1
|
Hao M, Wang W, Liu J, Wang H, Zhou R, Mei D, Fu L, Hu Q, Cheng H. Auxin Biosynthesis Genes in Allotetraploid Oilseed Rape Are Essential for Plant Development and Response to Drought Stress. Int J Mol Sci 2022; 23:15600. [PMID: 36555242 PMCID: PMC9778849 DOI: 10.3390/ijms232415600] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Crucial studies have verified that IAA is mainly generated via the two-step pathway in Arabidopsis, in which tryptophan aminotransferase (TAA) and YUCCA (YUC) are the two crucial enzymes. However, the role of the TAA (or TAR) and YUC genes in allotetraploid oilseed rape underlying auxin biosynthesis and development regulation remains elusive. In the present study, all putative TAR and YUC genes were identified in B. napus genome. Most TAR and YUC genes were tissue that were specifically expressed. Most YUC and TAR proteins contained trans-membrane regions and were confirmed to be endoplasmic reticulum localizations. Enzymatic activity revealed that YUC and TAR protein members were involved in the conversion of IPA to IAA and Trp to IPA, respectively. Transgenic plants overexpressing BnaYUC6a in both Arabidopsis and B. napus displayed high auxin production and reduced plant branch angle, together with increased drought resistance. Moreover, mutation in auxin biosynthesis BnaTARs genes by CRISPR/Cas9 caused development defects. All these results suggest the convergent role of BnaYUC and BnaTAR genes in auxin biosynthesis. Different homoeologs of BnaYUC and BnaTAR may be divergent according to sequence and expression variation. Auxin biosynthesis genes in allotetraploid oilseed rape play a pivotal role in coordinating plant development processes and stress resistance.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| |
Collapse
|
2
|
Wang H, Cheng H, Wang W, Liu J, Hao M, Mei D, Zhou R, Fu L, Hu Q. Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq. Sci Rep 2016; 6:38493. [PMID: 27922076 PMCID: PMC5138835 DOI: 10.1038/srep38493] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 11/11/2016] [Indexed: 11/12/2022] Open
Abstract
Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population. Eighty-two genes were identified in the ba1 region. Among these genes, BnaA0639380D is a homolog of AtYUCCA6. Sequence comparison of BnaA0639380D from small- and big-branch angle oilseed rape lines identified six SNPs and four amino acid variation in the promoter and coding region, respectively. The expression level of BnaA0639380D is significantly higher in the small branch angle line Purler than in the big branch angle line Huyou19, suggesting that the genomic mutations may result in reduced activity of BnaA0639380D in Huyou19. Phytohormone determination showed that the IAA content in Purler was also obviously increased. Taken together, our results suggested BnaA0639380D is a possible candidate gene for branch angle in oilseed rape.
Collapse
Affiliation(s)
- Hui Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Wenxiang Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Rijin Zhou
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Li Fu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong 2nd Road, Wuhan 430062, P.R. China
| |
Collapse
|
3
|
Kim JI, Dolan WL, Anderson NA, Chapple C. Indole Glucosinolate Biosynthesis Limits Phenylpropanoid Accumulation in Arabidopsis thaliana. THE PLANT CELL 2015; 27:1529-46. [PMID: 25944103 PMCID: PMC4456644 DOI: 10.1105/tpc.15.00127] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/05/2015] [Accepted: 04/20/2015] [Indexed: 05/17/2023]
Abstract
Plants produce an array of metabolites (including lignin monomers and soluble UV-protective metabolites) from phenylalanine through the phenylpropanoid biosynthetic pathway. A subset of plants, including many related to Arabidopsis thaliana, synthesizes glucosinolates, nitrogen- and sulfur-containing secondary metabolites that serve as components of a plant defense system that deters herbivores and pathogens. Here, we report that the Arabidopsis thaliana reduced epidermal fluorescence5 (ref5-1) mutant, identified in a screen for plants with defects in soluble phenylpropanoid accumulation, has a missense mutation in CYP83B1 and displays defects in glucosinolate biosynthesis and in phenylpropanoid accumulation. CYP79B2 and CYP79B3 are responsible for the production of the CYP83B1 substrate indole-3-acetaldoxime (IAOx), and we found that the phenylpropanoid content of cyp79b2 cyp79b3 and ref5-1 cyp79b2 cyp79b3 plants is increased compared with the wild type. These data suggest that levels of IAOx or a subsequent metabolite negatively influence phenylpropanoid accumulation in ref5 and more importantly that this crosstalk is relevant in the wild type. Additional biochemical and genetic evidence indicates that this inhibition impacts the early steps of the phenylpropanoid biosynthetic pathway and restoration of phenylpropanoid accumulation in a ref5-1 med5a/b triple mutant suggests that the function of the Mediator complex is required for the crosstalk.
Collapse
Affiliation(s)
- Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Whitney L Dolan
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Nickolas A Anderson
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| |
Collapse
|
4
|
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. BIOINFORMATICS (OXFORD, ENGLAND) 2014; 151:3-12. [PMID: 24695404 DOI: 10.1111/ppl.12098] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/30/2013] [Accepted: 08/15/2013] [Indexed: 05/09/2023]
Abstract
MOTIVATION Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. RESULTS The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. AVAILABILITY AND IMPLEMENTATION Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Anthony M Bolger
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
| | - Marc Lohse
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
| | - Bjoern Usadel
- Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, GermanyDepartment Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm,Institut für Biologie I, RWTH Aachen, Worringer Weg 3, 52074 Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany
| |
Collapse
|
5
|
Tivendale ND, Ross JJ, Cohen JD. The shifting paradigms of auxin biosynthesis. TRENDS IN PLANT SCIENCE 2014; 19:44-51. [PMID: 24524164 DOI: 10.1016/j.tplants.2013.09.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Auxins are an important group of hormones found in all land plants and several soil-dwelling microbes. Although auxin was the first phytohormone identified, its biosynthesis remained unclear until recently. In the past few years, our understanding of auxin biosynthesis has im-proved dramatically, to the stage where many believe there is a single predominant pathway in Arabidopsis (Arabidopsis thaliana L.). However, there is still uncertainty over the applicability of these findings to other plant species. Indeed, it appears that in certain organs of some species, other pathways can operate. Here we review the key advances that have led to our current understanding of auxin biosynthesis and its many pro-posed pathways.
Collapse
|
6
|
Kim JI, Baek D, Park HC, Chun HJ, Oh DH, Lee MK, Cha JY, Kim WY, Kim MC, Chung WS, Bohnert HJ, Lee SY, Bressan RA, Lee SW, Yun DJ. Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit. MOLECULAR PLANT 2013; 6:337-49. [PMID: 22986790 DOI: 10.1093/mp/sss100] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Indole-3-acetic acid (IAA), a major plant auxin, is produced in both tryptophan-dependent and tryptophan-independent pathways. A major pathway in Arabidopsis thaliana generates IAA in two reactions from tryptophan. Step one converts tryptophan to indole-3-pyruvic acid (IPA) by tryptophan aminotransferases followed by a rate-limiting step converting IPA to IAA catalyzed by YUCCA proteins. We identified eight putative StYUC (Solanum tuberosum YUCCA) genes whose deduced amino acid sequences share 50%-70% identity with those of Arabidopsis YUCCA proteins. All include canonical, conserved YUCCA sequences: FATGY motif, FMO signature sequence, and FAD-binding and NADP-binding sequences. In addition, five genes were found with ~50% amino acid sequence identity to Arabidopsis tryptophan aminotransferases. Transgenic potato (Solanum tuberosum cv. Jowon) constitutively overexpressing Arabidopsis AtYUC6 displayed high-auxin phenotypes such as narrow downward-curled leaves, increased height, erect stature, and longevity. Transgenic potato plants overexpressing AtYUC6 showed enhanced drought tolerance based on reduced water loss. The phenotype was correlated with reduced levels of reactive oxygen species in leaves. The results suggest a functional YUCCA pathway of auxin biosynthesis in potato that may be exploited to alter plant responses to the environment.
Collapse
Affiliation(s)
- Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Mano Y, Nemoto K. The pathway of auxin biosynthesis in plants. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2853-72. [PMID: 22447967 DOI: 10.1093/jxb/ers091] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The plant hormone auxin, which is predominantly represented by indole-3-acetic acid (IAA), is involved in the regulation of plant growth and development. Although IAA was the first plant hormone identified, the biosynthetic pathway at the genetic level has remained unclear. Two major pathways for IAA biosynthesis have been proposed: the tryptophan (Trp)-independent and Trp-dependent pathways. In Trp-dependent IAA biosynthesis, four pathways have been postulated in plants: (i) the indole-3-acetamide (IAM) pathway; (ii) the indole-3-pyruvic acid (IPA) pathway; (iii) the tryptamine (TAM) pathway; and (iv) the indole-3-acetaldoxime (IAOX) pathway. Although different plant species may have unique strategies and modifications to optimize their metabolic pathways, plants would be expected to share evolutionarily conserved core mechanisms for auxin biosynthesis because IAA is a fundamental substance in the plant life cycle. In this review, the genes now known to be involved in auxin biosynthesis are summarized and the major IAA biosynthetic pathway distributed widely in the plant kingdom is discussed on the basis of biochemical and molecular biological findings and bioinformatics studies. Based on evolutionarily conserved core mechanisms, it is thought that the pathway via IAM or IPA is the major route(s) to IAA in plants.
Collapse
Affiliation(s)
- Yoshihiro Mano
- Graduate School of Bioscience, Tokai University, 317 Nishino, Numazu, Shizuoka 410-0321, Japan.
| | | |
Collapse
|