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Li L, Liu Z, Pan X, Yao K, Wang Y, Yang T, Huang G, Liao W, Wang C. Genome-Wide Identification and Characterization of Tomato Fatty Acid β-Oxidase Family Genes KAT and MFP. Int J Mol Sci 2024; 25:2273. [PMID: 38396949 PMCID: PMC10889323 DOI: 10.3390/ijms25042273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Fatty acids and their derivatives play a variety of roles in living organisms. Fatty acids not only store energy but also comprise membrane lipids and act as signaling molecules. There are three main proteins involved in the fatty acid β-oxidation pathway in plant peroxisomes, including acyl-CoA oxidase (ACX), multifunctional protein (MFP), and 3-ketolipoyl-CoA thiolase (KAT). However, genome-scale analysis of KAT and MFP has not been systemically investigated in tomatoes. Here, we conducted a bioinformatics analysis of KAT and MFP genes in tomatoes. Their physicochemical properties, protein secondary structure, subcellular localization, gene structure, phylogeny, and collinearity were also analyzed. In addition, a conserved motif analysis, an evolutionary pressure selection analysis, a cis-acting element analysis, tissue expression profiling, and a qRT-PCR analysis were conducted within tomato KAT and MFP family members. There are five KAT and four MFP family members in tomatoes, which are randomly distributed on four chromosomes. By analyzing the conserved motifs of tomato KAT and MFP family members, we found that both KAT and MFP members are highly conserved. In addition, the results of the evolutionary pressure selection analysis indicate that the KAT and MFP family members have evolved mainly from purifying selection, which makes them more structurally stable. The results of the cis-acting element analysis show that SlKAT and SlMFP with respect may respond to light, hormones, and adversity stresses. The tissue expression analysis showed that KAT and MFP family members have important roles in regulating the development of floral organs as well as fruit ripening. The qRT-PCR analysis revealed that the expressions of SlKAT and SlMFP genes can be regulated by ABA, MeJA, darkness, NaCl, PEG, UV, cold, heat, and H2O2 treatments. These results provide a basis for the involvement of the SlKAT and SlMFP genes in tomato floral organ development and abiotic stress response, which lay a foundation for future functional study of SlKAT and SlMFP in tomatoes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Yinmen Village, Anning District, Lanzhou 730070, China; (L.L.); (Z.L.); (X.P.); (K.Y.); (Y.W.); (T.Y.); (G.H.); (W.L.)
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Xiang F, Liu WC, Liu X, Song Y, Zhang Y, Zhu X, Wang P, Guo S, Song CP. Direct balancing of lipid mobilization and reactive oxygen species production by the epoxidation of fatty acid catalyzed by a cytochrome P450 protein during seed germination. THE NEW PHYTOLOGIST 2023; 237:2104-2117. [PMID: 36495066 DOI: 10.1111/nph.18669] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Fatty acid (FA) β-oxidation provides energy for oil seed germination but also produces massive byproduct reactive oxygen species (ROS), posing potential oxidative damage to plant cells. How plants overcome the contradiction between energy supply and ROS production during seed germination remains unclear. In this study, we identified an Arabidopsis mvs1 (methylviologen-sensitive) mutant that was hypersensitive to ROS and caused by a missense mutation (G1349 substituted as A) of a cytochrome P450 gene, CYP77A4. CYP77A4 was highly expressed in germinating seedling cotyledons, and its protein is localized in the endoplasmic reticulum. As CYP77A4 catalyzes the epoxidation of unsaturated FA, disruption of CYP77A4 resulted in increased unsaturated FA abundance and over accumulated ROS in the mvs1 mutant. Consistently, scavenging excess ROS or blocking FA β-oxidation could repress the ROS overaccumulation and hypersensitivity in the mvs1 mutant. Furthermore, H2 O2 transcriptionally upregulated CYP77A4 expression and post-translationally modified CYP77A4 by sulfenylating its Cysteine-456, which is necessary for CYP77A4's role in modulating FA abundance and ROS production. Together, our study illustrates that CYP77A4 mediates direct balancing of lipid mobilization and ROS production by the epoxidation of FA during seed germination.
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Affiliation(s)
- Fuyou Xiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Wen-Cheng Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Xin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Yuwei Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
- College of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Yu Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Xiaojing Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Pengtao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
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3
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Sreeja S, Shylaja MR, Nazeem PA, Mathew D. Peroxisomal KAT2 (3-ketoacyl-CoA thiolase 2) gene has a key role in gingerol biosynthesis in ginger ( Zingiber officinale Rosc.). JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2023; 32:1-16. [PMID: 36685987 PMCID: PMC9838548 DOI: 10.1007/s13562-022-00825-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Ginger is an important spice crop with medicinal values and gingerols are the most abundant pungent polyphenols present in ginger, responsible for most of its pharmacological properties. The present study focuses on the molecular mechanism of gingerol biosynthesis in ginger using transcriptome analysis. Suppression Subtractive Hybridization (SSH) was done in leaf and rhizome tissues using high gingerol-producing ginger somaclone B3 as the tester and parent cultivar Maran as the driver and generated high-quality leaf and rhizome Expressed Sequence Tags (ESTs). The Blast2GO annotations of the ESTs revealed the involvement of leaf ESTs in secondary metabolite production, identifying the peroxisomal KAT2 gene (Leaf EST 9) for the high gingerol production in ginger. Rhizome ESTs mostly coded for DNA metabolic processes and differential genes for high gingerol production were not observed in rhizomes. In the qRT-PCR analysis, somaclone B3 had shown high chalcone synthase (CHS: rate-limiting gene in gingerol biosynthetic pathway) activity (0.54 fold) in the leaves of rhizome sprouts. The presence of a high gingerol gene in leaf ESTs and high expression of CHS in leaves presumed that the site of synthesis of gingerols in ginger is the leaves. A modified pathway for gingerol/polyketide backbone formation has been constructed explaining the involvement of KAT gene isoforms KAT2 and KAT5 in gingerol/flavonoid biosynthesis, specifically the KAT2 gene which is otherwise thought to be involved mainly in β-oxidation. The results of the present investigations have the potential of utilizing KAT/thiolase superfamily enzymes for protein/metabolic pathway engineering in ginger for large-scale production of gingerols. Supplementary Information The online version contains supplementary material available at 10.1007/s13562-022-00825-x.
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Affiliation(s)
- S. Sreeja
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - M. R. Shylaja
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - P. A. Nazeem
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - Deepu Mathew
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
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Wang Y, Ye X, Takano T, Liu S, Bu Y. Biotinylated subunit of 3-methylcrotonyl-CoA carboxylase encoding gene (AtMCCA) participating in Arabidopsis resistance to carbonate Stress by transcriptome analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111130. [PMID: 35067300 DOI: 10.1016/j.plantsci.2021.111130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/09/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
Soil salinization is a major factor impacting modern agricultural production, and alkaline soils contain large amounts of NaHCO3. Therefore, understanding plant tolerance to high levels of NaHCO3 is essential. In this study, a transcriptome analysis of shoot and root tissues of wild-type Arabidopsis thaliana was conducted at 0, 4, 12, 24 and 48 h after exposure to a 3 mM NaHCO3 stress. We focused on differentially expressed genes (DEGs) in roots identified in the early stages (4 h and 12 h) of the NaHCO3 stress response that were enriched in GO term, carboxylic acid metabolic process, and utilize HCO3-. Six genes were identified that exhibited similar expression patterns in both the RNA-seq and qRT-PCR data. We also characterized the phenotypic response of AtMCCA-overexpressing plants to carbonate stress, and found that the ability of AtMCCA-overexpressing plants to tolerate carbonate stress was enhanced by the addition of biotin to the growth medium.
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Affiliation(s)
- Yao Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xiaoxue Ye
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), University of Tokyo, Nishitokyo, Tokyo, 188-0002, Japan
| | - Shenkui Liu
- Department of Silviculture, State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin'an, Zhejiang, 311300, China.
| | - Yuanyuan Bu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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5
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Khan AH, Min L, Ma Y, Wu Y, Ding Y, Li Y, Xie S, Ullah A, Shaban M, Manghwar H, Shahid M, Zhao Y, Wang C, Zhang X. High day and night temperatures distinctively disrupt fatty acid and jasmonic acid metabolism, inducing male sterility in cotton. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6128-6141. [PMID: 32640017 DOI: 10.1093/jxb/eraa319] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/06/2020] [Indexed: 05/22/2023]
Abstract
High temperature stress is an inevitable environmental factor in certain geographical regions. To study the effect of day and night high temperature stress on male reproduction, the heat-sensitive cotton line H05 was subjected to high temperature stress. High day/normal night (HN) and normal day/high night (NH) temperature treatments were compared with normal day/normal night (NN) temperature as a control. At the anther dehiscence stage, significant differences were observed, with a reduction in flower size and filament length, and sterility in pollen, seen in NH more than in HN. A total of 36 806 differentially expressed genes were screened, which were mainly associated with fatty acid and jasmonic acid (JA) metabolic pathways. Fatty acid and JA contents were reduced more in NH than HN. Under NH, ACYL-COA OXIDASE 2 (ACO2), a JA biosynthesis gene, was down-regulated. Interestingly, aco2 CRISPR-Cas9 mutants showed male sterility under the NN condition. The exogenous application of methyl jasmonate to early-stage buds of mutants rescued the sterile pollen and indehiscent anther phenotypes at the late stage. These data show that high temperature at night may affect fatty acid and JA metabolism in anthers by suppressing GhACO2 and generate male sterility more strongly than high day temperature.
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Affiliation(s)
- Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanlong Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanhao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanlong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Sai Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Department of Botany, University of Malakand, Dir Lower, Khyber Pakhtunkwa, Pakistan
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Muhammad Shahid
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yunlong Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chaozhi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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6
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Perez de Souza L, Garbowicz K, Brotman Y, Tohge T, Fernie AR. The Acetate Pathway Supports Flavonoid and Lipid Biosynthesis in Arabidopsis. PLANT PHYSIOLOGY 2020; 182:857-869. [PMID: 31719153 PMCID: PMC6997690 DOI: 10.1104/pp.19.00683] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/31/2019] [Indexed: 05/21/2023]
Abstract
The phenylpropanoid pathway of flavonoid biosynthesis has been the subject of considerable research attention. By contrast, the proposed polyketide pathway, also known as the acetate pathway, which provides malonyl-CoA moieties for the C2 elongation reaction catalyzed by chalcone synthase, is less well studied. Here, we identified four genes as candidates for involvement in the supply of cytosolic malonyl-CoA from the catabolism of acyl-CoA, based on coexpression analysis with other flavonoid-related genes. Two of these genes, ACC and KAT5, have been previously characterized with respect to their involvement in lipid metabolism, but no information concerning their relationship to flavonoid biosynthesis is available. To assess the occurrence and importance of the acetate pathway, we characterized the metabolomes of two mutant or transgenic Arabidopsis lines for each of the four enzymes of this putative pathway using a hierarchical approach covering primary and secondary metabolites as well as lipids. Intriguingly, not only flavonoid content but also glucosinolate content was altered in lines deficient in the acetate pathway, as were levels of lipids and most primary metabolites. We discuss these data in the context of our current understanding of flavonoids and lipid metabolism as well as with regard to improving human nutrition.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Karolina Garbowicz
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653 Beersheba, Israel
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
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7
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Willems P, Horne A, Van Parys T, Goormachtig S, De Smet I, Botzki A, Van Breusegem F, Gevaert K. The Plant PTM Viewer, a central resource for exploring plant protein modifications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:752-762. [PMID: 31004550 DOI: 10.1111/tpj.14345] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 05/15/2023]
Abstract
Post-translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site-specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry-based PTM data to remain at pace with future PTM plant studies.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
| | - Alison Horne
- VIB Bioinformatics Core, VIB, 9052, Ghent, Belgium
| | | | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | | | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
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8
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Vaneechoutte D, Estrada AR, Lin YC, Loraine AE, Vandepoele K. Genome-wide characterization of differential transcript usage in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1218-1231. [PMID: 29031026 DOI: 10.1111/tpj.13746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 05/21/2023]
Abstract
Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of differential transcript usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes, and have been linked to development and stress response. However, neither the characteristics of these genes, nor the implications of DTU on their protein coding sequences or functions, are currently well understood. Here we present a dataset of isoform dominance and DTU for all genes in the AtRTD2 reference transcriptome based on a protocol that was benchmarked on simulated data and validated through comparison with a published reverse transciptase-polymerase chain reaction panel. We report DTU events for 8148 genes across 206 public RNA-Seq samples, and find that protein sequences are affected in 22% of the cases. The observed DTU events show high consistency across replicates, and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different evolutionary ages, expression breadths and functions show large differences in the frequency at which they undergo DTU, and in the effect that these events have on their protein sequences. Finally, we showcase how the generated dataset can be used to explore DTU events for genes of interest or to find genes with specific DTU in samples of interest.
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Affiliation(s)
- Dries Vaneechoutte
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - April R Estrada
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Ying-Chen Lin
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
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9
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Horn PJ, Liu J, Cocuron JC, McGlew K, Thrower NA, Larson M, Lu C, Alonso AP, Ohlrogge J. Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:322-348. [PMID: 26991237 DOI: 10.1111/tpj.13163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 03/02/2016] [Accepted: 03/07/2016] [Indexed: 06/05/2023]
Abstract
Two Brassicaceae species, Physaria fendleri and Camelina sativa, are genetically very closely related to each other and to Arabidopsis thaliana. Physaria fendleri seeds contain over 50% hydroxy fatty acids (HFAs), while Camelina sativa and Arabidopsis do not accumulate HFAs. To better understand how plants evolved new biochemical pathways with the capacity to accumulate high levels of unusual fatty acids, transcript expression and protein sequences of developing seeds of Physaria fendleri, wild-type Camelina sativa, and Camelina sativa expressing a castor bean (Ricinus communis) hydroxylase were analyzed. A number of potential evolutionary adaptations within lipid metabolism that probably enhance HFA production and accumulation in Physaria fendleri, and, in their absence, limit accumulation in transgenic tissues were revealed. These adaptations occurred in at least 20 genes within several lipid pathways from the onset of fatty acid synthesis and its regulation to the assembly of triacylglycerols. Lipid genes of Physaria fendleri appear to have co-evolved through modulation of transcriptional abundances and alterations within protein sequences. Only a handful of genes showed evidence for sequence adaptation through gene duplication. Collectively, these evolutionary changes probably occurred to minimize deleterious effects of high HFA amounts and/or to enhance accumulation for physiological advantage. These results shed light on the evolution of pathways for novel fatty acid production in seeds, help explain some of the current limitations to accumulation of HFAs in transgenic plants, and may provide improved strategies for future engineering of their production.
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Affiliation(s)
- Patrick J Horn
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Jinjie Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
| | | | - Kathleen McGlew
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Nicholas A Thrower
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
| | - Matt Larson
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA
| | - Ana P Alonso
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, USA
| | - John Ohlrogge
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
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10
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Li Z, Cheng Y, Cui J, Zhang P, Zhao H, Hu S. Comparative transcriptome analysis reveals carbohydrate and lipid metabolism blocks in Brassica napus L. male sterility induced by the chemical hybridization agent monosulfuron ester sodium. BMC Genomics 2015; 16:206. [PMID: 25880309 PMCID: PMC4376087 DOI: 10.1186/s12864-015-1388-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chemical hybridization agents (CHAs) are often used to induce male sterility for the production of hybrid seeds. We previously discovered that monosulfuron ester sodium (MES), an acetolactate synthase (ALS) inhibitor of the herbicide sulfonylurea family, can induce rapeseed (Brassica napus L.) male sterility at approximately 1% concentration required for its herbicidal activity. To find some clues to the mechanism of MES inducing male sterility, the ultrastructural cytology observations, comparative transcriptome analysis, and physiological analysis on carbohydrate content were carried out in leaves and anthers at different developmental stages between the MES-treated and mock-treated rapeseed plants. RESULTS Cytological analysis revealed that the plastid ultrastructure was abnormal in pollen mother cells and tapetal cells in male sterility anthers induced by MES treatment, with less material accumulation in it. However, starch granules were observed in chloroplastids of the epidermis cells in male sterility anthers. Comparative transcriptome analysis identified 1501 differentially expressed transcripts (DETs) in leaves and anthers at different developmental stages, most of these DETs being localized in plastid and mitochondrion. Transcripts involved in metabolism, especially in carbohydrate and lipid metabolism, and cellular transport were differentially expressed. Pathway visualization showed that the tightly regulated gene network for metabolism was reprogrammed to respond to MES treatment. The results of cytological observation and transcriptome analysis in the MES-treated rapeseed plants were mirrored by carbohydrate content analysis. MES treatment led to decrease in soluble sugars content in leaves and early stage buds, but increase in soluble sugars content and decrease in starch content in middle stage buds. CONCLUSIONS Our integrative results suggested that carbohydrate and lipid metabolism were influenced by CHA-MES treatment during rapeseed anther development, which might responsible for low concentration MES specifically inducing male sterility. A simple action model of CHA-MES inducing male sterility in B. napus was proposed. These results will help us to understand the mechanism of MES inducing male sterility at low concentration, and might provide some potential targets for developing new male sterility inducing CHAs and for genetic manipulation in rapeseed breeding.
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Affiliation(s)
- Zhanjie Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China. .,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
| | - Yufeng Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China. .,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
| | - Jianmin Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China. .,College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
| | - Peipei Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China. .,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
| | - Huixian Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China. .,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
| | - Shengwu Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China. .,College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
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Wiszniewski AAG, Bussell JD, Long RL, Smith SM. Knockout of the two evolutionarily conserved peroxisomal 3-ketoacyl-CoA thiolases in Arabidopsis recapitulates the abnormal inflorescence meristem 1 phenotype. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6723-33. [PMID: 25297549 PMCID: PMC4246196 DOI: 10.1093/jxb/eru397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A specific function for peroxisomal β-oxidation in inflorescence development in Arabidopsis thaliana is suggested by the mutation of the abnormal inflorescence meristem 1 gene, which encodes one of two peroxisomal multifunctional proteins. Therefore, it should be possible to identify other β-oxidation mutants that recapitulate the aim1 phenotype. Three genes encode peroxisomal 3-ketoacyl-CoA thiolase (KAT) in Arabidopsis. KAT2 and KAT5 are present throughout angiosperms whereas KAT1 is a Brassicaceae-specific duplication of KAT2 expressed at low levels in Arabidopsis. KAT2 plays a dominant role in all known aspects of peroxisomal β-oxidation, including that of fatty acids, pro-auxins, jasmonate precursor oxophytodienoic acid, and trans-cinnamic acid. The functions of KAT1 and KAT5 are unknown. Since KAT5 is conserved throughout vascular plants and expressed strongly in flowers, kat2 kat5 double mutants were generated. These were slow growing, had abnormally branched inflorescences, and ectopic organ growth. They made viable pollen, but produced no seed indicating that infertility was due to defective gynaecium function. These phenotypes are strikingly similar to those of aim1. KAT5 in the Brassicaceae encodes both cytosolic and peroxisomal proteins and kat2 kat5 defects could be complemented by the re-introduction of peroxisomal (but not cytosolic) KAT5. It is concluded that peroxisomal KAT2 and KAT5 have partially redundant functions and operate downstream of AIM1 to provide β-oxidation functions essential for inflorescence development and fertility.
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Affiliation(s)
- Andrew A G Wiszniewski
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia Max-Planck Institute for Molecular Plant Physiology, Wissenschaftpark Golm, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - John D Bussell
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Rowena L Long
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Steven M Smith
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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Bussell JD, Reichelt M, Wiszniewski AA, Gershenzon J, Smith SM. Peroxisomal ATP-binding cassette transporter COMATOSE and the multifunctional protein abnormal INFLORESCENCE MERISTEM are required for the production of benzoylated metabolites in Arabidopsis seeds. PLANT PHYSIOLOGY 2014; 164:48-54. [PMID: 24254312 PMCID: PMC3875823 DOI: 10.1104/pp.113.229807] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Secondary metabolites derived from benzoic acid (BA) are of central importance in the interactions of plants with pests, pathogens, and symbionts and are potentially important in plant development. Peroxisomal β-oxidation has recently been shown to contribute to BA biosynthesis in plants, but not all of the enzymes involved have been defined. In this report, we demonstrate that the peroxisomal ATP-binding cassette transporter COMATOSE is required for the accumulation of benzoylated secondary metabolites in Arabidopsis (Arabidopsis thaliana) seeds, including benzoylated glucosinolates and substituted hydroxybenzoylcholines. The ABNORMAL INFLORESCENCE MERISTEM protein, one of two multifunctional proteins encoded by Arabidopsis, is essential for the accumulation of these compounds, and MULTIFUNCTIONAL PROTEIN2 contributes to the synthesis of substituted hydroxybenzoylcholines. Of the two major 3-ketoacyl coenzyme A thiolases, KAT2 plays the primary role in BA synthesis. Thus, BA biosynthesis in Arabidopsis employs the same core set of β-oxidation enzymes as in the synthesis of indole-3-acetic acid from indole-3-butyric acid.
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Aghamirzaie D, Nabiyouni M, Fang Y, Klumas C, Heath LS, Grene R, Collakova E. Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos. BIOLOGY 2013; 2:1311-37. [PMID: 24833227 PMCID: PMC4009788 DOI: 10.3390/biology2041311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/06/2013] [Accepted: 11/12/2013] [Indexed: 12/17/2022]
Abstract
Developing soybean seeds accumulate oils, proteins, and carbohydrates that are used as oxidizable substrates providing metabolic precursors and energy during seed germination. The accumulation of these storage compounds in developing seeds is highly regulated at multiple levels, including at transcriptional and post-transcriptional regulation. RNA sequencing was used to provide comprehensive information about transcriptional and post-transcriptional events that take place in developing soybean embryos. Bioinformatics analyses lead to the identification of different classes of alternatively spliced isoforms and corresponding changes in their levels on a global scale during soybean embryo development. Alternative splicing was associated with transcripts involved in various metabolic and developmental processes, including central carbon and nitrogen metabolism, induction of maturation and dormancy, and splicing itself. Detailed examination of selected RNA isoforms revealed alterations in individual domains that could result in changes in subcellular localization of the resulting proteins, protein-protein and enzyme-substrate interactions, and regulation of protein activities. Different isoforms may play an important role in regulating developmental and metabolic processes occurring at different stages in developing oilseed embryos.
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Affiliation(s)
- Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Mahdi Nabiyouni
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Yihui Fang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Curtis Klumas
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
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Bussell JD, Keech O, Fenske R, Smith SM. Requirement for the plastidial oxidative pentose phosphate pathway for nitrate assimilation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:578-91. [PMID: 23621281 DOI: 10.1111/tpj.12222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 05/08/2023]
Abstract
Sugar metabolism and the oxidative pentose phosphate pathway (OPPP) are strongly implicated in N assimilation, although the relationship between them and the roles of the plastidial and cytosolic OPPP have not been established genetically. We studied a knock-down mutant of the plastid-localized OPPP enzyme 6-phosphogluconolactonase 3 (PGL3). pgl3-1 plants exhibited relatively greater resource allocation to roots but were smaller than the wild type. They had a lower content of amino acids and free NO3 - in leaves than the wild type, despite exhibiting comparable photosynthetic rates and efficiency, and normal levels of many other primary metabolites. When N-deprived plants were fed via the roots with 15NO3 -, pgl3-1 exhibited normal induction of OPPP and nitrate assimilation genes in roots, and amino acids in roots and shoots were labeled with (15) N at least as rapidly as in the wild type. However, when N-replete plants were fed via the roots with sucrose, expression of specific OPPP and N assimilation genes in roots increased in the wild type but not in pgl3-1. Thus, sugar-dependent expression of N assimilation genes requires OPPP activity and the specificity of the effect of the pgl3-1 mutation on N assimilation genes establishes that it is not the result of general energy deficiency or accumulation of toxic intermediates. We conclude that expression of specific nitrate assimilation genes in the nucleus of root cells is positively regulated by a signal emanating from OPPP activity in the plastid.
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Affiliation(s)
- John D Bussell
- Australian Research Council Centre of Excellence in Plant Energy Biology (M316), University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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