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Zhou L, Tian S, Qin G. RNA methylomes reveal the m 6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening. Genome Biol 2019; 20:156. [PMID: 31387610 PMCID: PMC6683476 DOI: 10.1186/s13059-019-1771-7] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay between 5mC and m6A remain uncharacterized. RESULTS Here, we show that mRNA m6A methylation exhibits dynamic changes similar to DNA methylation during tomato fruit ripening. RNA methylome analysis reveals that m6A methylation is a prevalent modification in the mRNA of tomato fruit, and the m6A sites are enriched around the stop codons and within the 3' untranslated regions. In the fruit of the ripening-deficient epimutant Colorless non-ripening (Cnr) which harbors DNA hypermethylation, over 1100 transcripts display increased m6A levels, while only 134 transcripts show decreased m6A enrichment, suggesting a global increase in m6A. The m6A deposition is generally negatively correlated with transcript abundance. Further analysis demonstrates that the overall increase in m6A methylation in Cnr mutant fruit is associated with the decreased expression of RNA demethylase gene SlALKBH2, which is regulated by DNA methylation. Interestingly, SlALKBH2 has the ability to bind the transcript of SlDML2, a DNA demethylase gene required for tomato fruit ripening, and modulates its stability via m6A demethylation. Mutation of SlALKBH2 decreases the abundance of SlDML2 mRNA and delays fruit ripening. CONCLUSIONS Our study identifies a novel layer of gene regulation for key ripening genes and establishes an essential molecular link between DNA methylation and mRNA m6A methylation during fruit ripening.
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Affiliation(s)
- Leilei Zhou
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China.
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Constantin ME, de Lamo FJ, Vlieger BV, Rep M, Takken FLW. Endophyte-Mediated Resistance in Tomato to Fusarium oxysporum Is Independent of ET, JA, and SA. FRONTIERS IN PLANT SCIENCE 2019; 10:979. [PMID: 31417594 PMCID: PMC6685397 DOI: 10.3389/fpls.2019.00979] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 07/11/2019] [Indexed: 05/21/2023]
Abstract
Root endophytes can confer resistance against plant pathogens by direct antagonism or via the host by triggering induced resistance. The latter response typically relies on jasmonic acid (JA)/ethylene (ET)-depended signaling pathways, but can also be triggered via salicylic acid (SA)-dependent signaling pathways. Here, we set out to determine if endophyte-mediated resistance (EMR), conferred by the Fusarium endophyte Fo47, against Fusarium wilt disease in tomato is mediated via SA, ET or JA. To test the contribution of SA, ET, and JA in EMR we performed bioassays with Fo47 and Fusarium oxysporum f. sp. lycopersici in tomato plants impaired in SA accumulation (NahG), JA biosynthesis (def1) or ET-production (ACD) and -sensing (Nr). We observed that the colonization pattern of Fo47 in stems of wildtype plants was indistinguishable from that of the hormone mutants. Surprisingly, EMR was not compromised in the lines affected in JA, ET, or SA signaling. The independence of EMR on SA, JA, and ET implies that this induced resistance-response against Fusarium wilt disease is distinct from the classical Induced Systemic Resistance (ISR) response, providing exciting possibilities for control of wilt diseases independent of conventional defense pathways.
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Li S, Chen K, Grierson D. A critical evaluation of the role of ethylene and MADS transcription factors in the network controlling fleshy fruit ripening. THE NEW PHYTOLOGIST 2019; 221:1724-1741. [PMID: 30328615 DOI: 10.1111/nph.15545] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/28/2018] [Indexed: 05/18/2023]
Abstract
Contents Summary 1724 I. Introduction 1725 II. Ripening genes 1725 III. The importance of ethylene in controlling ripening 1727 IV. The importance of MADS-RIN in controlling ripening 1729 V. Interactions between components of the ripening regulatory network 1734 VI. Conclusions 1736 Acknowledgements 1738 Author contributions 1738 References 1738 SUMMARY: Understanding the regulation of fleshy fruit ripening is biologically important and provides insights and opportunities for controlling fruit quality, enhancing nutritional value for animals and humans, and improving storage and waste reduction. The ripening regulatory network involves master and downstream transcription factors (TFs) and hormones. Tomato is a model for ripening regulation, which requires ethylene and master TFs including NAC-NOR and the MADS-box protein MADS-RIN. Recent functional characterization showed that the classical RIN-MC gene fusion, previously believed to be a loss-of-function mutation, is an active TF with repressor activity. This, and other evidence, has highlighted the possibility that MADS-RIN itself is not important for ripening initiation but is required for full ripening. In this review, we discuss the diversity of components in the control network, their targets, and how they interact to control initiation and progression of ripening. Both hormones and individual TFs affect the status and activity of other network participants, which changes overall network signaling and ripening outcomes. MADS-RIN, NAC-NOR and ethylene play critical roles but there are still unanswered questions about these and other TFs. Further attention should be paid to relationships between ethylene, MADS-RIN and NACs in ripening control.
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Affiliation(s)
- Shan Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Don Grierson
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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Mukherjee S. Recent advancements in the mechanism of nitric oxide signaling associated with hydrogen sulfide and melatonin crosstalk during ethylene-induced fruit ripening in plants. Nitric Oxide 2019; 82:25-34. [DOI: 10.1016/j.niox.2018.11.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/11/2018] [Accepted: 11/18/2018] [Indexed: 12/11/2022]
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Chen Y, Rofidal V, Hem S, Gil J, Nosarzewska J, Berger N, Demolombe V, Bouzayen M, Azhar BJ, Shakeel SN, Schaller GE, Binder BM, Santoni V, Chervin C. Targeted Proteomics Allows Quantification of Ethylene Receptors and Reveals SlETR3 Accumulation in Never-Ripe Tomatoes. FRONTIERS IN PLANT SCIENCE 2019; 10:1054. [PMID: 31555314 PMCID: PMC6727826 DOI: 10.3389/fpls.2019.01054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/29/2019] [Indexed: 05/04/2023]
Abstract
Ethylene regulates fruit ripening and several plant functions (germination, plant growth, plant-microbe interactions). Protein quantification of ethylene receptors (ETRs) is essential to study their functions, but is impaired by low resolution tools such as antibodies that are mostly nonspecific, or the lack of sensitivity of shotgun proteomic approaches. We developed a targeted proteomic method, to quantify low-abundance proteins such as ETRs, and coupled this to mRNAs analyses, in two tomato lines: Wild Type (WT) and Never-Ripe (NR) which is insensitive to ethylene because of a gain-of-function mutation in ETR3. We obtained mRNA and protein abundance profiles for each ETR over the fruit development period. Despite a limiting number of replicates, we propose Pearson correlations between mRNA and protein profiles as interesting indicators to discriminate the two genotypes: such correlations are mostly positive in the WT and are affected by the NR mutation. The influence of putative post-transcriptional and post-translational changes are discussed. In NR fruits, the observed accumulation of the mutated ETR3 protein between ripening stages (Mature Green and Breaker + 8 days) may be a cause of NR tomatoes to stay orange. The label-free quantitative proteomics analysis of membrane proteins, concomitant to Parallel Reaction Monitoring analysis, may be a resource to study changes over tomato fruit development. These results could lead to studies about ETR subfunctions and interconnections over fruit development. Variations of RNA-protein correlations may open new fields of research in ETR regulation. Finally, similar approaches may be developed to study ETRs in whole plant development and plant-microorganism interactions.
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Affiliation(s)
- Yi Chen
- GBF, Université de Toulouse, INRA, Toulouse, France
| | - Valérie Rofidal
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Sonia Hem
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Julie Gil
- GBF, Université de Toulouse, INRA, Toulouse, France
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Nathalie Berger
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Vincent Demolombe
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Beenish J. Azhar
- Department of Biochemistry, Quaid-i-azam University, Islamabad, Pakistan
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Samina N. Shakeel
- Department of Biochemistry, Quaid-i-azam University, Islamabad, Pakistan
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - G. Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Brad M. Binder
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Véronique Santoni
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- *Correspondence: Véronique Santoni, ; Christian Chervin,
| | - Christian Chervin
- GBF, Université de Toulouse, INRA, Toulouse, France
- *Correspondence: Véronique Santoni, ; Christian Chervin,
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Harkey AF, Yoon GM, Seo DH, DeLong A, Muday GK. Light Modulates Ethylene Synthesis, Signaling, and Downstream Transcriptional Networks to Control Plant Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1094. [PMID: 31572414 PMCID: PMC6751313 DOI: 10.3389/fpls.2019.01094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 08/09/2019] [Indexed: 05/17/2023]
Abstract
The inhibition of hypocotyl elongation by ethylene in dark-grown seedlings was the basis of elegant screens that identified ethylene-insensitive Arabidopsis mutants, which remained tall even when treated with high concentrations of ethylene. This simple approach proved invaluable for identification and molecular characterization of major players in the ethylene signaling and response pathway, including receptors and downstream signaling proteins, as well as transcription factors that mediate the extensive transcriptional remodeling observed in response to elevated ethylene. However, the dark-adapted early developmental stage used in these experiments represents only a small segment of a plant's life cycle. After a seedling's emergence from the soil, light signaling pathways elicit a switch in developmental programming and the hormonal circuitry that controls it. Accordingly, ethylene levels and responses diverge under these different environmental conditions. In this review, we compare and contrast ethylene synthesis, perception, and response in light and dark contexts, including the molecular mechanisms linking light responses to ethylene biology. One powerful method to identify similarities and differences in these important regulatory processes is through comparison of transcriptomic datasets resulting from manipulation of ethylene levels or signaling under varying light conditions. We performed a meta-analysis of multiple transcriptomic datasets to uncover transcriptional responses to ethylene that are both light-dependent and light-independent. We identified a core set of 139 transcripts with robust and consistent responses to elevated ethylene across three root-specific datasets. This "gold standard" group of ethylene-regulated transcripts includes mRNAs encoding numerous proteins that function in ethylene signaling and synthesis, but also reveals a number of previously uncharacterized gene products that may contribute to ethylene response phenotypes. Understanding these light-dependent differences in ethylene signaling and synthesis will provide greater insight into the roles of ethylene in growth and development across the entire plant life cycle.
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Affiliation(s)
- Alexandria F. Harkey
- Department of Biology and Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, United States
| | - Gyeong Mee Yoon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Dong Hye Seo
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Alison DeLong
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Gloria K. Muday
- Department of Biology and Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, United States
- *Correspondence: Gloria K. Muday,
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57
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Alaguero-Cordovilla A, Gran-Gómez FJ, Tormos-Moltó S, Pérez-Pérez JM. Morphological Characterization of Root System Architecture in Diverse Tomato Genotypes during Early Growth. Int J Mol Sci 2018; 19:E3888. [PMID: 30563085 PMCID: PMC6321557 DOI: 10.3390/ijms19123888] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
Plant roots exploit morphological plasticity to adapt and respond to different soil environments. We characterized the root system architecture of nine wild tomato species and four cultivated tomato (Solanum lycopersicum L.) varieties during early growth in a controlled environment. Additionally, the root system architecture of six near-isogenic lines from the tomato 'Micro-Tom' mutant collection was also studied. These lines were affected in key genes of ethylene, abscisic acid, and anthocyanin pathways. We found extensive differences between the studied lines for a number of meaningful morphological traits, such as lateral root distribution, lateral root length or adventitious root development, which might represent adaptations to local soil conditions during speciation and subsequent domestication. Taken together, our results provide a general quantitative framework for comparing root system architecture in tomato seedlings and other related species.
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Affiliation(s)
| | | | - Sergio Tormos-Moltó
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain.
- OQOTECH Process Validation System, 03801 Alcoy, Spain.
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58
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Mata CI, Fabre B, Parsons HT, Hertog MLATM, Van Raemdonck G, Baggerman G, Van de Poel B, Lilley KS, Nicolaï BM. Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2018; 9:1626. [PMID: 30467512 PMCID: PMC6235968 DOI: 10.3389/fpls.2018.01626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
Ethylene, the plant ripening hormone of climacteric fruit, is perceived by ethylene receptors which is the first step in the complex ethylene signal transduction pathway. Much progress has been made in elucidating the mechanism of this pathway, but there is still a lot to be done in the proteomic quantification of the main proteins involved, particularly during fruit ripening. This work focuses on the mass spectrometry based identification and quantification of the ethylene receptors (ETRs) and the downstream components of the pathway, CTR-like proteins (CTRs) and ETHYLENE INSENSITIVE 2 (EIN2). We used tomato as a model fruit to study changes in protein abundance involved in the ethylene signal transduction during fruit ripening. In order to detect and quantify these low abundant proteins located in the membrane of the endoplasmic reticulum, we developed a workflow comprising sample fractionation and MS analysis using parallel reaction monitoring. This work shows the feasibility of the identification and absolute quantification of all seven ethylene receptors, three out of four CTRs and EIN2 in four ripening stages of tomato. In parallel, gene expression was analyzed through real-time qPCR. Correlation between transcriptomic and proteomic profiles during ripening was only observed for three of the studied proteins, suggesting that the other signaling proteins are likely post-transcriptionally regulated. Based on our quantification results we were able to show that the protein levels of SlETR3 and SlETR4 increased during ripening, probably to control ethylene sensitivity. The other receptors and CTRs showed either stable levels that could sustain, or decreasing levels that could promote fruit ripening.
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Affiliation(s)
- Clara I. Mata
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bertrand Fabre
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Harriet T. Parsons
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Maarten L. A. T. M. Hertog
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Geert Van Raemdonck
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Bram Van de Poel
- Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Bart M. Nicolaï
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
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59
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Wang N, Chen H, Nonaka S, Sato-Izawa K, Kusano M, Ezura H. Ethylene biosynthesis controlled by NON-RIPENING: A regulatory conflict between wounding and ripening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:720-726. [PMID: 30150109 DOI: 10.1016/j.plaphy.2018.07.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
The phytohormone ethylene is involved in multiple aspects of morphological and physiological processes in plants. Tomato rapidly and transiently increases ethylene production during fruit ripening and in plant defense responses. The transcription factor non-ripening (NOR) has significant effects on fruit ripening via regulation of ethylene biosynthesis-related genes. The nor loss-of-function allele produces a basal level of ethylene during ripening, in contrast to the induced ethylene evolution observed upon Agrobacterium tumefaciens infection. The use of ACC deaminase represses ethylene production and significantly improves the efficiency of Agrobacterium-mediated T-DNA transfer in nor plants. Analyses of the transcription levels of the ethylene biosynthesis genes ACC synthase (ACS) and ACC oxidase (ACO) in nor plants revealed that the induced ethylene production was largely due to transcriptional accumulation of ACS2 and ACO1. Accumulation of ACS2 and ACO1 mRNA opposes NOR-mediated regulation in tomato fruit during ripening, and the feedback regulation of NOR is rendered ineffective by defense responses, thereby precluding the control of its own expression. The ethylene synthesis mechanisms respond properly to NOR-mediated transcriptional regulation that is differed through the wound-induced and ripening-induced signaling pathway.
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Affiliation(s)
- Ning Wang
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Haoting Chen
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Satoko Nonaka
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kanna Sato-Izawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Miyako Kusano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan; RIKEN Center for Sustainable Resource Science (CSRS), Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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60
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Mubarok S, Hoshikawa K, Okabe Y, Yano R, Tri MD, Ariizumi T, Ezura H. Evidence of the functional role of the ethylene receptor genes SlETR4 and SlETR5 in ethylene signal transduction in tomato. Mol Genet Genomics 2018; 294:301-313. [PMID: 30382349 DOI: 10.1007/s00438-018-1505-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/21/2018] [Indexed: 12/24/2022]
Abstract
Ethylene receptors are key factors for ethylene signal transduction. In tomato, six ethylene receptor genes (SlETR1-SlETR6) have been identified. Mutations in different ethylene receptor genes result in different phenotypes that are useful for elucidating the roles of each gene. In this study, we screened mutants of two ethylene receptor genes, SLETR4 and SLETR5, from a Micro-Tom mutant library generated by TILLING. We identified two ethylene receptor mutants with altered phenotypes and named them Sletr4-1 and Sletr5-1. Sletr4-1 has a mutation between the transmembrane and GAF domains, while Sletr5-1 has a mutation within the GAF domain. Sletr4-1 showed increased hypocotyl and root lengths, compared to those of wild type plants, under ethylene exposure. Moreover, the fruit shelf life of this mutant was extended, titratable acidity was increased and total soluble solids were decreased, suggesting a reduced ethylene sensitivity. In contrast, in the absence of exogenous ethylene, the hypocotyl and root lengths of Sletr5-1 were shorter than those of the wild type, and the fruit shelf life was shorter, suggesting that these mutants have increased ethylene sensitivity. Gene expression analysis showed that SlNR was up-regulated in the Sletr5-1 mutant line, in contrast to the down-regulation observed in the Sletr4-1 mutant line, while the down-regulation of SlCTR1, SlEIN2, SlEIL1, SlEIL3, and SlERF.E4 was observed in Sletr4-1 mutant allele, suggesting that these two ethylene receptors have functional roles in ethylene signalling and demonstrating, for the first time, a function of the GAF domain of ethylene receptors. These results suggest that the Sletr4-1 and Sletr5-1 mutants are useful for elucidating the complex mechanisms of ethylene signalling through the analysis of ethylene receptors in tomato.
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Affiliation(s)
- Syariful Mubarok
- Department of Agronomy, Faculty of Agriculture, Padjadjaran University, Bandung, 45363, Indonesia.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Ken Hoshikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.,Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Yoshihiro Okabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.,Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Ryoichi Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | | | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.,Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan. .,Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan.
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Parida AP, Raghuvanshi U, Pareek A, Singh V, Kumar R, Sharma AK. Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses. Mol Biol Rep 2018; 45:2653-2669. [PMID: 30350236 DOI: 10.1007/s11033-018-4435-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/10/2018] [Indexed: 01/25/2023]
Abstract
In tomato, DNA methylation has an inhibitory effect on fruit ripening. The inhibition of DNA methyltransferase by 5-azacytidine results in premature fruit ripening. Methyl CpG binding domain (MBD) proteins are the readers of DNA methylation marks and help in the recruitment of chromatin-modifying enzymes which affect gene expression. Therefore, we investigate their contribution during fruit development. In this study, we identified and analyzed 18 putative genes of Solanum lycopersicum and Solanum pimpinellifolium encoding MBD proteins. We also identified tomato MBD syntelogs in Capsicum annum and Solanum tuberosum. Sixty-three MBD genes identified from four different species of solanaceae were classified into three groups. An analysis of the conserved domains in these proteins identified additional domains along with MBD motif. The transcript profiling of tomato MBDs in wild-type and two non-ripening mutants, rin and Nr, indicated constructive information regarding their involvement during fruit development. When we performed a stage-specific expression analysis during fruit ripening, a gradual decrease in transcript accumulation in the wild-type fruit was detected. However, a very low expression was observed in the ripening mutants. Furthermore, many ethylene-responsive cis-elements were found in SlMBD gene promoters, and some of them were induced in the presence of exogenous ethylene. Further, we detected the possible role of these MBDs in abiotic stresses. We found that few genes were differentially expressed under various abiotic stress conditions. Our results provide an evidence of the involvement of the tomato MBDs in fruit ripening and abiotic stress responses, which would be helpful in further studies on these genes in tomato fruit ripening.
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Affiliation(s)
- Adwaita Prasad Parida
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Amit Pareek
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Vijendra Singh
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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Guo H, Sun Y, Yan H, Li C, Ge F. O 3-Induced Leaf Senescence in Tomato Plants Is Ethylene Signaling-Dependent and Enhances the Population Abundance of Bemisia tabaci. FRONTIERS IN PLANT SCIENCE 2018; 9:764. [PMID: 29946327 PMCID: PMC6005859 DOI: 10.3389/fpls.2018.00764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/17/2018] [Indexed: 05/27/2023]
Abstract
Elevated ozone (O3) can alter the phenotypes of host plants particularly in induction of leaf senescence, but few reports examine the involvement of phytohormone in O3-induced changes in host phenotypes that influence the foraging quality for insects. Here, we used an ethylene (ET) receptor mutant Nr and its wild-type to determine the function of the ET signaling pathway in O3-induced leaf senescence, and bottom-up effects on the performance of Bemisia tabaci in field open-top chambers (OTCs). Our results showed that elevated O3 reduced photosynthetic efficiency and chlorophyll content and induced leaf senescence of plant regardless of plant genotype. Leaf senescence in Nr plants was alleviated relative to wild-type under elevated O3. Further analyses of foliar quality showed that elevated O3 had little effect on phytohormone-mediated defenses, but significantly increased the concentration of amino acids in two plant genotypes. Furthermore, Nr plants had lower amino acid content relative to wild-type under elevated O3. These results provided an explanation of O3-induced increase in abundance of B. tabaci. We concluded that O3-induced senescence of plant was ET signal-dependent, and positive effects of O3-induced leaf senescence on the performance of B. tabaci largely resulted from changes of nutritional quality of host plants.
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Affiliation(s)
- Honggang Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yucheng Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongyu Yan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Feng Ge
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Zhang L, Zhu M, Ren L, Li A, Chen G, Hu Z. The SlFSR gene controls fruit shelf-life in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2897-2909. [PMID: 29635354 PMCID: PMC5972576 DOI: 10.1093/jxb/ery116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/23/2018] [Indexed: 05/29/2023]
Abstract
Fruit ripening represents a process that changes flavor and appearance and also a process that dramatically increases fruit softening. Fruit softening and textural variations mainly result from disruptions to the cell walls of the fruit throughout ripening, but the exact mechanisms and specific modifications of the cell wall remain unclear. Plant-specific GRAS proteins play a critical role in development and growth. To date, few GRAS genes have been functionally categorized in tomato. The expression of a novel GRAS gene described in this study and designated as SlFSR (fruit shelf-life regulator) specifically increased during fruit ripening, but was significantly decreased in the tomato mutant rin (ripening inhibitor). RNAi repression of SlFSR resulted in reduced expression of multiple cell wall modification-related genes, decreased the activities of PG (polygalacturonase), TBG (tomato β-galactosidase), CEL (cellulase), and XYL (β-D-xylosidase), and significantly prolonged fruit shelf-life. Furthermore, overexpression of SlFSR in mutant rin gave rise to up-regulated expression of multiple cell wall modification-related genes, such as PG, TBG4, CEL2, XYL1, PL, PE, MAN1, EXP1, and XTH5, and significantly shortened the fruit shelf-life. These findings reveal some of the genetic mechanisms underlying fruit cell wall metabolism and suggest that the SlFSR gene is another potential biotechnological target for the control of tomato fruit shelf-life.
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Affiliation(s)
- Lincheng Zhang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Mingku Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Lijun Ren
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Anzhou Li
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Guoping Chen
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Zongli Hu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
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Saraiva LA, Castelan FP, Gomes BL, Purgatto E, Cordenunsi-Lysenko BR. Thap Maeo bananas: Fast ripening and full ethylene perception at low doses. Food Res Int 2018; 105:384-392. [DOI: 10.1016/j.foodres.2017.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/19/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
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A tomato MADS-box protein, SlCMB1, regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening. Sci Rep 2018; 8:3413. [PMID: 29467500 PMCID: PMC5821886 DOI: 10.1038/s41598-018-21672-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/07/2018] [Indexed: 12/30/2022] Open
Abstract
The MADS-box transcription factors play essential roles in many physiological and biochemical processes of plants, especially in fruit ripening. Here, a tomato MADS-box gene, SlCMB1, was isolated. SlCMB1 expression declined with the fruit ripening from immature green to B + 7 (7 days after Breaker) fruits in the wild type (WT) and was lower in Nr and rin mutants fruits. Tomato plants with reduced SlCMB1 mRNA displayed delayed fruit ripening, reduced ethylene production and carotenoid accumulation. The ethylene production in SlCMB1-RNAi fruits decreased by approximately 50% as compared to WT. The transcripts of ethylene biosynthesis genes (ACS2, ACS4, ACO1 and ACO3), ethylene-responsive genes (E4, E8 and ERF1) and fruit ripening-related genes (RIN, TAGL1, FUL1, FUL2, LoxC and PE) were inhibited in SlCMB1-RNAi fruits. The carotenoid accumulation was decreased and two carotenoid synthesis-related genes (PSY1 and PDS) were down-regulated while three lycopene cyclase genes (CYCB, LCYB and LCYE) were up-regulated in transgenic fruits. Furthermore, yeast two-hybrid assay showed that SlCMB1 could interact with SlMADS-RIN, SlMADS1, SlAP2a and TAGL1, respectively. Collectively, these results indicate that SlCMB1 is a new component to the current model of regulatory network that regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening.
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Yu W, Peng F, Xiao Y, Wang G, Luo J. Overexpression of PpSnRK1α in Tomato Promotes Fruit Ripening by Enhancing RIPENING INHIBITOR Regulation Pathway. FRONTIERS IN PLANT SCIENCE 2018; 9:1856. [PMID: 30619421 PMCID: PMC6304366 DOI: 10.3389/fpls.2018.01856] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/30/2018] [Indexed: 05/14/2023]
Abstract
As a conserved kinase complex, sucrose non-fermenting-1-related protein kinase 1 (SnRK1) is a major regulator of plant growth and development. In our previous study, overexpression of MhSnRK1 in tomato (Solanum lycopersicum L.) modified fruit maturation: the transgenic fruit ripened earlier than the wild type (WT). However, the mechanism by which fruit maturation is regulated by SnRK1 is not clear; therefore, the test materials used were the transgenic tomato lines (OE-1, OE-3, and OE-4) overexpressing the coding gene of peach [Prunus persica (L.) Batsch] SNF1-related kinase α subunit (PpSnRK1α). The activity of SnRK1 kinase in transgenic tomato lines OE-1, OE-3, and OE-4 was higher than that in the WT at different periods of fruit development; in the pink coloring period the SnRK1 kinase activity increased the most, with 23.5, 28.8, and 21.4% increases, respectively. The content of starch and soluble sugars in red ripe transgenic fruit significantly increased, while the soluble protein and titratable acid content decreased significantly. We also found that the tomatoes overexpressing PpSnRK1α matured approximately 10 days earlier than the WT. Moreover, the yeast-two-hybrid assay showed that PpSnRK1α interacted with the MADS-box transcription factor (TF) SIRIN, which acts as an essential regulator of tomato fruit ripening. The BiFC technology further validated the location of the PpSnRK1α interaction sites within the nucleus. The quantitative real-time PCR analysis showed that RIN expression was up-regulated by PpSnRK1α overexpression; the expression of RIN-targeted TF genes NOR and FUL1 increased during different stages of fruit development. The expression of key genes, ACS2, ACS4, and E8, in ethylene synthesis also changed accordingly, and the ethylene emitted by the red ripe fruit increased by 36.1-43.9% compared with the WT. These results suggest that PpSnRK1α interacts with SIRIN, increasing the expression of RIN, thereby regulating the expression of downstream ripening-related genes, finally promoting fruit ripening.
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Affiliation(s)
- Wen Yu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Futian Peng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- *Correspondence: Futian Peng, Yuansong Xiao,
| | - Yuansong Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- *Correspondence: Futian Peng, Yuansong Xiao,
| | | | - Jingjing Luo
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
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Ibort P, Imai H, Uemura M, Aroca R. Proteomic analysis reveals that tomato interaction with plant growth promoting bacteria is highly determined by ethylene perception. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:43-59. [PMID: 29145071 DOI: 10.1016/j.jplph.2017.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/27/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Feeding an increasing global population as well as reducing environmental impact of crops is the challenge for the sustainable intensification of agriculture. Plant-growth-promoting bacteria (PGPB) management could represent a suitable method but elucidation of their action mechanisms is essential for a proper and effective utilization. Furthermore, ethylene is involved in growth and response to environmental stimuli but little is known about the implication of ethylene perception in PGPB activity. The ethylene-insensitive tomato never ripe and its isogenic wild-type cv. Pearson lines inoculated with Bacillus megaterium or Enterobacter sp. C7 strains were grown until mature stage to analyze growth promotion, and bacterial inoculation effects on root proteomic profiles. Enterobacter C7 promoted growth in both plant genotypes, meanwhile Bacillus megaterium PGPB activity was only noticed in wt plants. Moreover, PGPB inoculation affected proteomic profile in a strain- and genotype-dependent manner modifying levels of stress-related and interaction proteins, and showing bacterial inoculation effects on antioxidant content and phosphorus acquisition capacity. Ethylene perception is essential for properly recognition of Bacillus megaterium and growth promotion mediated in part by increased levels of reduced glutathione. In contrast, Enterobacter C7 inoculation improves phosphorus nutrition keeping plants on growth independently of ethylene sensitivity.
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Affiliation(s)
- Pablo Ibort
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain.
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain.
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Guo JE, Hu Z, Yu X, Li A, Li F, Wang Y, Tian S, Chen G. A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation. PLANT CELL REPORTS 2018; 37:125-135. [PMID: 28932910 DOI: 10.1007/s00299-017-2211-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/12/2017] [Indexed: 05/04/2023]
Abstract
SlHDA3 functions as an inhibitor and regulates tomato fruit ripening and carotenoid accumulation. Post-translational modifications, including histones acetylation, play a pivotal role in the changes of chromatin structure dynamic modulation and gene activity. The regulation of histone acetylation is achieved by the action of histone acetyltransferases and deacetylases, which play crucial roles in the regulation of transcription activation. There is an increasing research focus on histone deacetylation in crops, but the role of histone deacetylase genes (HDACs) in tomato has not been elucidated. With the aim of characterizing the tomato RPD3/HDA1 family histone deacetylase genes, SlHDA3 was isolated and its RNA interference (RNAi) lines was obtained. The fruit of SlHDA3 RNAi lines exhibited accelerated ripening process along with short shelf life characteristics. The accumulation of carotenoid was increased due to the alteration of the carotenoid pathway flux. Climacteric ethylene production also stimulated along with significantly up-regulated expression of ethylene biosynthetic genes (ACS2, ACS4, ACO1 and ACO3) and fruit ripening-associated genes (RIN, E4, E8, PG, Pti4, LOXB, Cnr and TAGL1) in SlHDA3 RNAi lines. Besides, fruit cell wall metabolism-associated genes (HEX, MAN, TBG4, XTH5 and XYL) were enhanced in transgenic lines. Relative to wild type (WT) plants, SlHDA3 RNAi seedlings displayed shorter hypocotyls and more sensitivity to ACC (1-aminocyclopropane-1-carboxylate). These results indicated that SlHDA3 is involved in the regulation of fruit ripening by affecting ethylene biosynthesis and carotenoid accumulation.
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Affiliation(s)
- Jun-E Guo
- Room 523, Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Zongli Hu
- Room 523, Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Xiaohui Yu
- Room 523, Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Anzhou Li
- Room 523, Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Fenfen Li
- Room 523, Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Yunshu Wang
- Room 523, Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China
| | - Shibing Tian
- The Institute of Vegetable Research, Chongqing Academy of Agricultural Sciences, Chongqing, 401329, People's Republic of China
| | - Guoping Chen
- Room 523, Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400044, People's Republic of China.
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69
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Guo JE, Hu Z, Li F, Zhang L, Yu X, Tang B, Chen G. Silencing of histone deacetylase SlHDT3 delays fruit ripening and suppresses carotenoid accumulation in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:29-38. [PMID: 29223340 DOI: 10.1016/j.plantsci.2017.09.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 05/15/2023]
Abstract
The acetylation levels of histones on lysine residues are regulated by histone acetyltransferases and histone deacetylases, which play an important but understudied role in the control of gene expression in plants. There is an increasing research focus on histone deacetylation in crops, but to date, there is little information regarding tomato. With the aim of characterizing the tomato HD2 family of histone deacetylases, an RNA interference (RNAi) expression vector of SlHDT3 was constructed and transformed into tomato plants. The time of fruit ripening was delayed and the shelf life of the fruit was prolonged in SlHDT3 RNAi lines. The accumulation of carotenoid was decreased by altering of the carotenoid pathway flux. Ethylene content was also reduced and expression of ethylene biosynthetic genes (ACS2, ACS4 and ACO1, ACO3) and ripening-associated genes (RIN, E4, E8, PG, Pti4 and LOXB) was significantly down-regulated in SlHDT3 RNAi lines. The expression of genes involved in fruit cell wall metabolism (HEX, MAN, TBG4, XTH5 and XYL) was inhibited compared with wild type. These results indicate that SlHDT3 functions as a positive regulator of fruit ripening by affecting ethylene synthesis and carotenoid accumulation and that SlHDT3 lies upstream of SlMADS-RIN in the fruit ripening regulatory network.
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Affiliation(s)
- Jun-E Guo
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
| | - Zongli Hu
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
| | - Fenfen Li
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
| | - Lincheng Zhang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
| | - Xiaohui Yu
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
| | - Boyan Tang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
| | - Guoping Chen
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China.
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Liu J, Zhang J, Miao H, Jia C, Wang J, Xu B, Jin Z. Elucidating the Mechanisms of the Tomato ovate Mutation in Regulating Fruit Quality Using Proteomics Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10048-10057. [PMID: 29120173 DOI: 10.1021/acs.jafc.7b03656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The ovate mutation has frequently been used to study changes in fruit shape but not fruit quality. A deterioration in fruit quality associated with the ovate mutation was discovered in this study. To elucidate how ovate influences the quality of fruit, we performed a proteomics analysis of the fruits of the ovate mutant (LA3543) and wild-type ("Ailsa Craig", LA2838A) using tandem mass tag analysis. The results indicated that the ovate mutation significantly influences fruit quality in a number of ways, including by reducing the expression of 1-aminocyclopropane-1-carboxylic acid oxidase 3 (ACO3) in ethylene biosynthesis, improving firmness by reducing the amount of pectinesterase and polygalacturonase, reducing sugar accumulation by downregulating the abundance of mannan endo-1,4-β-mannosidase 4, β-galactosidase, and β-amylase, and reducing the malic acid content by downregulating the accumulation of malic enzymes and malate synthase. These findings could inform future improvements in fruit quality.
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Affiliation(s)
- Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Jing Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , 4 Xueyuan Road, Haikou 571101, China
- Key Laboratory of Genetic Improvement of Bananas, Chinese Academy of Tropical Agricultural Sciences , Haikou Experimental Station, Haikou, Hainan Province 570102, China
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Calvo-Polanco M, Ibort P, Molina S, Ruiz-Lozano JM, Zamarreño AM, García-Mina JM, Aroca R. Ethylene sensitivity and relative air humidity regulate root hydraulic properties in tomato plants. PLANTA 2017; 246:987-997. [PMID: 28735369 DOI: 10.1007/s00425-017-2746-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
The effect of ethylene and its precursor ACC on root hydraulic properties, including aquaporin expression and abundance, is modulated by relative air humidity and plant sensitivity to ethylene. Relative air humidity (RH) is a main factor contributing to water balance in plants. Ethylene (ET) is known to be involved in the regulation of root water uptake and stomatal opening although its role on plant water balance under different RH is not very well understood. We studied, at the physiological, hormonal and molecular levels (aquaporins expression, abundance and phosphorylation state), the plant responses to exogenous 1-aminocyclopropane-1-carboxylic acid (ACC; precursor of ET) and 2-aminoisobutyric acid (AIB; inhibitor of ET biosynthesis), after 24 h of application to the roots of tomato wild type (WT) plants and its ET-insensitive never ripe (nr) mutant, at two RH levels: regular (50%) and close to saturation RH. Highest RH induced an increase of root hydraulic conductivity (Lpo) of non-treated WT plants, and the opposite effect in nr mutants. The treatment with ACC reduced Lpo in WT plants at low RH and in nr plants at high RH. The application of AIB increased Lpo only in nr plants at high RH. In untreated plants, the RH treatment changed the abundance and phosphorylation of aquaporins that affected differently both genotypes according to their ET sensitivity. We show that RH is critical in regulating root hydraulic properties, and that Lpo is affected by the plant sensitivity to ET, and possibly to ACC, by regulating aquaporins expression and their phosphorylation status. These results incorporate the relationship between RH and ET in the response of Lpo to environmental changes.
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Affiliation(s)
- Monica Calvo-Polanco
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
- SupAgro/INRA UMR 5004, Biochimie et Physiologie Moléculaire des Plantes, 2, Place Viala, 34060, Montpellier Cedex 2, France
| | - Pablo Ibort
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Sonia Molina
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Juan Manuel Ruiz-Lozano
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Angel María Zamarreño
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain
| | - Jose María García-Mina
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain
| | - Ricardo Aroca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain.
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Yin W, Hu Z, Cui B, Guo X, Hu J, Zhu Z, Chen G. Suppression of the MADS-box gene SlMBP8 accelerates fruit ripening of tomato (Solanum lycopersicum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:235-244. [PMID: 28649000 DOI: 10.1016/j.plaphy.2017.06.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 05/21/2023]
Abstract
MADS-box genes encode important transcription factors that are involved in many biological processes of plants, including fruit ripening. In our research, a MADS-box gene, SlMBP8, was identified, and its tissue-specific expression profiles were analysed. SlMBP8 was highly expressed in fruits of the B+4 stage, in senescent leaves and in sepals. To further characterize its function, an RNA interference (RNAi) expression vector of SlMBP8 was constructed and transferred into tomato. In the transgenic plants, the ripening of fruits was shortened by 2-4 days compared to that of wild type. At the same time, carotenoids accumulated to higher levels and the expression of phytone synthase 1 (PSY1), phytoene desaturase (PDS) and ς-carotene desaturase (ZDS) was enhanced in RNAi fruits. The transgenic fruits and seedlings showed more ethylene production compared with that of the wild type. Furthermore, SlMBP8-silenced seedlings displayed shorter hypocotyls due to higher endogenous ethylene levels, suggesting that SlMBP8 may modulates the ethylene triple response negatively. A yeast two-hybrid assay indicated that SlMBP8 could interact with SlMADS-RIN. Besides, the expression of ethylene-related genes, including ACO1, ACO3, ACS2, ERF1, E4 and E8, was simultaneously up-regulated in transgenic plants. In addition, SlMBP8-silenced fruits showed higher ethylene production, suggesting that suppressed expression of SlMBP8 promotes carotenoid and ethylene biosynthesis. In addition, the fruits of transgenic plants displayed more rapid water loss and decreased storability compared to wild type, which was due to the significantly induced expressions of cell wall metabolism genes such as PG, EXP, HEX, TBG4, XTH5 and XYL. These results suggest that SlMBP8 plays an important role in fruit ripening and softening.
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Affiliation(s)
- Wencheng Yin
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Baolu Cui
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Xuhu Guo
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Jingtao Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Zhiguo Zhu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, PR China.
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73
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Di X, Gomila J, Takken FLW. Involvement of salicylic acid, ethylene and jasmonic acid signalling pathways in the susceptibility of tomato to Fusarium oxysporum. MOLECULAR PLANT PATHOLOGY 2017; 18:1024-1035. [PMID: 28390170 PMCID: PMC6638294 DOI: 10.1111/mpp.12559] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/27/2017] [Accepted: 04/03/2017] [Indexed: 05/05/2023]
Abstract
Phytohormones, such as salicylic acid (SA), ethylene (ET) and jasmonic acid (JA), play key roles in plant defence following pathogen attack. The involvement of these hormones in susceptibility following Fusarium oxysporum (Fo) infection has mostly been studied in Arabidopsis thaliana. However, Fo causes vascular wilt disease in a broad range of crops, including tomato (Solanum lycopersicum). Surprisingly little is known about the involvement of these phytohormones in the susceptibility of tomato towards Fo f. sp. lycopersici (Fol). Here, we investigate their involvement by the analysis of the expression of ET, JA and SA marker genes following Fol infection, and by bioassays of tomato mutants affected in either hormone production or perception. Fol inoculation triggered the expression of SA and ET marker genes, showing the activation of these pathways. NahG tomato, in which SA is degraded, became hypersusceptible to Fol infection and showed stronger disease symptoms than wild-type. In contrast, ACD and Never ripe (Nr) mutants, in which ET biosynthesis and perception, respectively, are impaired, showed decreased disease symptoms and reduced fungal colonization on infection. The susceptibility of the def1 tomato mutant, and a prosystemin over-expressing line, in which JA signalling is compromised or constitutively activated, respectively, was unaltered. Our results show that SA is a negative and ET a positive regulator of Fol susceptibility. The SA and ET signalling pathways appear to act synergistically, as an intact ET pathway is required for the induction of an SA marker gene, and vice versa.
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Affiliation(s)
- Xiaotang Di
- Molecular Plant Pathology, Faculty of ScienceSwammerdam Institute for Life Sciences, University of AmsterdamPO Box 94215, 1090GEAmsterdamthe Netherlands
| | - Jo Gomila
- Molecular Plant Pathology, Faculty of ScienceSwammerdam Institute for Life Sciences, University of AmsterdamPO Box 94215, 1090GEAmsterdamthe Netherlands
| | - Frank L. W. Takken
- Molecular Plant Pathology, Faculty of ScienceSwammerdam Institute for Life Sciences, University of AmsterdamPO Box 94215, 1090GEAmsterdamthe Netherlands
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74
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Guo JE, Hu Z, Zhu M, Li F, Zhu Z, Lu Y, Chen G. The tomato histone deacetylase SlHDA1 contributes to the repression of fruit ripening and carotenoid accumulation. Sci Rep 2017; 7:7930. [PMID: 28801625 PMCID: PMC5554242 DOI: 10.1038/s41598-017-08512-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
Histone deacetylation is one of the well characterized post-translational modifications related to transcriptional repression in eukaryotes. The process of histone deacetylation is achieved by histone deacetylases (HDACs). Over the last decade, substantial advances in our understanding of the mechanism of fruit ripening have been achieved, but the role of HDACs in this process has not been elucidated. In our study, an RNA interference (RNAi) expression vector targeting SlHDA1 was constructed and transformed into tomato plants. Shorter fruit ripening time and decreased storability were observed in SlHDA1 RNAi lines. The accumulation of carotenoid was increased through an alteration of the carotenoid pathway flux. Ethylene content, ethylene biosynthesis genes (ACS2, ACS4 and ACO1, ACO3) and ripening-associated genes (RIN, E4, E8, Cnr, TAGL1, PG, Pti4 and LOXB) were significantly up-regulated in SlHDA1 RNAi lines. In addition, the expression of fruit cell wall metabolism genes (HEX, MAN, TBG4, XTH5 and XYL) was enhanced compared with wild type. Furthermore, SlHDA1 RNAi seedlings displayed shorter hypocotyls and were more sensitive to ACC (1-aminocyclopropane-1-carboxylate) than the wild type. The results of our study indicate that SlHDA1 functions as a negative regulator of fruit ripening by affecting ethylene synthesis and carotenoid accumulation.
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Affiliation(s)
- Jun-E Guo
- Laboratory of molecular biology of tomato (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Zongli Hu
- Laboratory of molecular biology of tomato (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Mingku Zhu
- Laboratory of molecular biology of tomato (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Fenfen Li
- Laboratory of molecular biology of tomato (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Zhiguo Zhu
- Laboratory of molecular biology of tomato (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Yu Lu
- Laboratory of molecular biology of tomato (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Guoping Chen
- Laboratory of molecular biology of tomato (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China.
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75
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Shukla V, Upadhyay RK, Tucker ML, Giovannoni JJ, Rudrabhatla SV, Mattoo AK. Transient regulation of three clustered tomato class-I small heat-shock chaperone genes by ethylene is mediated by SlMADS-RIN transcription factor. Sci Rep 2017; 7:6474. [PMID: 28743906 PMCID: PMC5527083 DOI: 10.1038/s41598-017-06622-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/27/2017] [Indexed: 11/24/2022] Open
Abstract
Clustered class-I small heat-shock protein (sHSP) chaperone genes, SlHSP17.6, SlHSP20.0 and SlHSP20.1, in tomato are demonstrated to be transcriptionally regulated by ethylene during mature green (MG) fruit transition into ripening. These genes are constitutively expressed at MG fruit stage in two different tomato genotypes as well as in their ripening mutants, including rin, nor and Nr, and an ethylene-deficient transgenic line, ACS2-antisense. Notably, ethylene treatment of the MG fruit led to significant sHSP gene suppression in both wild-types, ACS2-antisense, nor/nor and Nr/Nr, but not the rin/rin mutant. Inability of ethylene to suppress sHSP genes in rin/rin mutant, which harbors MADS-RIN gene mutation, suggests that MADS-RIN transcription factor regulates the expression of these genes. Treatment of the wild type and ACS2-antisense fruit with the ethylene-signaling inhibitor, 1-methylcyclopropane (1-MCP), reversed the sHSP gene suppression. Transcripts of representative ethylene-responsive and ripening-modulated genes confirmed and validated sHSP transcript profile patterns. In silico analysis in conjunction with chromatin immunoprecipitation demonstrated MADS-RIN protein binding to specific CArG motifs present in the promoters of these chaperone genes. The results establish MADS-RIN protein as a transcriptional regulator of these chaperone genes in an ethylene-dependent manner, and that MADS-RIN protein-regulation of sHSPs is integral to tomato fruit ripening.
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Affiliation(s)
- Vijaya Shukla
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA.,Department of Biology, Penn State University at Harrisburg, Middletown, PA, 170-57, USA
| | - Rakesh K Upadhyay
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA.,Department of Biology, Penn State University at Harrisburg, Middletown, PA, 170-57, USA
| | - Mark L Tucker
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - James J Giovannoni
- USDA-ARS Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Cornell University campus, Ithaca, NY, 14853, USA
| | - Sairam V Rudrabhatla
- Department of Biology, Penn State University at Harrisburg, Middletown, PA, 170-57, USA
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA.
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Ibort P, Molina S, Núñez R, Zamarreño ÁM, García-Mina JM, Ruiz-Lozano JM, Orozco-Mosqueda MDC, Glick BR, Aroca R. Tomato ethylene sensitivity determines interaction with plant growth-promoting bacteria. ANNALS OF BOTANY 2017; 120:101-122. [PMID: 28586422 PMCID: PMC5737082 DOI: 10.1093/aob/mcx052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/20/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Plant growth-promoting bacteria (PGPB) are soil micro-organisms able to interact with plants and stimulate their growth, positively affecting plant physiology and development. Although ethylene plays a key role in plant growth, little is known about the involvement of ethylene sensitivity in bacterial inoculation effects on plant physiology. Thus, the present study was pursued to establish whether ethylene perception is critical for plant-bacteria interaction and growth induction by two different PGPB strains, and to assess the physiological effects of these strains in juvenile and mature tomato ( Solanum lycopersicum ) plants. METHODS An experiment was performed with the ethylene-insensitive tomato never ripe and its isogenic wild-type line in which these two strains were inoculated with either Bacillus megaterium or Enterobacter sp. C7. Plants were grown until juvenile and mature stages, when biomass, stomatal conductance, photosynthesis as well as nutritional, hormonal and metabolic statuses were analysed. KEY RESULTS Bacillus megaterium promoted growth only in mature wild type plants. However, Enterobacter C7 PGPB activity affected both wild-type and never ripe plants. Furthermore, PGPB inoculation affected physiological parameters and root metabolite levels in juvenile plants; meanwhile plant nutrition was highly dependent on ethylene sensitivity and was altered at the mature stage. Bacillus megaterium inoculation improved carbon assimilation in wild-type plants. However, insensitivity to ethylene compromised B. megaterium PGPB activity, affecting photosynthetic efficiency, plant nutrition and the root sugar content. Nevertheless, Enterobacter C7 inoculation modified the root amino acid content in addition to stomatal conductance and plant nutrition. CONCLUSIONS Insensitivity to ethylene severely impaired B. megaterium interaction with tomato plants, resulting in physiological modifications and loss of PGPB activity. In contrast, Enterobacter C7 inoculation stimulated growth independently of ethylene perception and improved nitrogen assimilation in ethylene-insensitive plants. Thus, ethylene sensitivity is a determinant for B. megaterium , but is not involved in Enterobacter C7 PGPB activity.
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Affiliation(s)
- Pablo Ibort
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Sonia Molina
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Rafael Núñez
- Scientific Instrumental Service, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Ángel María Zamarreño
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain
| | - José María García-Mina
- Department of Environmental Biology, Agricultural Chemistry and Biology Group-CMI Roullier, Faculty of Sciences, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain
| | - Juan Manuel Ruiz-Lozano
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | | | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain
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Szymanski J, Levin Y, Savidor A, Breitel D, Chappell-Maor L, Heinig U, Töpfer N, Aharoni A. Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:396-417. [PMID: 28112434 DOI: 10.1111/tpj.13490] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 05/18/2023]
Abstract
Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large-scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages. The depth of our assay enabled identification of 61 differentially expressed transcription factors, including renowned ripening-related regulators and elements of ethylene signaling. Significantly, we measured proteins involved in 83% of all predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were identified, including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns, which is most significant in light of the weak transcript-protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique view of skin and flesh tissues in developing fruit. This study adds a new dimension to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post-translational research in tomato and additional species, which is presently focused on transcription.
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Affiliation(s)
- Jedrzej Szymanski
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Alon Savidor
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dario Breitel
- Metabolic Biology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Louise Chappell-Maor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Uwe Heinig
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nadine Töpfer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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78
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Jue D, Sang X, Shu B, Liu L, Wang Y, Jia Z, Zou Y, Shi S. Characterization and expression analysis of genes encoding ubiquitin conjugating domain-containing enzymes in Carica papaya. PLoS One 2017; 12:e0171357. [PMID: 28231288 PMCID: PMC5322903 DOI: 10.1371/journal.pone.0171357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/18/2017] [Indexed: 11/25/2022] Open
Abstract
Background Ripening affects the quality and nutritional contents of fleshy fruits and is a crucial process of fruit development. Although several studies have suggested that ubiquitin-conjugating enzyme (E2s or UBC enzymes) are involved in the regulation of fruit ripening, little is known about the function of E2s in papaya (Carica papaya). Methodology/Principal findings In the present study, we searched the papaya genome and identified 34 putative UBC genes, which were clustered into 17 phylogenetic subgroups. We also analyzed the nucleotide sequences of the papaya UBC (CpUBC) genes and found that both exon-intron junctions and sequence motifs were highly conserved among the phylogenetic subgroups. Using real-time PCR analysis, we also found that all the CpUBC genes were expressed in roots, stems, leaves, male and female flowers, and mature fruit, although the expression of some of the genes was increased or decreased in one or several specific organs. We also found that the expression of 13 and two CpUBC genes were incresesd or decreased during one and two ripening stages, respectively. Expression analyses indicates possible E2s playing a more significant role in fruit ripening for further studies. Conclusions To the best of our knowledge, this is the first reported genome-wide analysis of the papaya UBC gene family, and the results will facilitate further investigation of the roles of UBC genes in fruit ripening and will aide in the functional validation of UBC genes in papaya.
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Affiliation(s)
- Dengwei Jue
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Xuelian Sang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Bo Shu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Liqin Liu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Yicheng Wang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Zhiwei Jia
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Yu Zou
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shengyou Shi
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
- * E-mail:
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Kessenbrock M, Klein SM, Müller L, Hunsche M, Noga G, Groth G. Novel Protein-Protein Inhibitor Based Approach to Control Plant Ethylene Responses: Synthetic Peptides for Ripening Control. FRONTIERS IN PLANT SCIENCE 2017; 8:1528. [PMID: 28928762 PMCID: PMC5591945 DOI: 10.3389/fpls.2017.01528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/21/2017] [Indexed: 05/13/2023]
Abstract
Ethylene signaling is decisive for many plant developmental processes. Among these, control of senescence, abscission and fruit ripening are of fundamental relevance for global agriculture. Consequently, detailed knowledge of the signaling network along with the molecular processes of signal perception and transfer are expected to have high impact on future food production and agriculture. Recent advances in ethylene research have demonstrated that signaling of the plant hormone critically depends on the interaction of the ethylene receptor family with the NRAMP-like membrane protein ETHYLENE INSENSITIVE 2 (EIN2) at the ER membrane, phosphorylation-dependent proteolytic processing of ER-localized EIN2 and subsequent translocation of the cleaved EIN2 C-terminal polypeptide (EIN2-CEND) to the nucleus. EIN2 nuclear transport, but also interaction with the receptors sensing the ethylene signal, both, depend on a nuclear localization signal (NLS) located at the EIN2 C-terminus. Loss of the tight interaction between receptors and EIN2 affects ethylene signaling and impairs plant ethylene responses. Synthetic peptides derived from the NLS sequence interfere with the EIN2-receptor interaction and have utility in controlling plant ethylene responses such as ripening. Here, we report that a synthetic peptide (NOP-1) corresponding to the NLS motif of Arabidopsis EIN2 (aa 1262-1269) efficiently binds to tomato ethylene receptors LeETR4 and NR and delays ripening in the post-harvest phase when applied to the surface of sampled green fruits pre-harvest. In particular, degradation of chlorophylls was delayed by several days, as monitored by optical sensors and confirmed by analytical methods. Similarly, accumulation of β-carotene and lycopene in the fruit pulp after NOP-1 application was delayed, without having impact on the total pigment concentration in the completely ripe fruits. Likewise, the peptide had no negative effects on fruit quality. Our molecular and phenotypic studies reveal that peptide biologicals could contribute to the development of a novel family of ripening inhibitors and innovative ripening control in climacteric fruit.
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Affiliation(s)
- Mareike Kessenbrock
- Institute of Biochemical Plant Physiology, Heinrich Heine University DüsseldorfDüsseldorf, Germany
| | - Simone M. Klein
- Institute of Crop Science and Resource Conservation – Horticultural Science, University of BonnBonn, Germany
| | - Lena Müller
- Institute of Biochemical Plant Physiology, Heinrich Heine University DüsseldorfDüsseldorf, Germany
| | - Mauricio Hunsche
- Institute of Crop Science and Resource Conservation – Horticultural Science, University of BonnBonn, Germany
- COMPO EXPERT GmbHMünster, Germany
| | - Georg Noga
- Institute of Crop Science and Resource Conservation – Horticultural Science, University of BonnBonn, Germany
| | - Georg Groth
- Institute of Biochemical Plant Physiology, Heinrich Heine University DüsseldorfDüsseldorf, Germany
- Bioeconomy Science Center, Forschungszentrum JülichJülich, Germany
- *Correspondence: Georg Groth, ;
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80
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Yang L, Hu G, Li N, Habib S, Huang W, Li Z. Functional Characterization of SlSAHH2 in Tomato Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2017; 8:1312. [PMID: 28798762 PMCID: PMC5526918 DOI: 10.3389/fpls.2017.01312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/12/2017] [Indexed: 05/05/2023]
Abstract
S-adenosylhomocysteine hydrolase (SAHH) functions as an enzyme catalyzing the reversible hydrolysis of S-adenosylhomocysteine to homocysteine and adenosine. In the present work we have investigated its role in the ripening process of tomato fruit. Among the three SlSAHH genes we demonstrated that SlSAHH2 was highly accumulated during fruit ripening and strongly responded to ethylene treatment. Over-expression of SlSAHH2 enhanced SAHH enzymatic activity in tomato fruit development and ripening stages and resulted in a major phenotypic change of reduced ripening time from anthesis to breaker. Consistent with this, the content of lycopene was higher in SlSAHH2 over-expression lines than in wild-type at the same developmental stage. The expression of two ethylene inducible genes (E4 and E8) and three ethylene biosynthesis genes (SlACO1, SlACO3 and SlACS2) increased to a higher level in SlSAHH2 over-expression lines at breaker stage, and one transgenic line even produced much more ethylene than wild-type. Although inconsistency in gene expression and ethylene production existed between the two transgenic lines, the transcriptional changes of several important ripening regulators such as RIN, AP2a, TAGL1, CNR and NOR showed a consistent pattern. It was speculated that the influence of SlSAHH2 on ethylene production was downstream of the regulation of SlSAHH2 on these ripening regulator genes. The over-expressing lines displayed higher sensitivity to ethylene in both fruit and non-fruit tissues. Ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) treatment accelerated ripening faster in SlSAHH2 over-expressing fruit than in wild-type. Additionally, seedlings of transgenic lines displayed shorter hypocotyls and roots in ethylene triple response assay. In conclusion, SlSAHH2 played an important role in tomato fruit ripening.
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81
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Yuan XY, Wang RH, Zhao XD, Luo YB, Fu DQ. Role of the Tomato Non-Ripening Mutation in Regulating Fruit Quality Elucidated Using iTRAQ Protein Profile Analysis. PLoS One 2016; 11:e0164335. [PMID: 27732677 PMCID: PMC5061430 DOI: 10.1371/journal.pone.0164335] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/25/2016] [Indexed: 01/08/2023] Open
Abstract
Natural mutants of the Non-ripening (Nor) gene repress the normal ripening of tomato fruit. The molecular mechanism of fruit ripening regulation by the Nor gene is unclear. To elucidate how the Nor gene can affect ripening and fruit quality at the protein level, we used the fruits of Nor mutants and wild-type Ailsa Craig (AC) to perform iTRAQ (isobaric tags for relative and absolute quantitation) analysis. The Nor mutation altered tomato fruit ripening and affected quality in various respects, including ethylene biosynthesis by down-regulating the abundance of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), pigment biosynthesis by repressing phytoene synthase 1 (PSY1), ζ-carotene isomerase (Z-ISO), chalcone synthase 1 (CHS1) and other proteins, enhancing fruit firmness by increasing the abundance of cellulose synthase protein, while reducing those of polygalacturonase 2 (PG2) and pectate lyase (PL), altering biosynthesis of nutrients such as carbohydrates, amino acids, and anthocyanins. Conversely, Nor mutation also enhanced the fruit’s resistance to some pathogens by up-regulating the expression of several genes associated with stress and defense. Therefore, the Nor gene is involved in the regulation of fruit ripening and quality. It is useful in the future as a means to improve fruit quality in tomato.
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Affiliation(s)
- Xin-Yu Yuan
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
| | - Rui-Heng Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
| | - Xiao-Dan Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, People’s Republic of China
| | - Yun-Bo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
| | - Da-Qi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing 100083, PR China
- * E-mail:
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Folta KM, Klee HJ. Sensory sacrifices when we mass-produce mass produce. HORTICULTURE RESEARCH 2016; 3:16032. [PMID: 27602229 PMCID: PMC4942566 DOI: 10.1038/hortres.2016.32] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 06/14/2016] [Indexed: 05/17/2023]
Abstract
Plant breeders have been extremely successful at driving genetic improvements in crops. However, 'improvements' are truly a question of perspective. Over the last one-hundred years most plant genetic innovations have been driven by industry demand. Larger fruits, heavier yields, uniformity, increased resistance to disease and better shipping quality are just a few of the traits that have ensured profits on the farm and affordable food for consumers. However, these milestones have come at the expense of sensory qualities, which have been sacrificed in exchange for practical production objectives. With a base of industry-sufficient genetics, today's breeders can now turn to the consumer for guidance in defining critical desires. New approaches to plant breeding start with the analysis of consumer preferences, and then merge them with modern genomics and analytical chemistry tools. The result is the next generation of crops that meet supply chain demands while presenting improvements in flavor, nutrition, color, aroma and texture. This review analyzes the approach of consumer-assisted selection as it has been applied to tomato and strawberry, two complementary annual crops that have been intensively bred to meet industry expectations. Current breeding efforts start with the consumer, with the objective of reclaiming lost sensory qualities.
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Affiliation(s)
- Kevin M Folta
- Horticultural Sciences Department, Plant Innovation Center and The Graduate Program for Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32606, USA
| | - Harry J Klee
- Horticultural Sciences Department, Plant Innovation Center and The Graduate Program for Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32606, USA
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83
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Gao L, Zhao W, Qu H, Wang Q, Zhao L. The yellow-fruited tomato 1 (yft1) mutant has altered fruit carotenoid accumulation and reduced ethylene production as a result of a genetic lesion in ETHYLENE INSENSITIVE2. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:717-728. [PMID: 26743523 DOI: 10.1007/s00122-015-2660-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/14/2015] [Indexed: 05/16/2023]
Abstract
The isolated yft1 allele controls the formation of fruit color in n3122 via the regulation of response to ethylene, carotenoid accumulation and chromoplast development. Fruit color is one of the most important quality traits of tomato (Solanum lycopersicum) and is closely associated with both nutritional and market value. In this study, we characterized a tomato fruit color mutant n3122, named as yellow-fruited tomato 1 (yft1), which produces yellow colored mature fruit. Fruit color segregation of the progeny from an intra-specific cross (M82 × n3122) and an inter-specific cross (n3122 × LA1585) revealed that a single recessive nuclear gene determined the yellow fruit phenotype. Through map-based cloning, the yft1 locus was assigned to an 88.2 kb region at the top of chromosome 9 that was annotated as containing 12 genes. Sequencing revealed that one gene, Solyc09g007870, which encodes ETHYLENE INSENSITIVE2 (EIN2), contained two mutations in yft1: a 13 bp deletion and a 573 bp insertion at position -318 bp upstream of the translation initiation site. We detected that EIN2 expression was substantially lower in yft1 than in the red-fruited M82 wild type and that, in addition, carotenoid accumulation was decreased, ethylene synthesis and perception were impaired and chromoplast development was delayed. The results implied that the reduced expression of EIN2 in yft1 leads to suppressed ethylene signaling which results in abnormal carotenoid production.
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Affiliation(s)
- Lei Gao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weihua Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haiou Qu
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qishan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingxia Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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84
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Kumar V, Irfan M, Ghosh S, Chakraborty N, Chakraborty S, Datta A. Fruit ripening mutants reveal cell metabolism and redox state during ripening. PROTOPLASMA 2016; 253:581-94. [PMID: 26008650 DOI: 10.1007/s00709-015-0836-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
Ripening which leads to fruit senescence is an inimitable process characterized by vivid changes in color, texture, flavor, and aroma of the fleshy fruits. Our understanding of the mechanisms underlying the regulation of fruit ripening and senescence is far from complete. Molecular and biochemical studies on tomato (Solanum lycopersicum) ripening mutants such as ripening inhibitor (rin), nonripening (nor), and never ripe (Nr) have been useful in our understanding of fruit development and ripening. The MADS-box transcription factor RIN, a global regulator of fruit ripening, is vital for the broad aspects of ripening, in both ethylene-dependent and independent manners. Here, we have carried out microarray analysis to study the expression profiles of tomato genes during ripening of wild type and rin mutant fruits. Analysis of the differentially expressed genes revealed the role of RIN in regulation of several molecular and biochemical events during fruit ripening including fruit specialized metabolism and cellular redox state. The role of reactive oxygen species (ROS) during fruit ripening and senescence was further examined by determining the changes in ROS level during ripening of wild type and mutant fruits and by analyzing expression profiles of the genes involved in maintaining cellular redox state. Taken together, our findings suggest an important role of ROS during fruit ripening and senescence, and therefore, modulation of ROS level during ripening could be useful in achieving desired fruit quality.
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Affiliation(s)
- Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohammad Irfan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sumit Ghosh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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85
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Steffens B, Rasmussen A. The Physiology of Adventitious Roots. PLANT PHYSIOLOGY 2016; 170:603-17. [PMID: 26697895 PMCID: PMC4734560 DOI: 10.1104/pp.15.01360] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/27/2015] [Indexed: 05/17/2023]
Abstract
Adventitious roots are plant roots that form from any nonroot tissue and are produced both during normal development (crown roots on cereals and nodal roots on strawberry [Fragaria spp.]) and in response to stress conditions, such as flooding, nutrient deprivation, and wounding. They are important economically (for cuttings and food production), ecologically (environmental stress response), and for human existence (food production). To improve sustainable food production under environmentally extreme conditions, it is important to understand the adventitious root development of crops both in normal and stressed conditions. Therefore, understanding the regulation and physiology of adventitious root formation is critical for breeding programs. Recent work shows that different adventitious root types are regulated differently, and here, we propose clear definitions of these classes. We use three case studies to summarize the physiology of adventitious root development in response to flooding (case study 1), nutrient deficiency (case study 2), and wounding (case study 3).
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Affiliation(s)
- Bianka Steffens
- Plant Physiology, Philipps University, 35043 Marburg, Germany (B.S.); andDivision of Plant and Crop Science, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (A.R.)
| | - Amanda Rasmussen
- Plant Physiology, Philipps University, 35043 Marburg, Germany (B.S.); andDivision of Plant and Crop Science, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (A.R.)
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86
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Irfan M, Ghosh S, Meli VS, Kumar A, Kumar V, Chakraborty N, Chakraborty S, Datta A. Fruit Ripening Regulation of α-Mannosidase Expression by the MADS Box Transcription Factor RIPENING INHIBITOR and Ethylene. FRONTIERS IN PLANT SCIENCE 2016; 7:10. [PMID: 26834776 PMCID: PMC4720780 DOI: 10.3389/fpls.2016.00010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/07/2016] [Indexed: 05/07/2023]
Abstract
α-Mannosidase (α-Man), a fruit ripening-specific N-glycan processing enzyme, is involved in ripening-associated fruit softening process. However, the regulation of fruit-ripening specific expression of α-Man is not well understood. We have identified and functionally characterized the promoter of tomato (Solanum lycopersicum) α-Man to provide molecular insights into its transcriptional regulation during fruit ripening. Fruit ripening-specific activation of the α-Man promoter was revealed by analysing promoter driven expression of beta-glucuronidase (GUS) reporter in transgenic tomato. We found that RIPENING INHIBITOR (RIN), a MADS box family transcription factor acts as positive transcriptional regulator of α-Man during fruit ripening. RIN directly bound to the α-Man promoter sequence and promoter activation/α-Man expression was compromised in rin mutant fruit. Deletion analysis revealed that a promoter fragment (567 bp upstream of translational start site) that contained three CArG boxes (binding sites for RIN) was sufficient to drive GUS expression in fruits. In addition, α-Man expression was down-regulated in fruits of Nr mutant which is impaired in ethylene perception and promoter activation/α-Man expression was induced in wild type following treatment with a precursor of ethylene biosynthesis, 1-aminocyclopropane-1-carboxylic acid (ACC). Although, α-Man expression was induced in rin mutant after ACC treatment, the transcript level was less as compared to ACC-treated wild type. Taken together, these results suggest RIN-mediated direct transcriptional regulation of α-Man during fruit ripening and ethylene may acts in RIN-dependent and -independent ways to regulate α-Man expression.
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Affiliation(s)
- Mohammad Irfan
- National Institute of Plant Genome Research New Delhi, India
| | - Sumit Ghosh
- Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial ResearchLucknow, India
| | - Vijaykumar S. Meli
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los AngelesCA, USA
| | - Anil Kumar
- National Institute of Plant Genome Research New Delhi, India
| | - Vinay Kumar
- National Institute of Plant Genome Research New Delhi, India
| | | | | | - Asis Datta
- National Institute of Plant Genome Research New Delhi, India
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87
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Ma Y, Zhou L, Wang Z, Chen J, Qu G. Oligogalacturonic acids promote tomato fruit ripening through the regulation of 1-aminocyclopropane-1-carboxylic acid synthesis at the transcriptional and post-translational levels. BMC PLANT BIOLOGY 2016; 16:13. [PMID: 26748512 PMCID: PMC4706653 DOI: 10.1186/s12870-015-0634-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/30/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Oligogalacturonic acids (OGs) are oligomers of alpha-1,4-linked galacturonosyl residues that are released from cell walls by the hydrolysis of polygalacturonic acids upon fruit ripening and under abiotic/biotic stress. OGs may induce ethylene production and fruit ripening, however, the mechanism(s) behind these processes is unknown. RESULTS Tomato cultivar 'Ailsa Craig' (AC) and mutant Neverripe, ripening inhibitor, non-ripening, and colorless non-ripening fruits were treated with OGs at different stages. Only AC fruits at mature green stage 1 showed an advanced ripening phenomenon, although transient ethylene production was detected in all of the tomato fruits. Ethylene synthesis genes LeACS2 and LeACO1 were rapidly up-regulated, and the phosphorylated LeACS2 protein was detected after OGs treatment. Protein kinase/phosphatase inhibitors significantly affected the ripening process induced by the OGs. As a potential receptor of OGs, LeWAKL2 was also up-regulated in their presence. CONCLUSIONS We demonstrated that OGs promoted tomato fruit ripening by inducing ethylene synthesis through the regulation of LeACS2 at transcriptional and post-translational levels.
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Affiliation(s)
- Yingxuan Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
| | - Leilei Zhou
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
| | - Zhichao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
| | - Jianting Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
| | - Guiqin Qu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
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88
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Fiebig A, Dodd IC. Inhibition of tomato shoot growth by over-irrigation is linked to nitrogen deficiency and ethylene. PHYSIOLOGIA PLANTARUM 2016; 156:70-83. [PMID: 25950248 DOI: 10.1111/ppl.12343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 03/25/2015] [Accepted: 04/03/2015] [Indexed: 05/09/2023]
Abstract
Although physiological effects of acute flooding have been well studied, chronic effects of suboptimal soil aeration caused by over-irrigation of containerized plants have not, despite its likely commercial significance. By automatically scheduling irrigation according to soil moisture thresholds, effects of over-irrigation on soil properties (oxygen concentration, temperature and moisture), leaf growth, gas exchange, phytohormone [abscisic acid (ABA) and ethylene] relations and nutrient status of tomato (Solanum lycopersicum Mill. cv. Ailsa Craig) were studied. Over-irrigation slowly increased soil moisture and decreased soil oxygen concentration by 4%. Soil temperature was approximately 1°C lower in the over-irrigated substrate. Over-irrigating tomato plants for 2 weeks significantly reduced shoot height (by 25%) and fresh weight and total leaf area (by 60-70%) compared with well-drained plants. Over-irrigation did not alter stomatal conductance, leaf water potential or foliar ABA concentrations, suggesting that growth inhibition was not hydraulically regulated or dependent on stomatal closure or changes in ABA. However, over-irrigation significantly increased foliar ethylene emission. Ethylene seemed to inhibit growth, as the partially ethylene-insensitive genotype Never ripe (Nr) was much less sensitive to over-irrigation than the wild type. Over-irrigation induced significant foliar nitrogen deficiency and daily supplementation of small volumes of 10 mM Ca(NO3 )2 to over-irrigated soil restored foliar nitrogen concentrations, ethylene emission and shoot fresh weight of over-irrigated plants to control levels. Thus reduced nitrogen uptake plays an important role in inhibiting growth of over-irrigated plants, in part by stimulating foliar ethylene emission.
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Affiliation(s)
- Antje Fiebig
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Ian C Dodd
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
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89
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90
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Liu M, Chen G, Guo H, Fan B, Liu J, Fu Q, Li X, Lu X, Zhao X, Li G, Sun Z, Xia L, Zhu S, Yang D, Cao Z, Wang H, Suo Y, You J. Accurate Analysis and Evaluation of Acidic Plant Growth Regulators in Transgenic and Nontransgenic Edible Oils with Facile Microwave-Assisted Extraction-Derivatization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:8058-8067. [PMID: 26309068 DOI: 10.1021/acs.jafc.5b02489] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Determination of plant growth regulators (PGRs) in a signal transduction system (STS) is significant for transgenic food safety, but may be challenged by poor accuracy and analyte instability. In this work, a microwave-assisted extraction-derivatization (MAED) method is developed for six acidic PGRs in oil samples, allowing an efficient (<1.5 h) and facile (one step) pretreatment. Accuracies are greatly improved, particularly for gibberellin A3 (-2.72 to -0.65%) as compared with those reported (-22 to -2%). Excellent selectivity and quite low detection limits (0.37-1.36 ng mL(-1)) are enabled by fluorescence detection-mass spectrum monitoring. Results show the significant differences in acidic PGRs between transgenic and nontransgenic oils, particularly 1-naphthaleneacetic acid (1-NAA), implying the PGRs induced variations of components and genes. This study provides, for the first time, an accurate and efficient determination for labile PGRs involved in STS and a promising concept for objectively evaluating the safety of transgenic foods.
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Affiliation(s)
- Mengge Liu
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Guang Chen
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining 810001, China
| | - Hailong Guo
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Baolei Fan
- Hubei University of Science and Technology , Xianning, 437100 China
| | - Jianjun Liu
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Qiang Fu
- Qinghai Normal University , Xining, 810008 China
| | - Xiu Li
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Xiaomin Lu
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Xianen Zhao
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Guoliang Li
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Zhiwei Sun
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Lian Xia
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Shuyun Zhu
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Daoshan Yang
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Ziping Cao
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Hua Wang
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
| | - Yourui Suo
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining 810001, China
| | - Jinmao You
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University , Qufu 273165, Shandong, China
- Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine, Qufu Normal University , Qufu 273165, Shandong, China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining 810001, China
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Mubarok S, Okabe Y, Fukuda N, Ariizumi T, Ezura H. Potential Use of a Weak Ethylene Receptor Mutant, Sletr1-2, as Breeding Material To Extend Fruit Shelf Life of Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015. [PMID: 26208257 DOI: 10.1021/acs.jafc.5b02742] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mutations in the ethylene receptor gene (SlETR1), Sletr1-1 and Sletr1-2, are effective in reducing ethylene sensitivity and improving fruit shelf life. In this study the effect of Sletr1-1 and Sletr1-2 mutations was investigated in F1 hybrid lines. These two mutants and control were crossed with four commercial pure-line tomatoes. The Sletr1-1 mutation showed undesirable pleiotropic effects in the F1 hybrid lines. The Sletr1-2 mutation was effective in improving fruit shelf life of F1 hybrid lines for 4-5 days longer. It was also effective in improving fruit firmness without change in fruit size, ethylene production, respiration rate, and total soluble solids or a great reduction in fruit color, lycopene, and β-carotene, although the titratable acidity was increased by Sletr1-2 mutation. These results indicate that the Sletr1-2 mutant allele has the potential to improve fruit shelf life via incorporation in tomato breeding programs.
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Affiliation(s)
- Syariful Mubarok
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba, 305-8572 Japan
- Department of Agronomy, Faculty of Agriculture, Padjadjaran University , Bandung, 45363 Indonesia
| | - Yoshihiro Okabe
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba, 305-8572 Japan
| | - Naoya Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba, 305-8572 Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba, 305-8572 Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba, 305-8572 Japan
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92
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Thao NP, Khan MIR, Thu NBA, Hoang XLT, Asgher M, Khan NA, Tran LSP. Role of Ethylene and Its Cross Talk with Other Signaling Molecules in Plant Responses to Heavy Metal Stress. PLANT PHYSIOLOGY 2015; 169:73-84. [PMID: 26246451 PMCID: PMC4577409 DOI: 10.1104/pp.15.00663] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/05/2015] [Indexed: 05/18/2023]
Abstract
Excessive heavy metals (HMs) in agricultural lands cause toxicities to plants, resulting in declines in crop productivity. Recent advances in ethylene biology research have established that ethylene is not only responsible for many important physiological activities in plants but also plays a pivotal role in HM stress tolerance. The manipulation of ethylene in plants to cope with HM stress through various approaches targeting either ethylene biosynthesis or the ethylene signaling pathway has brought promising outcomes. This review covers ethylene production and signal transduction in plant responses to HM stress, cross talk between ethylene and other signaling molecules under adverse HM stress conditions, and approaches to modify ethylene action to improve HM tolerance. From our current understanding about ethylene and its regulatory activities, it is believed that the optimization of endogenous ethylene levels in plants under HM stress would pave the way for developing transgenic crops with improved HM tolerance.
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Affiliation(s)
- Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh 70000, Vietnam (N.P.T., N.B.A.T., X.L.T.H.);Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India (M.I.R.K., M.A., N.A.K.); andSignaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 2300045, Japan (L.-S.P.T.)
| | - M Iqbal R Khan
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh 70000, Vietnam (N.P.T., N.B.A.T., X.L.T.H.);Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India (M.I.R.K., M.A., N.A.K.); andSignaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 2300045, Japan (L.-S.P.T.)
| | - Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh 70000, Vietnam (N.P.T., N.B.A.T., X.L.T.H.);Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India (M.I.R.K., M.A., N.A.K.); andSignaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 2300045, Japan (L.-S.P.T.)
| | - Xuan Lan Thi Hoang
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh 70000, Vietnam (N.P.T., N.B.A.T., X.L.T.H.);Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India (M.I.R.K., M.A., N.A.K.); andSignaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 2300045, Japan (L.-S.P.T.)
| | - Mohd Asgher
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh 70000, Vietnam (N.P.T., N.B.A.T., X.L.T.H.);Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India (M.I.R.K., M.A., N.A.K.); andSignaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 2300045, Japan (L.-S.P.T.)
| | - Nafees A Khan
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh 70000, Vietnam (N.P.T., N.B.A.T., X.L.T.H.);Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India (M.I.R.K., M.A., N.A.K.); andSignaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 2300045, Japan (L.-S.P.T.)
| | - Lam-Son Phan Tran
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh 70000, Vietnam (N.P.T., N.B.A.T., X.L.T.H.);Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India (M.I.R.K., M.A., N.A.K.); andSignaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 2300045, Japan (L.-S.P.T.)
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93
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Tohge T, Fernie AR. Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality. PLANT & CELL PHYSIOLOGY 2015; 56:1681-96. [PMID: 26228272 DOI: 10.1093/pcp/pcv093] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/12/2015] [Indexed: 05/20/2023]
Abstract
Tomato was one of the first plant species to be evaluated using metabolomics and remains one of the best characterized, with tomato fruit being both an important source of nutrition in the human diet and a valuable model system for the development of fleshy fruits. Additionally, given the broad habitat range of members of the tomato clade and the extensive use of exotic germplasm in tomato genetic research, it represents an excellent genetic model system for understanding both metabolism per se and the importance of various metabolites in conferring stress tolerance. This review summarizes technical approaches used to characterize the tomato metabolome to date and details insights into metabolic pathway structure and regulation that have been obtained via analysis of tissue samples taken under different developmental or environmental circumstance as well as following genetic perturbation. Particular attention is paid to compounds of importance for nutrition or the shelf-life of tomatoes. We propose furthermore how metabolomics information can be coupled to the burgeoning wealth of genome sequence data from the tomato clade to enhance further our understanding of (i) the shifts in metabolic regulation occurring during development and (ii) specialization of metabolism within the tomato clade as a consequence of either adaptive evolution or domestication.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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94
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Abstract
Ethylene is a hormone involved in numerous aspects of growth, development, and responses to biotic and abiotic stresses in plants. Ethylene is perceived through its binding to endoplasmic reticulum-localized receptors that function as negative regulators of ethylene signaling in the absence of the hormone. In Arabidopsis thaliana, five structurally and functionally different ethylene receptors are present. These differ in their primary sequence, in the domains present, and in the type of kinase activity exhibited, which may suggest functional differences among the receptors. Whereas ethylene receptors functionally overlap to suppress ethylene signaling, certain other responses are controlled by specific receptors. In this review, I examine the nature of these receptor differences, how the evolution of the ethylene receptor gene family may provide insight into their differences, and how expression of receptors or their accessory proteins may underlie receptor-specific responses.
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95
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Leida C, Moser C, Esteras C, Sulpice R, Lunn JE, de Langen F, Monforte AJ, Picó B. Variability of candidate genes, genetic structure and association with sugar accumulation and climacteric behavior in a broad germplasm collection of melon (Cucumis melo L.). BMC Genet 2015; 16:28. [PMID: 25886993 PMCID: PMC4380257 DOI: 10.1186/s12863-015-0183-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/18/2015] [Indexed: 11/15/2022] Open
Abstract
Background A collection of 175 melon (Cucumis melo L.) accessions (including wild relatives, feral types, landraces, breeding lines and commercial cultivars) from 50 countries was selected to study the phenotypic variability for ripening behavior and sugar accumulation. The variability of single nucleotide polymorphisms (SNPs) at 53 selected candidate genes involved in sugar accumulation and fruit ripening processes was studied, as well as their association with phenotypic variation of related traits. Results The collection showed a strong genetic structure, defining seven groups plus a number of accessions that could not be associated to any of the groups (admixture), which fitted well with the botanical classification of melon varieties. The variability in candidate genes for ethylene, cell wall and sugar-related traits was high and similar to SNPs located in reference genes. Variability at ripening candidate genes had an important weight on the genetic stratification of melon germplasm, indicating that traditional farmers might have selected for ripening traits during cultivar diversification. A strong relationship was also found between the genetic structure and phenotypic diversity, which could hamper genetic association studies. Accessions belonging to the ameri group are the most appropriate for association analysis given the high phenotypic and molecular diversity within the group, and lack of genetic structure. The most remarkable association was found between sugar content and SNPs in LG III, where a hotspot of sugar content QTLs has previously been defined. By studying the differences in allelic variation of SNPs within horticultural groups with specific phenotypic features, we also detected differential variation in sugar-related candidates located in LGIX and LGX, and in ripening-related candidates located in LGII and X, all in regions with previously mapped QTLs for the corresponding traits. Conclusions In the current study we have found an important variability at both the phenotypic and candidate gene levels for ripening behavior and sugar accumulation in melon fruit. By combination of differences in allelic diversity and association analysis, we have identified several candidate genes that may be involved in the melon phenotypic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0183-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carmen Leida
- Research and Innovation Center, Department Genomics and Biology of Fruit Crops, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele, Italy.
| | - Claudio Moser
- Research and Innovation Center, Department Genomics and Biology of Fruit Crops, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele, Italy.
| | - Cristina Esteras
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Ronan Sulpice
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam, Germany. .,Plant Systems Biology Research Laboratory, Department of Botany and Plant Science, Plant and AgriBiosciences Research Centre, National University of Galway, University Road, Galway, Ireland.
| | - John E Lunn
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam, Germany.
| | - Frank de Langen
- HMCLAUSE (Business Unit of Limagrain), Station de Mas Saint Pierre, La Galine, 13210, Saint-Rémy-de-Provence, France.
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
| | - Belen Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain.
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96
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Almeida J, Asís R, Molineri VN, Sestari I, Lira BS, Carrari F, Peres LEP, Rossi M. Fruits from ripening impaired, chlorophyll degraded and jasmonate insensitive tomato mutants have altered tocopherol content and composition. PHYTOCHEMISTRY 2015; 111:72-83. [PMID: 25432273 DOI: 10.1016/j.phytochem.2014.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 05/07/2023]
Abstract
Since isoprenoids are precursors in chlorophyll, carotenoid and tocopherol pathways, the study of their metabolism is of fundamental importance in understanding the regulatory cross-talk that contributes to the nutritional quality of tomato fruits. By means of an integrated analysis of metabolite and gene expression profiles, isoprenoid metabolism was dissected in ripening-impaired (ripening inhibitor and non-ripening), senescence-related (lutescent1 and green flesh) and jasmonate insensitive (jasmonic acid insensitive 1-1) tomato mutants, all in the Micro-Tom genetic background. It was found that the more upstream the location of the mutated gene, the more extensive the effect on the transcriptional profiles of the isoprenoid-related genes. Although there was a distinct effect in the analyzed mutations on chlorophyll, carotenoid and tocopherol metabolism, a metabolic adjustment was apparent such the antioxidant capacity mostly remained constant. Transcriptional profiles from fruits of ripening and senescence-related tomato mutants suggested that maintenance of the de novo phytyl diphosphate synthesis might, in later ripening stages, compensate for the lack of chlorophyll-derived phytol used in tocopherol production. Interestingly, an impairment in jasmonate perception led to higher total tocopherol levels in ripe fruits, accompanied by an increase in antioxidant capacity, highlighting the contribution of tocopherols to this nutritionally important trait.
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Affiliation(s)
- Juliana Almeida
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Ramón Asís
- CIBICI, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Virginia Noel Molineri
- CIBICI, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Ivan Sestari
- Universidade Federal de Santa Catarina, Campus Curitibanos, Curitibanos, SC, Brazil.
| | - Bruno Silvestre Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria and Consejo Nacional de Investigaciones Científicas y Técnicas, Hurlingham, Buenos Aires, Argentina.
| | - Lázaro Eustáquio Pereira Peres
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil.
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
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97
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Ma N, Feng H, Meng X, Li D, Yang D, Wu C, Meng Q. Overexpression of tomato SlNAC1 transcription factor alters fruit pigmentation and softening. BMC PLANT BIOLOGY 2014; 14:351. [PMID: 25491370 PMCID: PMC4272553 DOI: 10.1186/s12870-014-0351-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/25/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Fruit maturation and ripening are genetically regulated processes that involve a complex interplay of plant hormones, growth regulators and multiple biological and environmental factors. Tomato (Solanum lycopersicum) has been used as a model of biological and genetic studies on the regulation of specific ripening pathways, including ethylene, carotenoid and cell wall metabolism. This model has also been used to investigate the functions of upstream signalling and transcriptional regulators. Thus far, many ripening-associated transcription factors that influence fruit development and ripening have been reported. NAC transcription factors are plant specific and play important roles in many stages of plant growth and development, such as lateral root formation, secondary cell wall synthesis, and embryo, floral organ, vegetative organ and fruit development. RESULTS Tissue-specific analysis by quantitative real-time PCR showed that SlNAC1 was highly accumulated in immature green fruits; the expression of SlNAC1 increased with fruit ripening till to the highest level at 7 d after the breaker stage. The overexpression of SlNAC1 resulted in reduced carotenoids by altering carotenoid pathway flux and decreasing ethylene synthesis mediated mainly by the reduced expression of ethylene biosynthetic genes of system-2, thus led to yellow or orange mature fruits. The results of yeast one-hybrid experiment demonstrated that SlNAC1 can interact with the regulatory regions of genes related lycopene and ethylene synthesis. These results also indicated that SlNAC1 inhibited fruit ripening by affecting ethylene synthesis and carotenoid accumulation in SlNAC1 overexpression lines. In addition, the overexpression of SlNAC1 reduced the firmness of the fruits and the thickness of the pericarp and produced more abscisic acid, resulting in the early softening of fruits. Hence, in SlNAC1 overexpression lines, both ethylene-dependent and abscisic acid-dependent pathways are regulated by SlNAC1 in fruit ripening regulatory network. CONCLUSIONS SlNAC1 had a broad influence on tomato fruit ripening and regulated SlNAC1 overexpression tomato fruit ripening through both ethylene-dependent and abscisic acid-dependent pathways. Thus, this study provided new insights into the current model of tomato fruit ripening regulatory network.
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Affiliation(s)
- Nana Ma
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Hailong Feng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Xia Meng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Dong Li
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Dongyue Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai’an, 271018 Shandong P. R. China
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98
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Yang T, Peng H, Bauchan GR. Functional analysis of tomato calmodulin gene family during fruit development and ripening. HORTICULTURE RESEARCH 2014; 1:14057. [PMID: 26504554 PMCID: PMC4596335 DOI: 10.1038/hortres.2014.57] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 05/09/2023]
Abstract
Calmodulin is a ubiquitous calcium sensor to recognize the different developmental and/or stimulus-triggered calcium changes and regulate plant growth and development. However, the function of calmodulin remains elusive for fleshy fruit development. We performed expression studies of a family of six calmodulin genes (SlCaMs) in tomato fruit. All calmodulins showed a double peak expression pattern. The first flat peak appeared at 10-30 days after anthesis, but their expression rapidly declined at mature green and breaker. Then a sharp and even higher peak came at turning/pink stages. Among six calmodulins, SlCaM1 had the highest expression during fruit enlargement, whereas SlCaM2 was the major calmodulin during fruit ripening. However, SlCaMs showed different patterns in three ripening mutants rin, Nor and Nr. In particular, at the stages corresponding to mature green and breaker, the expression levels of SlCaMs in those mutants were significantly higher than wild-type. Furthermore, SlCaMs, especially SlCaM2 were upregulated by ethylene. Transiently overexpressing SlCaM2 in mature green fruit delayed ripening, while reducing SlCaM2 expression accelerated ripening. Our results suggest that SlCaMs play double roles to regulate fruit ripening. Prior to the ethylene burst, the ethylene-independent repression of SlCaMs might be critical for fruit to initiate the ripening process. After the ethylene burst, SlCaMs could participate in the ethylene coordinated rapid ripening.
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Affiliation(s)
- Tianbao Yang
- Food Quality Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Hui Peng
- Food Quality Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
- College of Life Sciences, Guangxi Normal University, Guilin 541004, China
| | - Gary R Bauchan
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
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99
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Irfan M, Ghosh S, Kumar V, Chakraborty N, Chakraborty S, Datta A. Insights into transcriptional regulation of β-D-N-acetylhexosaminidase, an N-glycan-processing enzyme involved in ripening-associated fruit softening. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5835-48. [PMID: 25129131 PMCID: PMC4203122 DOI: 10.1093/jxb/eru324] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Tomato (Solanum lycopersicum) fruit ripening-specific N-glycan processing enzyme, β-D-N-acetylhexosaminidase (β-Hex), plays an important role in the ripening-associated fruit-softening process. However, the regulation of fruit ripening-specific expression of β-Hex is not well understood. We have identified and functionally characterized the fruit ripening-specific promoter of β-Hex and provided insights into its transcriptional regulation during fruit ripening. Our results demonstrate that RIPENING INHIBITOR (RIN), a global fruit ripening regulator, and ABSCISIC ACID STRESS RIPENING 1 (SlASR1), a poorly characterized ripening-related protein, are the transcriptional regulators of β-Hex. Both RIN and SlASR1 directly bound to the β-Hex promoter fragments containing CArG and C₂₋₃(C/G)A cis-acting elements, the binding sites for RIN and SlASR1, respectively. Moreover, β-Hex expression/promoter activity in tomato fruits was downregulated once expression of either RIN or SlASR1 was suppressed; indicating that RIN and SlASR1 positively regulate the transcription of β-Hex during fruit ripening. Interestingly, RIN could also bind to the SlASR1 promoter, which contains several CArG cis-acting elements, and SlASR1 expression was suppressed in rin mutant fruits, indicating that RIN also acts as a positive regulator of SlASR1 expression during fruit ripening. Taken together, these results suggest that RIN, both directly and indirectly, through SlASR1, regulates the transcription of β-Hex during fruit ripening. The fruit ripening-specific promoter of β-Hex could be a useful tool in regulating gene expression during fruit ripening.
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Affiliation(s)
- Mohammad Irfan
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Sumit Ghosh
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, New Delhi 110067, India
| | | | | | - Asis Datta
- National Institute of Plant Genome Research, New Delhi 110067, India
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100
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González-Pérez L, Perrotta L, Acosta A, Orellana E, Spadafora N, Bruno L, Bitonti BM, Albani D, Cabrera JC, Francis D, Rogers HJ. In tobacco BY-2 cells xyloglucan oligosaccharides alter the expression of genes involved in cell wall metabolism, signalling, stress responses, cell division and transcriptional control. Mol Biol Rep 2014; 41:6803-16. [PMID: 25008996 DOI: 10.1007/s11033-014-3566-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/25/2014] [Indexed: 02/02/2023]
Abstract
Xyloglucan oligosaccharides (XGOs) are breakdown products of XGs, the most abundant hemicelluloses of the primary cell walls of non-Poalean species. Treatment of cell cultures or whole plants with XGOs results in accelerated cell elongation and cell division, changes in primary root growth, and a stimulation of defence responses. They may therefore act as signalling molecules regulating plant growth and development. Previous work suggests an interaction with auxins and effects on cell wall loosening, however their mode of action is not fully understood. The effect of an XGO extract from tamarind (Tamarindus indica) on global gene expression was therefore investigated in tobacco BY-2 cells using microarrays. Over 500 genes were differentially regulated with similar numbers and functional classes of genes up- and down-regulated, indicating a complex interaction with the cellular machinery. Up-regulation of a putative XG endotransglycosylase/hydrolase-related (XTH) gene supports the mechanism of XGO action through cell wall loosening. Differential expression of defence-related genes supports a role for XGOs as elicitors. Changes in the expression of genes related to mitotic control and differentiation also support previous work showing that XGOs are mitotic inducers. XGOs also affected expression of several receptor-like kinase genes and transcription factors. Hence, XGOs have significant effects on expression of genes related to cell wall metabolism, signalling, stress responses, cell division and transcriptional control.
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Affiliation(s)
- Lien González-Pérez
- Plant Biology Department, Faculty of Biology, University of Havana, Havana City, Cuba
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