding an anti-pAMT antibody to the reaction system. The amino donor specificity and affinity for vanillin of rpAMT were similar to those of the placenta extract. We thus confirmed that pAMT is the enzyme responsible for the conversion of vanillin to vanillylamine in capsaicinoid synthesis in Capsicum fruits. Therefore, we propose that pAMT should henceforth be named vanillin aminotransferase (VAMT).
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Affiliation(s)
- Ryota Nakaniwa
- Graduate School of Pharmaceutical Sciences, Josai University, Saitama 350-0295, Japan
| | - Yuki Misawa
- Graduate School of Pharmaceutical Sciences, Josai University, Saitama 350-0295, Japan
| | - Saika Nakasato
- Graduate School of Pharmaceutical Sciences, Josai University, Saitama 350-0295, Japan
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, Saitama 350-0295, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Sachie Nakatani
- Graduate School of Pharmaceutical Sciences, Josai University, Saitama 350-0295, Japan
| | - Kenji Kobata
- Graduate School of Pharmaceutical Sciences, Josai University, Saitama 350-0295, Japan
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MYB24 Negatively Regulates the Biosynthesis of Lignin and Capsaicin by Affecting the Expression of Key Genes in the Phenylpropanoid Metabolism Pathway in Capsicum chinense. Molecules 2023; 28:molecules28062644. [PMID: 36985616 PMCID: PMC10054932 DOI: 10.3390/molecules28062644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The wide application of pepper is mostly related to the content of capsaicin, and phenylpropanoid metabolism and its branch pathways may play an important role in the biosynthesis of capsaicin. The expression level of MYB24, a transcription factor screened from the transcriptome data of the pepper fruit development stage, was closely related to the spicy taste. In this experiment, CcMYB24 was cloned from Hainan Huangdenglong pepper, a hot aromatic pepper variety popular in the world for processing, and its function was confirmed by tissue expression characteristics, heterologous transformation in Arabidopsis thaliana, and VIGS technology. The results showed that the relative expression level of CcMYB24 was stable in the early stage of pepper fruit development, and increased significantly from 30 to 50 days after flowering. Heterologous expression led to a significant increase in the expression of CcMYB24 and decrease in lignin content in transgenic Arabidopsis thaliana plants. CcMYB24 silencing led to a significant increase in the expression of phenylpropanoid metabolism pathway genes PAL, 4CL, and pAMT; lignin branch CCR1 and CAD; and capsaicin pathway CS, AT3, and COMT genes in the placenta of pepper, with capsaicin content increased by more than 31.72% and lignin content increased by 20.78%. However, the expression of PAL, pAMT, AT3, COMT, etc., in the corresponding pericarps did not change significantly. Although CS, CCR1, and CAD increased significantly, the relative expression amount was smaller than that in placental tissue, and the lignin content did not change significantly. As indicated above, CcMYB24 may negatively regulate the formation of capsaicin and lignin by regulating the expression of genes from phenylpropanoid metabolism and its branch pathways.
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Shams M, Yuksel EA, Agar G, Ekinci M, Kul R, Turan M, Yildirim E. Biosynthesis of capsaicinoids in pungent peppers under salinity stress. PHYSIOLOGIA PLANTARUM 2023; 175:e13889. [PMID: 36905231 DOI: 10.1111/ppl.13889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
The synthesis of capsaicinoids occurs in the placenta of the fruits of pungent peppers. However, the mechanism of capsaicinoids' biosynthesis in pungent peppers under salinity stress conditions is unknown. The Habanero and Maras genotypes, the hottest peppers in the world, were chosen as plant material for this study, and they were grown under normal and salinity (5 dS m-1 ) conditions. The results showed that salinity stress harmed plant growth but increased the capsaicin content by 35.11% and 37.00%, as well as the dihydrocapsaicin content by 30.82% and 72.89% in the fruits of the Maras and Habanero genotypes, respectively, at 30 days after planting. The expression analysis of key genes in capsaicinoids biosynthesis revealed that the PAL1, pAMT, KAS, and PUN1 genes were overexpressed in the vegetative and reproductive organs of pungent peppers under normal conditions. However, under salinity stress, overexpression of PAL1, pAMT, and PUN1 genes was identified in the roots of both genotypes, which was accompanied by an increase in capsaicin and dihydrocapsaicin content. The findings showed that salinity stress caused an enhancement in the capsaicin and dihydrocapsaicin contents in the roots, leaves, and fruits of pungent peppers. Nonetheless, it was found that the production of capsaicinoids is generally not restricted to the fruits of pungent peppers.
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Affiliation(s)
- Mostafakamal Shams
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Esra Arslan Yuksel
- Department of Biotechnology, Faculty of Agriculture, Atatürk University, Erzurum, 25240, Turkey
| | - Guleray Agar
- Department of Biology, Faculty of Science, Atatürk University, Erzurum, 25240, Turkey
| | - Melek Ekinci
- Department of Horticulture, Faculty of Agriculture, Atatürk University, Erzurum, 25240, Turkey
| | - Raziye Kul
- Department of Horticulture, Faculty of Agriculture, Atatürk University, Erzurum, 25240, Turkey
| | - Metin Turan
- Department of Genetic and Bioengineering, Yeditepe University, Istanbul, Turkey
| | - Ertan Yildirim
- Department of Horticulture, Faculty of Agriculture, Atatürk University, Erzurum, 25240, Turkey
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Zhang W, Wu D, Zhang L, Zhao C, Shu H, Cheng S, Wang Z, Zhu J, Liu P. Identification and expression analysis of capsaicin biosynthesis pathway genes at genome level in Capsicum chinense. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2071633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Wei Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Dan Wu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Liping Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Chengzhi Zhao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Jie Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Pingwu Liu
- Fang Zhiyuan Academician Team Innovation Center of Hainan Province, Haikou, Hainan, PR China
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Yi S, Lee DG, Back S, Hong JP, Jang S, Han K, Kang BC. Genetic mapping revealed that the Pun2 gene in Capsicum chacoense encodes a putative aminotransferase. FRONTIERS IN PLANT SCIENCE 2022; 13:1039393. [PMID: 36388488 PMCID: PMC9664168 DOI: 10.3389/fpls.2022.1039393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Several genes regulating capsaicinoid biosynthesis including Pun1 (also known as CS), Pun3, pAMT, and CaKR1 have been studied. However, the gene encoded by Pun2 in the non-pungent Capsicum chacoense is unknown. This study aimed to identify the Pun2 gene by genetic mapping using interspecific (C. chacoense × Capsicum annuum) and intraspecific (C. chacoense × C. chacoense) populations. QTL mapping using the interspecific F2 population revealed two major QTLs on chromosomes 3 and 9. Two bin markers within the QTL regions on two chromosomes were highly correlated with the capsaicinoid content in the interspecific population. The major QTL, Pun2_PJ_Gibbs_3.11 on chromosome 3, contained the pAMT gene, indicating that the non-pungency of C. chacoense may be attributed to a mutation in the pAMT gene. Sequence analysis revealed a 7 bp nucleotide insertion in the 8th exon of pAMT of the non-pungent C. chacoense. This mutation resulted in the generation of an early stop codon, resulting in a truncated mutant lacking the PLP binding site, which is critical for pAMT enzymatic activity. This insertion co-segregated with the pungency phenotype in the intraspecific F2 population. We named this novel pAMT allele pamt11 . Taken together, these data indicate that the non-pungency of C. chacoense is due to the non-functional pAMT allele, and Pun2 encodes the pAMT gene.
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Affiliation(s)
| | | | | | | | | | | | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, South Korea
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Sun B, Chen C, Song J, Zheng P, Wang J, Wei J, Cai W, Chen S, Cai Y, Yuan Y, Zhang S, Liu S, Lei J, Cheng G, Zhu Z. The Capsicum MYB31 regulates capsaicinoid biosynthesis in the pepper pericarp. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 176:21-30. [PMID: 35190336 DOI: 10.1016/j.plaphy.2022.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Pepper (Capsicum) are consumed worldwide as vegetables and food additives due to their pungent taste. Capsaicinoids are the bioactive compounds that confer the desired pungency to pepper fruits. Capsaicinoid biosynthesis was thought to occur exclusively in fruit placenta. Recently, biosynthesis in the pericarp of extremely pungent varieties was discovered, however, the mechanism of capsaicinoid biosynthesis regulation in the pericarp remains largely unknown. Here, the capsaicinoid contents of placenta and pericarp were analyzed. The results indicated that the Capsicum chinense pericarp accumulated a vast amount of capsaicinoids. Expression of the master regulator MYB31 and capsaicinoid biosynthesis genes (CBGs) were significantly upregulated in the pericarp in C. chinense accessions compared to accessions in other tested species. Moreover, in fruit of extremely-pungent 'Trinidad Moruga Scorpion' (C. chinense) and low-pungent '59' inbred line (C. annuum), the capsaicinoid accumulation patterns in the pericarp were consistent with expression levels of CBGs and MYB31. Silencing MYB31 in 'Trinidad Moruga Scorpion' pericarp leads to a significantly decreased CBGs transcription level and capsaicinoids content. Taken together, our results provide insights into the molecular mechanism arising from the expression of MYB31 in the pericarp that results in exceedingly hot peppers.
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Affiliation(s)
- Binmei Sun
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Changming Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiali Song
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Peng Zheng
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Juntao Wang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianlang Wei
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Cai
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Siping Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yutong Cai
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yuan Yuan
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Shuanglin Zhang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Shaoqun Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianjun Lei
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Guoju Cheng
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Zhangsheng Zhu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Bhattacharjee B, Hallan V. Geminivirus-Derived Vectors as Tools for Functional Genomics. Front Microbiol 2022; 13:799345. [PMID: 35432267 PMCID: PMC9010885 DOI: 10.3389/fmicb.2022.799345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
A persistent issue in the agricultural sector worldwide is the intensive damage caused to crops by the geminivirus family of viruses. The diverse types of viruses, rapid virus evolution rate, and broad host range make this group of viruses one of the most devastating in nature, leading to millions of dollars' worth of crop damage. Geminiviruses have a small genome and can be either monopartite or bipartite, with or without satellites. Their ability to independently replicate within the plant without integration into the host genome and the relatively easy handling make them excellent candidates for plant bioengineering. This aspect is of great importance as geminiviruses can act as natural nanoparticles in plants which can be utilized for a plethora of functions ranging from vaccine development systems to geminivirus-induced gene silencing (GIGS), through deconstructed viral vectors. Thus, the investigation of these plant viruses is pertinent to understanding their crucial roles in nature and subsequently utilizing them as beneficial tools in functional genomics. This review, therefore, highlights some of the characteristics of these viruses that can be deemed significant and the subsequent successful case studies for exploitation of these potentially significant pathogens for role mining in functional biology.
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Affiliation(s)
- Bipasha Bhattacharjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vipin Hallan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
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Paudel L, Kerr S, Prentis P, Tanurdžić M, Papanicolaou A, Plett JM, Cazzonelli CI. Horticultural innovation by viral-induced gene regulation of carotenogenesis. HORTICULTURE RESEARCH 2022; 9:uhab008. [PMID: 35043183 PMCID: PMC8769041 DOI: 10.1093/hr/uhab008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/31/2021] [Accepted: 09/24/2021] [Indexed: 06/14/2023]
Abstract
Multipartite viral vectors provide a simple, inexpensive and effective biotechnological tool to transiently manipulate (i.e. reduce or increase) gene expression in planta and characterise the function of genetic traits. The development of virus-induced gene regulation (VIGR) systems usually involve the targeted silencing or overexpression of genes involved in pigment biosynthesis or degradation in plastids, thereby providing rapid visual assessment of success in establishing RNA- or DNA-based VIGR systems in planta. Carotenoids pigments provide plant tissues with an array of yellow, orange, and pinkish-red colours. VIGR-induced transient manipulation of carotenoid-related gene expression has advanced our understanding of carotenoid biosynthesis, regulation, accumulation and degradation, as well as plastid signalling processes. In this review, we describe mechanisms of VIGR, the importance of carotenoids as visual markers of technology development, and knowledge gained through manipulating carotenogenesis in model plants as well as horticultural crops not always amenable to transgenic approaches. We outline how VIGR can be utilised in plants to fast-track the characterisation of gene function(s), accelerate fruit tree breeding programs, edit genomes, and biofortify plant products enriched in carotenoid micronutrients for horticultural innovation.
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Affiliation(s)
- Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Stephanie Kerr
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, 2 George Street, Brisbane City, QLD 4000, Australia
- School of Biology and Environmental Sciences, Faculty of Science,
Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, Australia
| | - Peter Prentis
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, 2 George Street, Brisbane City, QLD 4000, Australia
- School of Biology and Environmental Sciences, Faculty of Science,
Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, Australia
| | - Miloš Tanurdžić
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Christopher I Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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Wen J, Lv J, Zhao K, Zhang X, Li Z, Zhang H, Huo J, Wan H, Wang Z, Zhu H, Deng M. Ethylene-Inducible AP2/ERF Transcription Factor Involved in the Capsaicinoid Biosynthesis in Capsicum. FRONTIERS IN PLANT SCIENCE 2022; 13:832669. [PMID: 35310674 PMCID: PMC8928445 DOI: 10.3389/fpls.2022.832669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/14/2022] [Indexed: 05/17/2023]
Abstract
Ethylene is very important in the process of plant development and regulates the biosynthesis of many secondary metabolites. In these regulatory mechanisms, transcription factors (TFs) that mediate ethylene signals play a very important role. Capsaicinoids (CAPs) are only synthesized and accumulated in Capsicum species, causing their fruit to have a special pungent taste, which can protect against attack from herbivores and pathogens. In this study, we identified the TF CcERF2, which is induced by ethylene, and demonstrated its regulatory effect on CAPs biosynthesis. Transcriptome sequencing analysis revealed that the expression patterns of CcERF2 and multiple genes associated with CAPs biosynthesis were basically the same. The spatiotemporal expression results showed CcERF2 was preferentially expressed in the placenta of the spicy fruit. Ethylene can induce the expression of CcERF2 and CAPs biosynthesis genes (CBGs). CcERF2 gene silencing and 1-methylcyclopropene (1-MCP) and pyrazinamide (PZA) treatments caused a decrease in expression of CBGs and a sharp decrease in content of CAPs. The results indicated that CcERF2 was indeed involved in the regulation of structural genes of the CAPs biosynthetic pathway.
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Affiliation(s)
- Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming, China
| | - Junheng Lv
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Kai Zhao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Xiang Zhang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Zuosen Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Hong Zhang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Jinlong Huo
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Hongjian Wan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ziran Wang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Haishan Zhu
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Minghua Deng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
- *Correspondence: Minghua Deng, , orcid.org/0000-0001-8293-9035
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13
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Tanaka Y, Watachi M, Nemoto W, Goto T, Yoshida Y, Yasuba KI, Ohno S, Doi M. Capsaicinoid biosynthesis in the pericarp of chili pepper fruits is associated with a placental septum-like transcriptome profile and tissue structure. PLANT CELL REPORTS 2021; 40:1859-1874. [PMID: 34283265 DOI: 10.1007/s00299-021-02750-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
CAP biosynthesis in the pericarp of chili pepper fruits occurs with an ambiguous boundary in the placental septum and pericarp. Capsaicinoid (CAP) is a pungent ingredient of chili pepper fruits. Generally, CAP biosynthesis is limited to the placental septum of fruits, but it has been reported that its biosynthesis occurs even in the pericarp of some extremely pungent varieties, resulting in a substantial increase in total content. To examine the mechanism of CAP biosynthesis in the pericarp, comparative transcriptome analysis of a variety that produces CAP in the pericarp (MY) and a variety that does not (HB) was carried out. RNA-seq revealed that 2264 genes were differentially expressed in the MY pericarp compared with the HB pericarp. PCA analysis and GO enrichment analysis indicated that the MY pericarp has a gene expression profile more like placental septum than the HB pericarp. The gene expression of CAP biosynthesis-related genes in the MY pericarp changed coordinately with the placental septum during fruit development. In most Capsicum accessions including HB, the distribution of slender epidermal cells producing CAP was limited to the placental septum, and the morphological boundary between the placental septum and pericarp was clear. In some extremely pungent varieties such as MY, slender epidermal cells ranged from the placental septum to the pericarp region, and the pericarp was morphologically similar to the placental septum, such as the absence of large sub-epidermal cells and abundant spaces in the parenchymal tissue. Our data suggest that CAP biosynthesis in the pericarp occurred with an ambiguous boundary in the placental septum and pericarp. These findings contribute to further enhancement of CAP production in chili pepper fruits.
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Affiliation(s)
- Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
| | - Mayuko Watachi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Wakana Nemoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tanjuro Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuichi Yoshida
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Ken-Ichiro Yasuba
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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14
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Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening. PLoS One 2021; 16:e0256319. [PMID: 34428253 PMCID: PMC8384167 DOI: 10.1371/journal.pone.0256319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.
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15
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The pungent-variable sweet chili pepper 'Shishito' (Capsicum annuum) provides insights regarding the relationship between pungency, the number of seeds, and gene expression involving capsaicinoid biosynthesis. Mol Genet Genomics 2021; 296:591-603. [PMID: 33599813 DOI: 10.1007/s00438-021-01763-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Pungent traits caused by capsaicinoids are characteristic of chili peppers (Capsicum spp.), and the pungent-variable sweet chili pepper 'Shishito' (Capsicum annuum) is unique in being known for the pungency in fruits with few seeds. In the present study, we tried to clarify the relationship between the number of seeds and pungency in 'Shishito'. First, we investigated the pungency of 'Shishito' by simple sensory evaluations and quantifications of capsaicinoids by high-performance liquid chromatography. As a result, few-seeded fruits had a larger fluctuation of capsaicinoid content than many-seeded ones. This indicates that the number of seeds, in particular a decrease of the seeds, has some sort of connection with the pungency of 'Shishito'. Then, we analyzed the relationship between pungency and gene expression involving capsaicinoid biosynthesis at the individual fruit level. We vertically separated the placental septum in which capsaicinoids are synthesized and performed quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for 18 genes involved in capsaicinoid biosynthesis. We also used the placental septum for capsaicinoid quantification so that the gene expression levels and capsaicinoid contents in the same fruits were obtained, and their correlations were analyzed using 20 biological replicates. Among the 18 genes, expression levels of 11 genes (WRKY9, CaMYB31, AT3, BCAT, BCKDH, KAS I, KAS III, ACL, CaKR1, FAT, and pAMT) had a significant positive correlation with the capsaicinoid concentration, and they were considered to upregulate capsaicinoid biosynthesis. These results provide new insights regarding the environmental variation of the pungency traits in chili peppers and the relationship between pungency, the number of seeds, and gene expression involved in capsaicinoid biosynthesis.
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16
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Sun B, Zhou X, Chen C, Chen C, Chen K, Chen M, Liu S, Chen G, Cao B, Cao F, Lei J, Zhu Z. Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers. HORTICULTURE RESEARCH 2020; 7:162. [PMID: 33082969 PMCID: PMC7527512 DOI: 10.1038/s41438-020-00381-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/18/2020] [Accepted: 07/13/2020] [Indexed: 05/24/2023]
Abstract
Plant biosynthesis involves numerous specialized metabolites with diverse chemical natures and biological activities. The biosynthesis of metabolites often exclusively occurs in response to tissue-specific combinatorial developmental cues that are controlled at the transcriptional level. Capsaicinoids are a group of specialized metabolites that confer a pungent flavor to pepper fruits. Capsaicinoid biosynthesis occurs in the fruit placenta and combines its developmental cues. Although the capsaicinoid biosynthetic pathway has been largely characterized, the regulatory mechanisms that control capsaicinoid metabolism have not been fully elucidated. In this study, we combined fruit placenta transcriptome data with weighted gene coexpression network analysis (WGCNA) to generate coexpression networks. A capsaicinoid-related gene module was identified in which the MYB transcription factor CaMYB48 plays a critical role in regulating capsaicinoid in pepper. Capsaicinoid biosynthetic gene (CBG) and CaMYB48 expression primarily occurs in the placenta and is consistent with capsaicinoid biosynthesis. CaMYB48 encodes a nucleus-localized protein that primarily functions as a transcriptional activator through its C-terminal activation motif. CaMYB48 regulates capsaicinoid biosynthesis by directly regulating the expression of CBGs, including AT3a and KasIa. Taken together, the results of this study indicate ways to generate robust networks optimized for the mining of CBG-related regulators, establishing a foundation for future research elucidating capsaicinoid regulation.
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Affiliation(s)
- Binmei Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Xin Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Jiangxi Agricultural Engineering College, Zhangshu, 331200 Jiangxi China
| | - Changming Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Chengjie Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Kunhao Chen
- Guangdong Helinong Seeds, Co., Ltd., Shantou, 515800 Guangdong China
- Guangdong Helinong Agricultural Research Institute, Co., Ltd., Shantou, 515800 Guangdong China
| | - Muxi Chen
- Guangdong Helinong Seeds, Co., Ltd., Shantou, 515800 Guangdong China
- Guangdong Helinong Agricultural Research Institute, Co., Ltd., Shantou, 515800 Guangdong China
| | - Shaoqun Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Guoju Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Bihao Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Fanrong Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jianjun Lei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Henry School of Agricultural Science and Engineering, Shaoguan University, Guangdong, 512005 China
| | - Zhangsheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Peking University—Southern University of Science and Technology Joint Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055 China
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17
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Li D, Zhou C, Zhang J, An Q, Wu Y, Li JQ, Pan C. Nanoselenium Foliar Applications Enhance the Nutrient Quality of Pepper by Activating the Capsaicinoid Synthetic Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9888-9895. [PMID: 32809823 DOI: 10.1021/acs.jafc.0c03044] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Increasing the crop quality through enhancement of plant health is a challenging task. In this study, nanoselenium (nano-Se) was sprayed on pepper leaves, and the pepper components were compared to those of selenite. It was found that nano-Se (20 mg/L) resulted in a greater performance of plant health. It increased the chlorophyll and soluble sugar levels, which could activate phenylpropane and branched-chain fatty acid pathways, as well as AT3-related enzymes and gene expressions. These led to an enhancement for the synthesis of capsaicinoids, flavonoids, and total phenols. The nano-Se treatment also significantly promoted the expression of phyto-hormones synthesis genes, and consequently increased jasmonic, abscisic, and salicylic acid levels. Proline pathway-related compounds were increased, which could decrease the malondialdehyde and hydroxyl radical levels in crops. This study shows that nano-Se activated capsaicinoid pathways by enhancing photosynthesis and raising soluble sugar levels. The capsaicinoid contents in peppers were then increased, which consequently promoted the accumulation of secondary metabolites and antioxidants.
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Affiliation(s)
- Dong Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Chunran Zhou
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Jingbang Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Quanshun An
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yangliu Wu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Jia-Qi Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Canping Pan
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
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18
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Misra RC, Sharma S, Garg A, Ghosh S. Virus-Induced Gene Silencing in Sweet Basil (Ocimum basilicum). Methods Mol Biol 2020; 2172:123-138. [PMID: 32557366 DOI: 10.1007/978-1-0716-0751-0_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Virus-induced gene silencing (VIGS) is a powerful reverse genetic tool for rapid functional analysis of plant genes. Over the last decade, VIGS has been widely used for conducting rapid gene knockdown experiment in plants and played a crucial role in advancing applied and basic research in plant science. VIGS was studied extensively in model plants Arabidopsis and tobacco. Moreover, several non-model plants such as Papaver (Hileman et al., Plant J 44:334-341, 2005), Aquilegia (Gould and Kramer, Plant Methods 3:6, 2007), Catharanthus (Liscombe and O'Connor, Phytochemistry 72:1969-1977, 2011), Withania (Singh et al., Plant Biol J 13:1287-1299, 2015), and Ocimum (Misra et al., New Phytol 214:706-720, 2017) were also successfully explored. We have recently developed a robust protocol for VIGS in sweet basil (Ocimum basilicum). Sweet basil, a popular medicinal/aromatic herb, is being studied for the diversity of specialized metabolites produced in it.
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Affiliation(s)
- Rajesh Chandra Misra
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Metabolic Biology Department,, John Innes Centre, Norwich, United Kingdom
| | - Shubha Sharma
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Anchal Garg
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Sumit Ghosh
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.
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19
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Arce-Rodríguez ML, Ochoa-Alejo N. Virus-Induced Gene Silencing (VIGS) in Chili Pepper (Capsicum spp.). Methods Mol Biol 2020; 2172:27-38. [PMID: 32557359 DOI: 10.1007/978-1-0716-0751-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Virus-induced gene silencing (VIGS) is a transcript suppression technique that enables the functional characterization of genes in recalcitrant transformation plants. This technique consists in cloning a short fragment of a gene of interest into a viral vector, such as TRV (Tobacco rattle virus), and this viral construction is used to agro-infiltrate the plant. VIGS induces posttranscriptional gene silencing (PTGS) that results in the specific sequence degradation of target RNAs. Here we describe a VIGS protocol using the Gateway-based TRV vector for the study of genes in chili pepper plants.
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Affiliation(s)
- Magda Lisette Arce-Rodríguez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Gto., Mexico
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Gto., Mexico.
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20
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Arce-Rodríguez ML, Ochoa-Alejo N. Biochemistry and molecular biology of capsaicinoid biosynthesis: recent advances and perspectives. PLANT CELL REPORTS 2019; 38:1017-1030. [PMID: 30941502 DOI: 10.1007/s00299-019-02406-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
The most widely known characteristic of chili pepper fruits is their capacity to produce capsaicinoids, which are responsible for the pungent sensation. The capsaicinoids have several uses in different areas, such as the pharmaceutical, cosmetic and agronomic industries, among others. They are synthesized by the condensation of vanillylamine (derived from phenylalanine) with a branched-chain fatty acid (from valine or leucine precursors), and they generally accumulate in the placental tissue of the chili pepper fruits. The pungency grade depends on the genotype of the plant but is also affected by external stimuli. In recent years, new structural and regulatory genes have been hypothesized to participate in the capsaicinoid biosynthetic pathway. Moreover, the role of some of these genes has been investigated. Substantial progress has been made in discerning the molecular biology of this pathway; however, many questions remain unsolved. We previously reviewed some aspects of the biochemistry and molecular biology of capsaicinoid biosynthesis (Aza-González et al. Plant Cell Rep 30:695-706. Aza-González et al., Plant Cell Rep 30:695-706, 2011), and in this review, we describe advances made by different researchers since our previous review, including the contribution of omics to the knowledge of this pathway.
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Affiliation(s)
- Magda Lisette Arce-Rodríguez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Km 9.6 libramiento norte carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Km 9.6 libramiento norte carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.
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21
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Li C, Hirano H, Kasajima I, Yamagishi N, Yoshikawa N. Virus-induced gene silencing in chili pepper by apple latent spherical virus vector. J Virol Methods 2019; 273:113711. [PMID: 31404574 DOI: 10.1016/j.jviromet.2019.113711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/01/2019] [Accepted: 07/25/2019] [Indexed: 12/30/2022]
Abstract
Apple latent spherical virus (ALSV) can infect a variety of crops, usually without inducing symptoms. Partial gene sequences can be introduced into ALSV vectors for the induction of virus-induced gene silencing (VIGS). These features are beneficial for the estimation of gene functions in plants, with relatively concise experimental manipulations. Given that the infectability of chili peppers (Capsicum spp.) by ALSV was unknown, an ALSV infectivity test was performed on the highly pungent Capsicum chinense cultivar 'Habanero'. The chili pepper plants were not infected after rub-inoculation with a crude homogenate of ALSV-infected Chenopodium quinoa leaves, whereas inoculating them with a concentrated ALSV virus preparation caused an infection. Inoculation with an ALSV RNA preparation by gold particle bombardment resulted in high infection rates (about 90%). The infection was systemic and the infected plants were symptomless. For the induction of VIGS, 201-nucleotide fragments of the putative aminotransferase (pAMT) gene were introduced into the ALSV vector. These ALSV vectors infected 80-90% of RNA-inoculated chili pepper seedlings. Expression of pAMT-mRNA was repressed in the placenta of immature fruit of infected plants. The silencing of pAMT in the infected plants caused a substantial decrease in capsaicin content and a concomitant moderate accumulation of the non-pungent bioactive metabolite capsiate in these plants. These results showed that ALSV could be used to study gene functions by VIGS and to enhance capsiate accumulation in chili pepper through genetic modification.
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Affiliation(s)
- Chunjiang Li
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Hiroto Hirano
- Frontier Research Laboratories, Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa 210-8681, Japan
| | - Ichiro Kasajima
- Agri-Innovation Center, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Noriko Yamagishi
- Agri-Innovation Center, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Nobuyuki Yoshikawa
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan; Agri-Innovation Center, Iwate University, Morioka, Iwate 020-8550, Japan.
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Zhu Z, Sun B, Cai W, Zhou X, Mao Y, Chen C, Wei J, Cao B, Chen C, Chen G, Lei J. Natural variations in the MYB transcription factor MYB31 determine the evolution of extremely pungent peppers. THE NEW PHYTOLOGIST 2019; 223:922-938. [PMID: 31087356 DOI: 10.1111/nph.15853] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 04/05/2019] [Indexed: 05/13/2023]
Abstract
Plants produce countless specialized metabolites crucial for their development and fitness, and many are useful bioactive compounds. Capsaicinoids are intriguing genus-specialized metabolites that confer a pungent flavor to Capsicum fruits, and they are widely applied in different areas. Among the five domesticated Capsicum species, Capsicum chinense has a high content of capsaicinoids, which results in an extremely hot flavor. However, the species-specific upregulation of capsaicinoid-biosynthetic genes (CBGs) and the evolution of extremely pungent peppers are not well understood. We conducted genetic and functional analyses demonstrating that the quantitative trait locus Capsaicinoid1 (Cap1), which is identical to Pun3 contributes to the level of pungency. The Cap1/Pun3 locus encodes the Solanaceae-specific MYB transcription factor MYB31. Capsicum species have evolved placenta-specific expression of MYB31, which directly activates expression of CBGs and results in genus-specialized metabolite production. The capsaicinoid content depends on MYB31 expression. Natural variations in the MYB31 promoter increase MYB31 expression in C. chinense via the binding of the placenta-specific expression of transcriptional activator WRKY9 and augmentation of CBG expression, which promotes capsaicinoid biosynthesis. Our findings provide insights into the evolution of extremely pungent C. chinense, which is due to natural variations in the master regulator, and offers targets for engineering or selecting flavor in Capsicum.
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Affiliation(s)
- Zhangsheng Zhu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Binmei Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Cai
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Zhou
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yanhui Mao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chengjie Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianlang Wei
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bihao Cao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Changming Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Guoju Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianjun Lei
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
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Tsurumaki K, Sasanuma T. Discovery of novel unfunctional pAMT allele pamt 10 causing loss of pungency in sweet bell pepper ( Capsicum annuum L.). BREEDING SCIENCE 2019; 69:133-142. [PMID: 31086491 PMCID: PMC6507711 DOI: 10.1270/jsbbs.18150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/10/2018] [Indexed: 05/29/2023]
Abstract
Pungency is a characteristic trait of pepper (Capsicum spp.). Two genes, Pun1 and pAMT, are known as determinative factors of pepper pungency. To date, it has been considered that most bell-type sweet peppers (called piman and paprika, in Japan) possess the identical mutated Pun1 allele, pun1, whereas pAMT mutated non-pungent pepper has been found only in non-bell-type pepper. In this study, to reconsider the uniformity of the source of non-pungency in sweet bell pepper and explore new genetic resources, the presence of pun1 was investigated in 26 sweet bell pepper varieties. Among them, a seemingly common sweet bell pepper 'Color Piman Yellow' had the intact Pun1, in spite of its non-pungency. Sequencing and linkage analyses revealed that 'Color Piman Yellow' possessed a novel mutated pAMT allele, pamt 10 , that has a nonsense substitution at the 11th exon responsible for non-pungency. This is the first pAMT mutant to be found in sweet bell pepper. The finding that there was a pAMT mutant in sweet bell pepper suggests the possibility that more pAMT mutants exist unconsciously in other sweet bell peppers. The discovery of a new factor of non-pungency contributes to expanding the genetic diversity of sweet pepper varieties.
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Affiliation(s)
- Keiichi Tsurumaki
- United Graduate School of Agricultural Sciences, Iwate University,
3-18-8 Ueda, Morioka, Iwate 020-8550,
Japan
| | - Tsuneo Sasanuma
- United Graduate School of Agricultural Sciences, Iwate University,
3-18-8 Ueda, Morioka, Iwate 020-8550,
Japan
- Faculty of Agriculture, Yamagata University,
1-23 Wakabamachi, Tsuruoka, Yamagata 997-8555,
Japan
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24
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Koeda S, Sato K, Saito H, Nagano AJ, Yasugi M, Kudoh H, Tanaka Y. Mutation in the putative ketoacyl-ACP reductase CaKR1 induces loss of pungency in Capsicum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:65-80. [PMID: 30267113 DOI: 10.1007/s00122-018-3195-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/20/2018] [Indexed: 05/13/2023]
Abstract
A putative ketoacyl-ACP reductase (CaKR1) that was not previously known to be associated with pungency of Capsicum was identified from map-based cloning and functional characterization. The pungency of chili pepper fruits is due to the presence of capsaicinoids, which are synthesized through the convergence of the phenylpropanoid and branched-chain fatty acid pathways. The extensive, global use of pungent and non-pungent peppers underlines the importance of understanding the genetic mechanism underlying capsaicinoid biosynthesis for breeding pepper cultivars. Although Capsicum is one of the earliest domesticated plant genera, the only reported genetic causes of its loss of pungency are mutations in acyltransferase (Pun1) and putative aminotransferase (pAMT). In this study, a single recessive gene responsible for the non-pungency of pepper No.3341 (C. chinense) was identified on chromosome 10 using an F2 population derived from a cross between Habanero and No.3341. Five candidate genes were identified in the target region, within a distance of 220 kb. A candidate gene, a putative ketoacyl-ACP reductase (CaKR1), of No.3341 had an insertion of a 4.5-kb transposable element (TE) sequence in the first intron, resulting in the production of a truncated transcript missing the region coding the catalytic domain. Virus-induced gene silencing of CaKR1 in pungent peppers resulted in the decreased accumulation of capsaicinoids, a phenotype consistent with No.3341. Moreover, GC-MS analysis of 8-methyl-6-nonenoic acid, which is predicted to be synthesized during the elongation cycle of branched-chain fatty acid biosynthesis, revealed that its deficiency in No.3341. Genetic, genomic, transcriptional, silencing, and biochemical precursor analyses performed in combination provide a solid ground for the conclusion that CaKR1 is involved in capsaicinoid biosynthesis and that its disruption results in a loss of pungency.
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Affiliation(s)
- Sota Koeda
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, 619-0218, Japan.
| | - Kosuke Sato
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, 619-0218, Japan
| | - Hiroki Saito
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, 619-0218, Japan
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Okinawa, 907-0002, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
| | - Masaki Yasugi
- Faculty of Engineering, Utsunomiya University, Utsunomiya, Tochigi, 321-8585, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
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25
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Zunun-Pérez AY, Guevara-Figueroa T, Jimenez-Garcia SN, Feregrino-Pérez AA, Gautier F, Guevara-González RG. Effect of foliar application of salicylic acid, hydrogen peroxide and a xyloglucan oligosaccharide on capsiate content and gene expression associated with capsinoids synthesis in Capsicum annuum L. J Biosci 2017; 42:245-250. [DOI: 10.1007/s12038-017-9682-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Kushwaha NK, Chakraborty S. Chilli leaf curl virus-based vector for phloem-specific silencing of endogenous genes and overexpression of foreign genes. Appl Microbiol Biotechnol 2017; 101:2121-2129. [PMID: 27878582 DOI: 10.1007/s00253-016-7964-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/05/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
Geminiviruses are the largest and most devastating group of plant viruses which contain ssDNA as a genetic material. Geminivirus-derived virus-induced gene silencing (VIGS) vectors have emerged as an efficient and simple tool to study functional genomics in various plants. However, previously developed VIGS vectors have certain limitations, owing to their inability to be used in tissue-specific functional study. In the present study, we developed a Chilli leaf curl virus (ChiLCV)-based VIGS vector for its tissue-specific utilization by replacing the coat protein gene (open reading frame (ORF) AV1) with the gene of interest for phytoene desaturase (PDS) of Nicotiana benthamiana. Functional validation of ChiLCV-based VIGS in N. benthamiana resulted in systemic silencing of PDS exclusively in the phloem region of inoculated plants. Furthermore, expression of enhanced green fluorescence protein (EGFP) using the same ChiLCV vector was verified in the phloem region of the inoculated plants. Our results also suggested that, during the early phase of infection, ChiLCV was associated with the phloem region, but at later stage of pathogenesis, it can spread into the adjoining non-vascular tissues. Taken together, the newly developed ChiLCV-based vector provides an efficient and versatile tool, which can be exploited to unveil the unknown functions of several phloem-specific genes.
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Affiliation(s)
- Nirbhay Kumar Kushwaha
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India.
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27
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Kim J, Park M, Jeong ES, Lee JM, Choi D. Harnessing anthocyanin-rich fruit: a visible reporter for tracing virus-induced gene silencing in pepper fruit. PLANT METHODS 2017; 13:3. [PMID: 28053648 PMCID: PMC5209810 DOI: 10.1186/s13007-016-0151-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 11/24/2016] [Indexed: 05/26/2023]
Abstract
BACKGROUND Virus-induced gene silencing (VIGS) has become a powerful tool for post-genomic technology in plant species. This is important, especially in select plants, such as the pepper plant, that are recalcitrant to Agrobacterium-mediated transformation. Although VIGS in plants has been widely employed as a powerful tool for functional genomics, scattering phenotypic effects by uneven gene silencing has been implemented in order to overcome challenges in experiments with fruit tissues. RESULTS We improved the VIGS system based on the tobacco rattle virus (TRV) containing the An2 MYB transcription factor, which is the genetic determinant of purple colored- or anthocyanin-rich pepper. Silencing of endogenous An2 in the anthocyanin-rich pepper with the modified TRV vector for ligation-independent cloning (LIC) lacked purple pigment in its leaves, flowers, and fruits. Infection with TRV-LIC containing a tandem construct of An2 and phytoene desaturase (PDS) resulted in a typical photobleaching event in leaves without the purple pigment, whereas silencing of PDS led to the presence of photobleached and purple-colored leaves. Cosilencing of endogenous An2 and capsaicin synthase in fruits resulted in decreased levels of capsaicin and dihydrocapsaicin as assessed by high performance liquid chromatography analysis coupled with the absence of the purple pigment in fruits. CONCLUSIONS VIGS with tandem constructs harboring An2 as a visible reporter in anthocyanin-rich pepper plants can facilitate the application of functional genomics in the study of metabolic pathways and fruit biology.
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Affiliation(s)
- Jihyun Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
| | - Minkyu Park
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Department of Genetics, University of Georgia, Athens, GA 30602-7223 USA
| | - Eun Soo Jeong
- Department of Horticultural Science, Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566 Korea
| | - Je Min Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Department of Horticultural Science, Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566 Korea
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, Korea
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28
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Cheng Y, Pang X, Wan H, Ahammed GJ, Yu J, Yao Z, Ruan M, Ye Q, Li Z, Wang R, Yang Y, Zhou G. Identification of Optimal Reference Genes for Normalization of qPCR Analysis during Pepper Fruit Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1128. [PMID: 28706523 PMCID: PMC5489665 DOI: 10.3389/fpls.2017.01128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
Due to its high sensitivity and reproducibility, quantitative real-time PCR (qPCR) is practiced as a useful research tool for targeted gene expression analysis. For qPCR operations, the normalization with suitable reference genes (RGs) is a crucial step that eventually determines the reliability of the obtained results. Although pepper is considered an ideal model plant for the study of non-climacteric fruit development, at present no specific RG have been developed or validated for the qPCR analyses of pepper fruit. Therefore, this study aimed to identify stably expressed genes for their potential use as RGs in pepper fruit studies. Initially, a total of 35 putative RGs were selected by mining the pepper transcriptome data sets derived from the PGP (Pepper Genome Platform) and PGD (Pepper Genome Database). Their expression stabilities were further measured in a set of pepper (Capsicum annuum L. var. 007e) fruit samples, which represented four different fruit developmental stages (IM: Immature; MG: Mature green; B: Break; MR: Mature red) using the qPCR analysis. Then, based on the qPCR results, three different statistical algorithms, namely geNorm, Normfinder, and boxplot, were chosen to evaluate the expression stabilities of these putative RGs. It should be noted that nine genes were proven to be qualified as RGs during pepper fruit development, namely CaREV05 (CA00g79660); CaREV08 (CA06g02180); CaREV09 (CA06g05650); CaREV16 (Capana12g002666); CaREV21 (Capana10g001439); CaREV23 (Capana05g000680); CaREV26 (Capana01g002973); CaREV27 (Capana11g000123); CaREV31 (Capana04g002411); and CaREV33 (Capana08g001826). Further analysis based on geNorm suggested that the application of the two most stably expressed genes (CaREV05 and CaREV08) would provide optimal transcript normalization in the qPCR experiments. Therefore, a new and comprehensive strategy for the identification of optimal RGs was developed. This strategy allowed for the effective normalization of the qPCR analysis of the pepper fruit development at the whole pepper genome level. This study not only explored the optimal RGs specific for studying pepper fruit development, but also introduced a referable strategy of RG mining which could potentially be implicated in other plant species.
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Affiliation(s)
- Yuan Cheng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xin Pang
- Suzhou Polytechnic Institute of AgricultureSuzhou, China
| | - Hongjian Wan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | | | - Jiahong Yu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Zhuping Yao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Meiying Ruan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Qingjing Ye
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Zhimiao Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Rongqing Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yuejian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Guozhi Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
- *Correspondence: Guozhi Zhou
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29
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M S, Gaur R, Sharma V, Chhapekar SS, Das J, Kumar A, Yadava SK, Nitin M, Brahma V, Abraham SK, Ramchiary N. Comparative Analysis of Fruit Metabolites and Pungency Candidate Genes Expression between Bhut Jolokia and Other Capsicum Species. PLoS One 2016; 11:e0167791. [PMID: 27936081 PMCID: PMC5147997 DOI: 10.1371/journal.pone.0167791] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/20/2016] [Indexed: 11/19/2022] Open
Abstract
Bhut jolokia, commonly known as Ghost chili, a native Capsicum species found in North East India was recorded as the naturally occurring hottest chili in the world by the Guinness Book of World Records in 2006. Although few studies have reported variation in pungency content of this particular species, no study till date has reported detailed expression analysis of candidate genes involved in capsaicinoids (pungency) biosynthesis pathway and other fruit metabolites. Therefore, the present study was designed to evaluate the diversity of fruit morphology, fruiting habit, capsaicinoids and other metabolite contents in 136 different genotypes mainly collected from North East India. Significant intra and inter-specific variations for fruit morphological traits, fruiting habits and 65 fruit metabolites were observed in the collected Capsicum germplasm belonging to three Capsicum species i.e., Capsicum chinense (Bhut jolokia, 63 accessions), C. frutescens (17 accessions) and C. annuum (56 accessions). The pungency level, measured in Scoville Heat Unit (SHU) and antioxidant activity measured by 2, 2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assay showed maximum levels in C. chinense accessions followed by C. frutescens accessions, while C. annuum accessions showed the lowest value for both the traits. The number of different fruit metabolites detected did not vary significantly among the different species but the metabolite such as benzoic acid hydroxyl esters identified in large percentage in majority of C. annuum genotypes was totally absent in the C. chinense genotypes and sparingly present in few genotypes of C. frutescens. Significant correlations were observed between fruit metabolites capsaicin, dihydrocapsaicin, hexadecanoic acid, cyclopentane, α-tocopherol and antioxidant activity. Furthermore, comparative expression analysis (through qRT-PCR) of candidate genes involved in capsaicinoid biosynthesis pathway revealed many fold higher expression of majority of the genes in C. chinense compared to C. frutescens and C. annuum suggesting that the possible reason for extremely high pungency might be due to the higher level of candidate gene(s) expression although nucleotide variation in pungency related genes may also be involved in imparting variations in level of pungency.
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Affiliation(s)
- Sarpras M
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rashmi Gaur
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vineet Sharma
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sushil Satish Chhapekar
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jharna Das
- Department of Biological Science, Gauhati University, Guwahati, Assam, India
| | - Ajay Kumar
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Periya, Kasaragod, Kerala, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, India
| | - Mukesh Nitin
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijaya Brahma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Suresh K. Abraham
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nirala Ramchiary
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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30
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Discovery of putative capsaicin biosynthetic genes by RNA-Seq and digital gene expression analysis of pepper. Sci Rep 2016; 6:34121. [PMID: 27756914 PMCID: PMC5069471 DOI: 10.1038/srep34121] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 09/07/2016] [Indexed: 11/23/2022] Open
Abstract
The Indian pepper ‘Guijiangwang’ (Capsicum frutescens L.), one of the world’s hottest chili peppers, is rich in capsaicinoids. The accumulation of the alkaloid capsaicin and its analogs in the epidermal cells of the placenta contribute to the pungency of Capsicum fruits. To identify putative genes involved in capsaicin biosynthesis, RNA-Seq was used to analyze the pepper’s expression profiles over five developmental stages. Five cDNA libraries were constructed from the total RNA of placental tissue and sequenced using an Illumina HiSeq 2000. More than 19 million clean reads were obtained from each library, and greater than 50% of the reads were assignable to reference genes. Digital gene expression (DGE) profile analysis using Solexa sequencing was performed at five fruit developmental stages and resulted in the identification of 135 genes of known function; their expression patterns were compared to the capsaicin accumulation pattern. Ten genes of known function were identified as most likely to be involved in regulating capsaicin synthesis. Additionally, 20 new candidate genes were identified related to capsaicin synthesis. We use a combination of RNA-Seq and DGE analyses to contribute to the understanding of the biosynthetic regulatory mechanism(s) of secondary metabolites in a nonmodel plant and to identify candidate enzyme-encoding genes.
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31
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Capsaicin: From Plants to a Cancer-Suppressing Agent. Molecules 2016; 21:molecules21080931. [PMID: 27472308 PMCID: PMC6274000 DOI: 10.3390/molecules21080931] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 01/07/2023] Open
Abstract
Capsaicinoids are plant secondary metabolites, capsaicin being the principal responsible for the pungency of chili peppers. It is biosynthesized through two pathways involved in phenylpropanoid and fatty acid metabolism. Plant capsaicin concentration is mainly affected by genetic, environmental and crop management factors. However, its synthesis can be enhanced by the use of elicitors. Capsaicin is employed as food additive and in pharmaceutical applications. Additionally, it has been found that capsaicin can act as a cancer preventive agent and shows wide applications against various types of cancer. This review is an approach in contextualizing the use of controlled stress on the plant to increase the content of capsaicin, highlighting its synthesis and its potential use as anticancer agent.
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32
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Mejía-Teniente L, Joaquin-Ramos ADJ, Torres-Pacheco I, Rivera-Bustamante RF, Guevara-Olvera L, Rico-García E, Guevara-Gonzalez RG. Silencing of a Germin-Like Protein Gene (CchGLP) in Geminivirus-Resistant Pepper (Capsicum chinense Jacq.) BG-3821 Increases Susceptibility to Single and Mixed Infections by Geminiviruses PHYVV and PepGMV. Viruses 2015; 7:6141-51. [PMID: 26610554 PMCID: PMC4690854 DOI: 10.3390/v7122930] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 11/16/2022] Open
Abstract
Germin-like proteins (GLPs) are encoded by a family of genes found in all plants, and in terms of function, the GLPs are implicated in the response of plants to biotic and abiotic stresses. CchGLP is a gene encoding a GLP identified in a geminivirus-resistant Capsicum chinense Jacq accession named BG-3821, and it is important in geminivirus resistance when transferred to susceptible tobacco in transgenic experiments. To characterize the role of this GLP in geminivirus resistance in the original accession from which this gene was identified, this work aimed at demonstrating the possible role of CchGLP in resistance to geminiviruses in Capsicum chinense Jacq. BG-3821. Virus-induced gene silencing studies using a geminiviral vector based in PHYVV component A, displaying that silencing of CchGLP in accession BG-3821, increased susceptibility to geminivirus single and mixed infections. These results suggested that CchGLP is an important factor for geminivirus resistance in C. chinense BG-3821 accession.
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Affiliation(s)
- Laura Mejía-Teniente
- C.A. Ingeniería de Biosistemas, Facultad de Ingeniería-Campus Amazcala, Carretera a Chichimequillas, Km. 1, S/N, El Marques, Queretaro C.P. 76229, Mexico.
| | - Ahuizolt de Jesús Joaquin-Ramos
- Instituto Tecnológico de Roque, Departamento de Ingeniería en Industrias Alimentarias, Km. 8 Carr. Celaya-J. Rosas, Roque, Celaya, Gto C.P. 38110, Mexico.
| | - Irineo Torres-Pacheco
- C.A. Ingeniería de Biosistemas, Facultad de Ingeniería-Campus Amazcala, Carretera a Chichimequillas, Km. 1, S/N, El Marques, Queretaro C.P. 76229, Mexico.
| | - Rafael F Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)-Unidad Irapuato, Carretera Irapuato-Leon, Km 9.6, Libramiento norte, Irapuato, Guanajuato A.P. 629, Mexico.
| | - Lorenzo Guevara-Olvera
- Departamento de Ingeniería Bioquímica, Instituto Tecnológico de Celaya, Ave. Tecnológico y A, Garcia-Cubas, S/N, Col. FOVISSSTE, Celaya, Gto A.P. 57, Mexico.
| | - Enrique Rico-García
- C.A. Ingeniería de Biosistemas, Facultad de Ingeniería-Campus Amazcala, Carretera a Chichimequillas, Km. 1, S/N, El Marques, Queretaro C.P. 76229, Mexico.
| | - Ramon G Guevara-Gonzalez
- C.A. Ingeniería de Biosistemas, Facultad de Ingeniería-Campus Amazcala, Carretera a Chichimequillas, Km. 1, S/N, El Marques, Queretaro C.P. 76229, Mexico.
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Zhirnov IV, Trifonova EA, Kochetov AV, Shumny VK. Virus-induced silencing as a method for studying gene functions in higher plants. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415050099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ogawa K, Murota K, Shimura H, Furuya M, Togawa Y, Matsumura T, Masuta C. Evidence of capsaicin synthase activity of the Pun1-encoded protein and its role as a determinant of capsaicinoid accumulation in pepper. BMC PLANT BIOLOGY 2015; 15:93. [PMID: 25884984 PMCID: PMC4386094 DOI: 10.1186/s12870-015-0476-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/17/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Capsaicinoids, including capsaicin and its analogs, are responsible for the pungency of pepper (Capsicum species) fruits. Even though capsaicin is familiar and used daily by humans, the genes involved in the capsaicin biosynthesis pathway have not been well characterized. The putative aminotransferase (pAMT) and Pungent gene 1 (Pun1) proteins are believed to catalyze the second to last and the last steps in the pathway, respectively, making the Pun1 protein the putative capsaicin synthase. However, there is no direct evidence that Pun1 has capsaicin synthase activity. RESULTS To verify that the Pun1 protein actually plays a role in capsaicin production, we generated anti-Pun1 antibodies against an Escherichia coli-synthesized Pun1 protein and used them to antagonize endogenous Pun1 activity. To confirm the anti-Pun1 antibodies' specificity, we targeted Pun1 mRNA using virus-induced gene silencing. In the Pun1-down-regulated placental tissues, the accumulated levels of the Pun1 protein, which was identified on a western blot using the anti-Pun1 antibodies, were reduced, and simultaneously, capsaicin accumulations were reduced in the same tissues. In the de novo capsaicin synthesis in vitro cell-free assay, which uses protoplasts isolated from placental tissues, capsaicin synthesis was inhibited by the addition of anti-Pun1 antibodies. We next analyzed the expression profiles of pAMT and Pun1 in various pepper cultivars and found that high levels of capsaicin accumulation always accompanied high expression levels of both pAMT and Pun1, indicating that both genes are important for capsaicin synthesis. However, comparisons of the accumulated levels of vanillylamine (a precursor of capsaicin) and capsaicin between pungent and nonpungent cultivars revealed that vanillylamine levels in the pungent cultivars were very low, probably owing to its rapid conversion to capsaicin by Pun1 soon after synthesis, and that in nonpungent cultivars, vanillylamine accumulated to quite high levels owing to the lack of Pun1. CONCLUSIONS Using a newly developed protoplast-based assay for de novo capsaicin synthesis and the anti-Pun1 antibodies, we successfully demonstrated that the Pun1 gene and its gene product are involved in capsaicin synthesis. The analysis of the vanillylamine accumulation relative to that of capsaicin indicated that Pun1 was the primary determinant of their accumulation levels.
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Affiliation(s)
- Kana Ogawa
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Katsunori Murota
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Hanako Shimura
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Misaki Furuya
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Yasuko Togawa
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Takeshi Matsumura
- Plant Molecular Technology Research Group, Research Institute of Bioproduction, National Institute of Advanced Industrial Science and Technology, Sapporo, 062-8517, Japan.
| | - Chikara Masuta
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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Synthesis of Stable Isotope-Labeled Precursors for the Biosyntheses of Capsaicinoids, Capsinoids, and Capsiconinoids. Biosci Biotechnol Biochem 2014; 75:1611-4. [DOI: 10.1271/bbb.110187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, Lee HY, Kim SY, Kim MS, Kang BC, Jo YD, Yang HB, Jeong HJ, Kang WH, Kwon JK, Shin C, Lim JY, Park JH, Huh JH, Kim JS, Kim BD, Cohen O, Paran I, Suh MC, Lee SB, Kim YK, Shin Y, Noh SJ, Park J, Seo YS, Kwon SY, Kim HA, Park JM, Kim HJ, Choi SB, Bosland PW, Reeves G, Jo SH, Lee BW, Cho HT, Choi HS, Lee MS, Yu Y, Do Choi Y, Park BS, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai HS, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sørensen I, Lee SJ, Kim RW, Choi IY, Choi BS, Lim JS, Lee YH, Choi D. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 2014; 46:270-8. [PMID: 24441736 DOI: 10.1038/ng.2877] [Citation(s) in RCA: 558] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/30/2013] [Indexed: 12/12/2022]
Abstract
Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.
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Affiliation(s)
- Seungill Kim
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Minkyu Park
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Seon-In Yeom
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Yong-Min Kim
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Je Min Lee
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Hyun-Ah Lee
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Eunyoung Seo
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kyeongchae Cheong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kyongyong Jung
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Gir-Won Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea
| | - Sang-Keun Oh
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Chungyun Bae
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Saet-Byul Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hye-Young Lee
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Shin-Young Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Myung-Shin Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Byoung-Cheorl Kang
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3] Vegetable Breeding Research Center, Seoul National University, Seoul, Korea
| | - Yeong Deuk Jo
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hee-Bum Yang
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hee-Jin Jeong
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Won-Hee Kang
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Jin-Kyung Kwon
- Vegetable Breeding Research Center, Seoul National University, Seoul, Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - June-Sik Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Byung-Dong Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Oded Cohen
- Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel
| | - Ilan Paran
- Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
| | - Saet Buyl Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
| | - Yeon-Ki Kim
- Genomics Genetics Institute, GreenGene BioTech, Inc., Yongin, Korea
| | | | | | | | - Young Sam Seo
- Ginseng Resources Research Laboratory, Korea Ginseng Corporation, Daejeon, Korea
| | - Suk-Yoon Kwon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun A Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jeong Mee Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Korea
| | - Paul W Bosland
- 1] Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA. [2] Chile Pepper Institute, New Mexico State University, Las Cruces, New Mexico, USA
| | - Gregory Reeves
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA
| | | | | | - Hyung-Taeg Cho
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hee-Seung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Min-Soo Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Yeisoo Yu
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA
| | - Yang Do Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Beom-Seok Park
- Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea
| | - Allen van Deynze
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Woo Taek Kim
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hee Kyung Ahn
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Inhwa Yeam
- Department of Horticulture and Breeding, Andong National University, Andong, Korea
| | - James J Giovannoni
- 1] US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, New York, USA. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Sang-Jik Lee
- Biotechnology Institute, Nongwoo Bio, Yeoju, Korea
| | - Ryan W Kim
- Genome Center, University of California, Davis, Davis, California, USA
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Beom-Soon Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Jong-Sung Lim
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Doil Choi
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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Martínez-López LA, Ochoa-Alejo N, Martínez O. Dynamics of the chili pepper transcriptome during fruit development. BMC Genomics 2014; 15:143. [PMID: 24555715 PMCID: PMC3936869 DOI: 10.1186/1471-2164-15-143] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/18/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. RESULTS RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueño 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. CONCLUSIONS In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.
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Affiliation(s)
| | | | - Octavio Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36821 Irapuato, Guanajuato, México.
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Reddy UK, Almeida A, Abburi VL, Alaparthi SB, Unselt D, Hankins G, Park M, Choi D, Nimmakayala P. Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections. PLoS One 2014; 9:e86393. [PMID: 24475113 PMCID: PMC3903536 DOI: 10.1371/journal.pone.0086393] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/06/2013] [Indexed: 11/23/2022] Open
Abstract
Pepper (Capsicum annuum L.) is an economically important crop with added nutritional value. Production of capsaicin is an important quantitative trait with high environmental variance, so the development of markers regulating capsaicinoid accumulation is important for pepper breeding programs. In this study, we performed association mapping at the gene level to identify single nucleotide polymorphisms (SNPs) associated with capsaicin pathway metabolites in a diverse Capsicum annuum collection during two seasons. The genes Pun1, CCR, KAS and HCT were sequenced and matched with the whole-genome sequence draft of pepper to identify SNP locations and for further characterization. The identified SNPs for each gene underwent candidate gene association mapping. Association mapping results revealed Pun1 as a key regulator of major metabolites in the capsaicin pathway mainly affecting capsaicinoids and precursors for acyl moieties of capsaicinoids. Six different SNPs in the promoter sequence of Pun1 were found associated with capsaicin in plants from both seasons. Our results support that CCR is an important control point for the flux of p-coumaric acid to specific biosynthesis pathways. KAS was found to regulate the major precursors for acyl moieties of capsaicinoids and may play a key role in capsaicinoid production. Candidate gene association mapping of Pun1 suggested that the accumulation of capsaicinoids depends on the expression of Pun1, as revealed by the most important associated SNPs found in the promoter region of Pun1.
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Affiliation(s)
- Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Aldo Almeida
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata L Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Suresh Babu Alaparthi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Desiree Unselt
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Gerald Hankins
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Minkyu Park
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
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Kobata K, Sugawara M, Mimura M, Yazawa S, Watanabe T. Potent production of capsaicinoids and capsinoids by Capsicum peppers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:11127-11132. [PMID: 24147886 DOI: 10.1021/jf403553w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The fundamental structure of capsinoids is a fatty acid ester with vanillyl alcohol, whereas in capsaicinoids, a fatty acid amide is linked to vanillylamine. To clarify the relationship between their biosynthesis in Capsicum plants, we carried out an in vivo tracer experiment using stable isotopically labeled putative precursors. Liquid chromatography-tandem mass spectrometry was used to measure the uptake of isotopes into metabolites after injection of the labeled precursors into intact fruits of a pungent cultivar, Peru, and a non-pungent cultivar, CH-19 Sweet. Labeled vanillylamine was incorporated into capsaicinoids in both cultivars. While labeled vanillyl alcohol was incorporated into capsinoids in both cultivars, the accumulation of intact capsaicinoids in Peru was suppressed by over 60% after administration of vanillyl alcohol. In Peru, labeled vanillin was converted to both vanillylamine and, in 5-fold excess, vanillyl alcohol. Moreover, labeled vanillin was converted exclusively to vanillyl alcohol in CH-19 Sweet. These data are consistent with the incorporation of labeled vanillin into capsaicinoids and capsinoids in both cultivars. We conclude that pungent cultivars are highly potent producers of vanillyl alcohol that is incorporated into capsinoids and that biosynthesis of capsinoids is catalyzed by capsaicin synthase.
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Affiliation(s)
- Kenji Kobata
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka , 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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Liu S, Li W, Wu Y, Chen C, Lei J. De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids. PLoS One 2013; 8:e48156. [PMID: 23349661 PMCID: PMC3551913 DOI: 10.1371/journal.pone.0048156] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/21/2012] [Indexed: 12/04/2022] Open
Abstract
The capsaicinoids are a group of compounds produced by chili pepper fruits and are used widely in many fields, especially in medical purposes. The capsaicinoid biosynthetic pathway has not yet been established clearly. To understand more knowledge in biosynthesis of capsaicinoids, we applied RNA-seq for the mixture of placenta and pericarp of pungent pepper (Capsicum frutescens L.). We have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for de novo assembly of transcriptome data. We obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (C. annuum) ESTs databases. Our results predicted 3 new structural genes (DHAD, TD, PAT), which filled gaps of the capsaicinoid biosynthetic pathway predicted by Mazourek, and revealed new candidate genes involved in capsaicinoid biosynthesis based on KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. A significant number of SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) markers were predicted in C. frutescens and C. annuum sequences, which will be helpful in the identification of polymorphisms within chili pepper populations. These data will provide new insights to the pathway of capsaicinoid biosynthesis and subsequent research of chili peppers. In addition, our strategy of de novo transcriptome assembly is applicable to a wide range of similar studies.
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Affiliation(s)
- Shaoqun Liu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wanshun Li
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yimin Wu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jianjun Lei
- College of Horticulture, South China Agricultural University, Guangzhou, China
- * E-mail:
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Gururaj HB, Padma MN, Giridhar P, Ravishankar GA. Functional validation of Capsicum frutescens aminotransferase gene involved in vanillylamine biosynthesis using Agrobacterium mediated genetic transformation studies in Nicotiana tabacum and Capsicum frutescens calli cultures. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 195:96-105. [PMID: 22921003 DOI: 10.1016/j.plantsci.2012.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/24/2012] [Accepted: 06/26/2012] [Indexed: 06/01/2023]
Abstract
Capsaicinoid biosynthesis involves the participation of two substrates viz. vanillylamine and C(9)-C(11) fatty acid moieties. Vanillylamine which is a derivative of vanillin is synthesized through a transaminase reaction in the phenylpropanoid pathway of capsaicinoid synthesis. Here we report the functional validation of earlier reported putative aminotransferase gene for vanillylamine biosynthesis in heterologous system using Agrobacterium mediated genetic transformation studies in Nicotiana tabacum and Capsicum frutescens calli cultures. Molecular analysis tools comprising PCR and Southern blot analysis have shown the integration of the foreign gene in N. tabacum and C. frutescens calli cultures. The study shows the production of vanillylamine in transformed N. tabacum callus cultures and also the reduction of vanillylamine production when whole gene based antisense binary vector construct was used in transformation of C. frutescens callus cultures. Vanillylamine production, aminotransferase assay with Western blot analysis for crude proteins of transformants established the production of putative aminotransferase (pAMT) protein in alternate plant. The result is a clear evidence of involvement of the reported putative aminotransferase responsible for vanillylamine biosynthesis in capsaicinoid biosynthesis pathway, confirming the gene function through functional validation.
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Affiliation(s)
- Harishchandra B Gururaj
- Plant Cell Biotechnology Department, Central Food Technological Research Institute, (Constituent laboratory of Council of Scientific and Industrial Research, CSIR), Mysore 570020, India
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Ma M, Yan Y, Huang L, Chen M, Zhao H. Virus-induced gene-silencing in wheat spikes and grains and its application in functional analysis of HMW-GS-encoding genes. BMC PLANT BIOLOGY 2012; 12:141. [PMID: 22882902 PMCID: PMC3462119 DOI: 10.1186/1471-2229-12-141] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 06/28/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Barley stripe mosaic virus (BSMV)-based vector has been developed and used for gene silencing in barley and wheat seedlings to assess gene functions in pathogen- or insect-resistance, but conditions for gene silencing in spikes and grains have not been evaluated. In this study, we explored the feasibility of using BSMV for gene silencing in wheat spikes or grains. RESULTS Apparent photobleaching on the spikes infected with BSMV:PDS at heading stage was observed after 13 days post inoculation (dpi), and persisted until 30 dpi, while the spikes inoculated with BSMV:00 remained green during the same period. Grains of BSMV:PDS infected spikes also exhibited photobleaching. Molecular analysis indicated that photobleached spikes or grains resulted from the reduction of endogenous PDS transcript abundances, suggesting that BSMV:PDS was able to induce PDS silencing in wheat spikes and grains. Inoculation onto wheat spikes from heading to flowering stage was optimal for efficient silencing of PDS in wheat spikes. Furthermore, we used the BSMV-based system to reduce the transcript level of 1Bx14, a gene encoding for High-molecular-weight glutenin subunit 1Bx14 (HMW-GS 1Bx14), by 97 % in the grains of the BSMV:1Bx14 infected spikes at 15 dpi, compared with that in BSMV:00 infected spikes, and the reduction persisted until at least 25 dpi. The amount of the HMW-GS 1Bx14 was also detectably decreased. The percentage of glutenin macropolymeric proteins in total proteins was significantly reduced in the grains of 1Bx14-silenced plants as compared with that in the grains of BSMV:00 infected control plants, indicating that HMW-GS 1Bx14 is one of major components participating in the formation of glutenin macropolymers in wheat grains. CONCLUSION This is one of the first reports of successful application of BSMV-based virus-induced-gene-silencing (VIGS) for gene knockdown in wheat spikes and grains and its application in functional analysis of the 1Bx14 gene. The established BSMV-VIGS system will be very useful in future research on functional analysis of genes contributing to grain quality and the metabolic networks in developing seeds of wheat.
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Affiliation(s)
- Meng Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Li Huang
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT59717, USA
| | - Mingshun Chen
- USDA-ARS and Department of Entomology, Kansas State University, Manhattan, KS66506, USA
| | - Huixian Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
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Huang C, Qian Y, Li Z, Zhou X. Virus-induced gene silencing and its application in plant functional genomics. SCIENCE CHINA-LIFE SCIENCES 2012; 55:99-108. [PMID: 22415680 DOI: 10.1007/s11427-012-4280-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 12/13/2011] [Indexed: 12/13/2022]
Abstract
Virus-induced gene silencing is regarded as a powerful and efficient tool for the analysis of gene function in plants because it is simple, rapid and transformation-free. It has been used to perform both forward and reverse genetics to identify plant functional genes. Many viruses have been developed into virus-induced gene silencing vectors and gene functions involved in development, biotic and abiotic stresses, metabolism, and cellular signaling have been reported. In this review, we discuss the development and application of virus-induced gene silencing in plant functional genomics.
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Affiliation(s)
- Changjun Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Hosseini Tafreshi SA, Shariati M, Mofid MR, Khayam Nekui M, Esmaeili A. Heterologous virus-induced gene silencing as a promising approach in plant functional genomics. Mol Biol Rep 2012; 39:2169-78. [PMID: 21655951 DOI: 10.1007/s11033-011-0965-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
VIGS (virus induced gene silencing) is considered as a powerful genomics tool for characterizing the function of genes in a few closely related plant species. The investigations have been carried out mainly in order to test if a pre-existing VIGS vector can serve as an efficient tool for gene silencing in a diverse array of plant species. Another route of investigation has been the constructing of new viral vectors to act in their hosts. Our approach was the creation of a heterologous system in which silencing of endogenous genes was achieved by sequences isolated from evolutionary remote species. In this study, we showed that a TRV-based vector cloned with sequences from a gymnosperm, Taxus baccata L. silenced the endogenous phytoene desaturase in an angiosperm, N. benthamiana. Our results showed that inserts of between 390 and 724 bp isolated from a conserved fragment of the Taxus PDS led to silencing of its homolog in tobacco. The real time analysis indicated that the expression of PDS was reduced 2.1- to 4.0-fold in pTRV-TbPDS infected plants compared with buffer treated plants. Once the best insert is identified and the conditions are optimized for heterologous silencing by pTRV-TbPDS in tobacco, then we can test if TRV can serve as an efficient silencing vector in Taxus. This strategy could also be used to silence a diverse array of genes from a wide range of species which have no VIGS protocol. The results also showed that plants silenced heterologously by the VIGS system a minimally affected with respect to plant growth which may be ideal for studying the genes that their complete loss of function may lead to decrease of plant growth or plant death.
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Abstract
Virus-induced gene silencing (VIGS) has emerged as a powerful method for studying gene function. VIGS is induced by infecting a plant with a plant virus that has had its genome modified to include a sequence from the host gene to be silenced. DNAβ and DNA1 are satellite and single-stranded DNA molecules associated with begomoviruses (family Geminiviridae). We converted DNAβ and DNA1 into gene-silencing vectors. The VIGS vectors can induce silencing efficiently in many solanaceous plants. Here, we describe procedures for the use of these two gene-silencing vectors for VIGS in different hosts.
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Affiliation(s)
- Xueping Zhou
- Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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46
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Chen C, Chen G, Hao X, Cao B, Chen Q, Liu S, Lei J. CaMF2, an anther-specific lipid transfer protein (LTP) gene, affects pollen development in Capsicum annuum L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:439-448. [PMID: 21889050 DOI: 10.1016/j.plantsci.2011.07.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/07/2011] [Accepted: 07/12/2011] [Indexed: 05/28/2023]
Abstract
Based on the gene differential expression analysis performed by cDNA-amplified fragment length polymorphism (cDNA-AFLP) in the genic male sterile-fertile line 114AB of Capsicum annuum L., a variety of differentially expressed cDNA fragments were detected in fertile or sterile lines. A transcript-derived fragment (TDF) specifically accumulated in the flower buds of fertile line was isolated, and the corresponding full-length cDNA and DNA were subsequently amplified. Bioinformatical analyses of this gene named CaMF2 showed that it encodes a lipid transfer protein with 94 amino acids. Spatial and temporal expression patterns analysis indicated that CaMF2 was an anther-specific gene and the expression of CaMF2 was detected only in flower buds at stage 3-7 of male fertile line with a peak expression at stage 4, but not detected in the roots, tender stems, fresh leaves, flower buds, open flowers, sepals, petals, anthers or pistils of male sterile line. Further, inhibition of the CaMF2 by virus-induced gene silencing (VIGS) method resulted in the low pollen germination ability and shriveled pollen grains. All these evidence showed that CaMF2 had a vital role in pollen development of C. annuum.
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MESH Headings
- Amino Acid Sequence
- Amplified Fragment Length Polymorphism Analysis
- Antigens, Plant/chemistry
- Antigens, Plant/genetics
- Antigens, Plant/metabolism
- Base Sequence
- Capsicum/anatomy & histology
- Capsicum/genetics
- Capsicum/growth & development
- Capsicum/ultrastructure
- Carrier Proteins/chemistry
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- DNA, Complementary/genetics
- Expressed Sequence Tags
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant/genetics
- Molecular Sequence Data
- Organ Specificity/genetics
- Plant Infertility/genetics
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Pollen/genetics
- Pollen/growth & development
- Pollen/ultrastructure
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
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Affiliation(s)
- Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
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Wahyuni Y, Ballester AR, Sudarmonowati E, Bino RJ, Bovy AG. Metabolite biodiversity in pepper (Capsicum) fruits of thirty-two diverse accessions: variation in health-related compounds and implications for breeding. PHYTOCHEMISTRY 2011; 72:1358-70. [PMID: 21514607 DOI: 10.1016/j.phytochem.2011.03.016] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/17/2011] [Accepted: 03/18/2011] [Indexed: 05/20/2023]
Abstract
A comprehensive study on morphology and biochemical compounds of 32 Capsicum spp. accessions has been performed. Accessions represented four pepper species, Capsicum annuum, Capsicum frutescens, Capsicum chinense and Capsicum baccatum which were selected by their variation in morphological characters such as fruit color, pungency and origin. Major metabolites in fruits of pepper, carotenoids, capsaicinoids (pungency), flavonoid glycosides, and vitamins C and E were analyzed and quantified by high performance liquid chromatography. The results showed that composition and level of metabolites in fruits varied greatly between accessions and was independent of species and geographical location. Fruit color was determined by the accumulation of specific carotenoids leading to salmon, yellow, orange, red and brown colored fruits. Levels of both O- and C-glycosides of quercetin, luteolin and apigenin varied strongly between accessions. All non-pungent accessions were devoid of capsaicins, whereas capsaicinoid levels ranged from 0.07 up to 80 mg/100g fr. wt. in fruit pericarp. In general, pungent accessions accumulated the highest capsaicinoid levels in placenta plus seed tissue compared to pericarp. The non-pungent capsaicinoid analogs, capsiates, could be detected at low levels in some pungent accessions. All accessions accumulated high levels of vitamin C, up to 200 mg/100g fr. wt. The highest vitamin E concentration found was 16 mg/100g fr. wt. Based on these metabolic data, five accessions were selected for further metabolic and molecular analysis, in order to isolate key genes involved in the production of these compounds and to assist future breeding programs aimed at optimizing the levels of health-related compounds in pepper fruit.
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Affiliation(s)
- Yuni Wahyuni
- Plant Research International, 6700 AA Wageningen, The Netherlands
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48
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Aza-González C, Núñez-Palenius HG, Ochoa-Alejo N. Molecular biology of capsaicinoid biosynthesis in chili pepper (Capsicum spp.). PLANT CELL REPORTS 2011; 30:695-706. [PMID: 21161234 DOI: 10.1007/s00299-010-0968-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/29/2010] [Accepted: 11/30/2010] [Indexed: 05/27/2023]
Abstract
Capsicum species produce fruits that synthesize and accumulate unique hot compounds known as capsaicinoids in placental tissues. The capsaicinoid biosynthetic pathway has been established, but the enzymes and genes participating in this process have not been extensively studied or characterized. Capsaicinoids are synthesized through the convergence of two biosynthetic pathways: the phenylpropanoid and the branched-chain fatty acid pathways, which provide the precursors phenylalanine, and valine or leucine, respectively. Capsaicinoid biosynthesis and accumulation is a genetically determined trait in chili pepper fruits as different cultivars or genotypes exhibit differences in pungency; furthermore, this characteristic is also developmentally and environmentally regulated. The establishment of cDNA libraries and comparative gene expression studies in pungent and non-pungent chili pepper fruits has identified candidate genes possibly involved in capsaicinoid biosynthesis. Genetic and molecular approaches have also contributed to the knowledge of this biosynthetic pathway; however, more studies are necessary for a better understanding of the regulatory process that accounts for different accumulation levels of capsaicinoids in chili pepper fruits.
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Affiliation(s)
- Cesar Aza-González
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav)-Unidad Irapuato, Km 9.6 libramiento norte carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
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Rentería-Canett I, Xoconostle-Cázares B, Ruiz-Medrano R, Rivera-Bustamante RF. Geminivirus mixed infection on pepper plants: synergistic interaction between PHYVV and PepGMV. Virol J 2011; 8:104. [PMID: 21385390 PMCID: PMC3061938 DOI: 10.1186/1743-422x-8-104] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 03/08/2011] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND PHYVV and PepGMV are plant viruses reported in Mexico and Southern US as causal agents of an important pepper disease known as "rizado amarillo". Mixed infections with PHYVV and PepGMV have been reported in several hosts over a wide geographic area. Previous work suggested that these viruses might interact at the replication and/or movement level in a complex manner. The aim of present report was to study some aspects of a synergistic interaction between PHYVV and PepGMV in pepper plants. These include analyses of symptom severity, viral DNA concentration and tissue localization of both viruses in single and mixed infections. RESULTS Mixed infections with PepGMV and PHYVV induced symptoms more severe than those observed in single viral infections. Whereas plants infected with either virus (single infection) presented a remission stage with a corresponding decrease in viral DNA levels, double-infected plants did not present symptom remission and both viral DNA concentrations dramatically increased. In situ hybridization experiments revealed that both viruses are restricted to the vascular tissue. Interestingly, the amount of viral DNA detected was higher in plants inoculated with PepGMV than that observed in PHYVV-infected plants. During mixed infections, the location of both viruses remained similar to the one observed in single infections, although the number of infected cells increases. Infections with the tripartite mixture PHYVV (A+B) + PepGMV A produced a similar synergistic infection to the one observed after inoculation with both full viruses. On the contrary, tripartite mixture PepGMV (A+B) + PHYVV A did not produce a synergistic interaction. In an attempt to study the contribution of individual genes to the synergism, several mutants of PHYVV or PepGMV were inoculated in combination with the corresponding wild type, second virus (wt PepGMV or wt PHYVV). All combinations tested resulted in synergistic infections, with exception of the TrAP mutant of PepGMV (PepGMV TrAP-) + PHYVV. CONCLUSION In this report, we have demonstrated that synergistic interaction between PHYVV and PepGMV during a mixed infection is mainly due to an increased DNA concentration of both viruses, without any noticeable effect on the localization of either virus on infected plant tissue. Our results have shown that the viral component A from PepGMV is important for synergism during PHYVV-PepGMV mixed infections.
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Affiliation(s)
- Ilenia Rentería-Canett
- Departamento de Ingeniería Genética. Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Unidad Irapuato, Km. 9.6 Libramiento Norte, 36821 Irapuato, Guanajuato
| | - Beatriz Xoconostle-Cázares
- Departamento de Biotecnología y Bioingeniería, Cinvestav-IPN, Av. IPN 2508, San Pedro Zacatenco, 07360 México, DF
| | - Roberto Ruiz-Medrano
- Departamento de Biotecnología y Bioingeniería, Cinvestav-IPN, Av. IPN 2508, San Pedro Zacatenco, 07360 México, DF
| | - Rafael F Rivera-Bustamante
- Departamento de Ingeniería Genética. Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Unidad Irapuato, Km. 9.6 Libramiento Norte, 36821 Irapuato, Guanajuato
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Tanaka Y, Hosokawa M, Miwa T, Watanabe T, Yazawa S. Novel loss-of-function putative aminotransferase alleles cause biosynthesis of capsinoids, nonpungent capsaicinoid analogues, in mildly pungent chili peppers (Capsicum chinense). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:11762-11767. [PMID: 20973559 DOI: 10.1021/jf1019642] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Capsinoids are a group of nonpungent capsaicinoid analogues produced in Capsicum fruits. They have similar bioactivities to capsaicinoids such as suppression of fat accumulation and antioxidant activity. They are more palatable ingredients in dietary supplements than capsaicinoids because of their low pungency. Previous studies on nonpungent Capsicum annuum cultivars showed that capsinoid biosynthesis is caused by loss-of-function putative aminotransferase (p-amt) alleles. This study showed that three mildly pungent cultivars of Capsicum chinense (Zavory Hot, Aji Dulce strain 2, and Belize Sweet) contain high levels of capsinoid. It was shown that these cultivars have novel p-amt alleles, which contain mutations that differ from those of C. annuum. Sequence analysis of p-amt in Belize Sweet revealed that a 5 bp insertion (TGGGC) results in a frameshift mutation. A transposable element (Tcc) was found in the p-amt of Zavory Hot and Aji Dulce strain 2. Tcc has features similar to those of the hAT transposon family. This was inserted in the fifth intron of Zavory Hot and in third intron of Aji Dulce strain 2. The p-amt alleles harboring Tcc cannot produce an active p-AMT. These mildly pungent cultivars will provide a new natural source of capsinoids.
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Affiliation(s)
- Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Kyoto 606-8502, Japan.
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