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Yu C, Liu G, Qin J, Wan X, Guo A, Wei H, Chen Y, Lian B, Zhong F, Zhang J. Genomic and transcriptomic studies on flavonoid biosynthesis in Lagerstroemia indica. BMC PLANT BIOLOGY 2024; 24:171. [PMID: 38443839 PMCID: PMC10913235 DOI: 10.1186/s12870-024-04776-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/29/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Lagerstroemia indica is a widely cultivated ornamental woody shrub/tree of the family Lythraceae that is used as a traditional medicinal plant in East Asia and Egypt. However, unlike other ornamental woody plants, its genome is not well-investigated, which hindered the discovery of the key genes that regulate important traits and the synthesis of bioactive compounds. RESULTS In this study, the genomic sequences of L. indica were determined using several next-generation sequencing technologies. Altogether, 324.01 Mb sequences were assembled and 98.21% (318.21 Mb) of them were placed in 24 pseudo-chromosomes. The heterozygosity, repeated sequences, and GC residues occupied 1.65%, 29.17%, and 38.64% of the genome, respectively. In addition, 28,811 protein-coding gene models, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs were identified. The intra- and interspecies synteny and Ks analysis revealed that L. indica exhibits a hexaploidy. The co-expression profiles of the genes involved in the phenylpropanoid (PA) and flavonoid/anthocyanin (ABGs) pathways with the R2R3 MYB genes (137 members) showed that ten R2R3 MYB genes positively regulate flavonoid/anthocyanin biosynthesis. The colors of flowers with white, purple (PB), and deep purplish pink (DPB) petals were found to be determined by the levels of delphinidin-based (Dp) derivatives. However, the substrate specificities of LiDFR and LiOMT probably resulted in the different compositions of flavonoid/anthocyanin. In L. indica, two LiTTG1s (LiTTG1-1 and LiTTG1-2) were found to be the homologs of AtTTG1 (WD40). LiTTG1-1 was found to repress anthocyanin biosynthesis using the tobacco transient transfection assay. CONCLUSIONS This study showed that the ancestor L. indica experienced genome triplication approximately 38.5 million years ago and that LiTTG1-1 represses anthocyanin biosynthesis. Furthermore, several genes such as LiDFR, LiOMTs, and R2R3 LiMYBs are related to anthocyanin biosynthesis. Further studies are required to clarify the mechanisms and alleles responsible for flower color development.
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Affiliation(s)
- Chunmei Yu
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Guoyuan Liu
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Jin Qin
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Xi Wan
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Anfang Guo
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Hui Wei
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Yanhong Chen
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Bolin Lian
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Fei Zhong
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China
| | - Jian Zhang
- School of Life Science, Nantong University, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China.
- Key Lab of Landscape Plant Genetics and Breeding of Nantong, No. 9 Seyuan Road, Nantong, Jiangsu Province, 226019, China.
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Cheng H, Cai S, Hao M, Cai Y, Wen Y, Huang W, Mei D, Hu Q. Targeted mutagenesis of BnTTG1 homologues generated yellow-seeded rapeseed with increased oil content and seed germination under abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108302. [PMID: 38171134 DOI: 10.1016/j.plaphy.2023.108302] [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: 09/02/2023] [Revised: 11/24/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
Yellow seed is one desirable trait with great potential to improve seed oil quality and yield. The present study surveys the redundant role of BnTTG1 genes in the proanthocyanidins (PA) biosynthesis, oil content and abiotic stress resistance. Stable yellow seed mutants were generated after mutating BnTTG1 by CRISPR/Cas9 genome editing system. Yellow seed phenotype could be obtained only when both functional homologues of BnTTG1 were simultaneously knocked out. Homozygous mutants of BnTTG1 homologues showed decreased thickness and PA accumulation in seed coat. Transcriptome and qRT-PCR analysis indicated that BnTTG1 mutation inhibited the expression of genes involved in phenylpropanoid and flavonoid biosynthetic pathways. Increased seed oil content and alteration of fatty acid (FA) composition were observed in homozygous mutants of BnTTG1 with enriched expression of genes involved in FA biosynthesis pathway. In addition, target mutation of BnTTG1 accelerated seed germination rate under salt and cold stresses. Enhanced seed germination capacity in BnTTG1 mutants was correlated with the change of expression level of ABA responsive genes. Overall, this study elucidated the redundant role of BnTTG1 in regulating seed coat color and established an efficient approach for generating yellow-seeded oilseed rape genetic resources with increase oil content, modified FA composition and resistance to multiple abiotic stresses.
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Affiliation(s)
- 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.
| | - Shengli Cai
- 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.
| | - 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 and Rural Affairs, Wuhan, 430062, China.
| | - Yating Cai
- 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.
| | - Yunfei Wen
- 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.
| | - Wei Huang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, 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 and Rural Affairs, Wuhan, 430062, 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 and Rural Affairs, Wuhan, 430062, China; Hubei Hongshan Laboratory, Wuhan, China.
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3
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Serna L. Evolution of gene regulatory network architectures regulating root hair patterning in superrosid species. THE NEW PHYTOLOGIST 2023; 240:940-944. [PMID: 37537753 DOI: 10.1111/nph.19183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Affiliation(s)
- Laura Serna
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, 45071, Spain
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Pietsch J, Deneer A, Fleck C, Hülskamp M. Comparative expression analysis in three Brassicaceae species revealed compensatory changes of the underlying gene regulatory network. FRONTIERS IN PLANT SCIENCE 2023; 13:1086004. [PMID: 36684738 PMCID: PMC9845631 DOI: 10.3389/fpls.2022.1086004] [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: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Trichomes are regularly distributed on the leaves of Arabidopsis thaliana. The gene regulatory network underlying trichome patterning involves more than 15 genes. However, it is possible to explain patterning with only five components. This raises the questions about the function of the additional components and the identification of the core network. In this study, we compare the relative expression of all patterning genes in A. thaliana, A. alpina and C. hirsuta by qPCR analysis and use mathematical modelling to determine the relative importance of patterning genes. As the involved proteins exhibit evolutionary conserved differential complex formation, we reasoned that the genes belonging to the core network should exhibit similar expression ratios in different species. However, we find several striking differences of the relative expression levels. Our analysis of how the network can cope with such differences revealed relevant parameters that we use to predict the relevant molecular adaptations in the three species.
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Affiliation(s)
- Jessica Pietsch
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Anna Deneer
- Biometris, Department of Mathematical and Statistical Methods, Wageningen University, Wageningen, Netherlands
| | - Christian Fleck
- Spatial Systems Biology Group, Center for Data Analysis and Modeling, University of Freiburg, Freiburg, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
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Yang S, Wang Y, Zhu H, Zhang M, Wang D, Xie K, Fan P, Dou J, Liu D, Liu B, Chen C, Yan Y, Zhao L, Yang L. A novel HD-Zip I/C2H2-ZFP/WD-repeat complex regulates the size of spine base in cucumber. THE NEW PHYTOLOGIST 2022; 233:2643-2658. [PMID: 35037268 DOI: 10.1111/nph.17967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Fruit spine is an important trait in cucumber, affecting not only commercial quality, but also fruit smoothness, transportation and storage. Spine size is determined by a multi-cellular base. However, the molecular mechanism underlying the regulation of cucumber spine base remains largely unknown. Here, we report map-based cloning and characterization of a spine base size 1 (SBS1) gene, encoding a C2H2 zinc-finger transcription factor. Near-isogenic lines of cucumber were used to map, identify and quantify cucumber spine base size 1 (CsSBS1). Yeast-hybrid, bimolecular fluorescence complementation (BiFC), co-immunoprecipitation (Co-IP) and RNA-sequencing assays were used to explore the molecular mechanism of CsSBS1 in regulating spine base size development. CsSBS1 was specifically expressed in cucumber ovaries with particularly high expression in fruit spines. Overexpression of CsSBS1 resulted in large fruit spine base, while RNA-interference silencing of CsSBS1 inhibited the expansion of fruit spine base. Sequence analysis of natural cucumber accessions revealed that CsSBS1 was lost in small spine base accessions, resulting from a 4895 bp fragment deletion in CsSBS1 locus. CsSBS1 can form a trimeric complex with two positive regulators CsTTG1 and CsGL1 to regulate spine base development through ethylene signaling. A novel regulator network is proposed that the CsGL1/CsSBS1/CsTTG1 complex plays a significant role in regulating spine base formation and size, which offers a strategy for cucumber breeders to develop smooth fruit.
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Affiliation(s)
- Sen Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Yueling Wang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Huayu Zhu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Minjuan Zhang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Dengke Wang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Kuixi Xie
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Pengfei Fan
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Junling Dou
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Dongming Liu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Bin Liu
- Department of Plant Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, 08193, Spain
| | - Chunhua Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yan Yan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lijun Zhao
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
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Han X, Wei X, Lu W, Wu Q, Mao L, Luo Z. Transcriptional regulation of KCS gene by bZIP29 and MYB70 transcription factors during ABA-stimulated wound suberization of kiwifruit (Actinidia deliciosa). BMC PLANT BIOLOGY 2022; 22:23. [PMID: 34998386 PMCID: PMC8742354 DOI: 10.1186/s12870-021-03407-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/09/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Our previous study has demonstrated that the transcription of AchnKCS involved in suberin biosynthesis was up-regulated by exogenous abscisic acid (ABA) during the wound suberization of kiwifruit, but the regulatory mechanism has not been fully elucidated. RESULTS Through subcellular localization analysis in this work, AchnbZIP29 and AchnMYB70 transcription factors were observed to be localized in the nucleus. Yeast one-hybrid and dual-luciferase assay proved the transcriptional activation of AchnMYB70 and transcriptional suppression of AchnbZIP29 on AchnKCS promoter. Furthermore, the transcription level of AchnMYB70 was enhanced by ABA during wound suberization of kiwifruit, but AchnbZIP29 transcription was reduced by ABA. CONCLUSIONS Therefore, it was believed that ABA enhanced the transcriptional activation of AchnMYB70 on AchnKCS by increasing AchnMYB70 expression. On the contrary, ABA relieved the inhibitory effect of AchnbZIP29 on transcription of AchnKCS by inhibiting AchnbZIP29 expression. These results gave further insight into the molecular regulatory network of ABA in wound suberization of kiwifruit.
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Affiliation(s)
- Xueyuan Han
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Xiaopeng Wei
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, Henan, China
| | - Wenjing Lu
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qiong Wu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China.
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China.
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
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Mapar M, Chopra D, Stephan L, Schrader A, Sun H, Schneeberger K, Albani M, Coupland G, Hülskamp M. Genetic and Molecular Analysis of Root Hair Development in Arabis alpina. FRONTIERS IN PLANT SCIENCE 2021; 12:767772. [PMID: 34721494 PMCID: PMC8554057 DOI: 10.3389/fpls.2021.767772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Root hair formation in Arabidopsis thaliana is a well-established model system for epidermal patterning and morphogenesis in plants. Over the last decades, many underlying regulatory genes and well-established networks have been identified by thorough genetic and molecular analysis. In this study, we used a forward genetic approach to identify genes involved in root hair development in Arabis alpina, a related crucifer species that diverged from A. thaliana approximately 26-40 million years ago. We found all root hair mutant classes known in A. thaliana and identified orthologous regulatory genes by whole-genome or candidate gene sequencing. Our findings indicate that the gene-phenotype relationships regulating root hair development are largely conserved between A. thaliana and A. alpina. Concordantly, a detailed analysis of one mutant with multiple hairs originating from one cell suggested that a mutation in the SUPERCENTIPEDE1 (SCN1) gene is causal for the phenotype and that AaSCN1 is fully functional in A. thaliana. Interestingly, we also found differences in the regulation of root hair differentiation and morphogenesis between the species, and a subset of root hair mutants could not be explained by mutations in orthologs of known genes from A. thaliana. This analysis provides insight into the conservation and divergence of root hair regulation in the Brassicaceae.
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Affiliation(s)
- Mona Mapar
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Divykriti Chopra
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Lisa Stephan
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Andrea Schrader
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Hequan Sun
- Faculty of Biology, LMU Munich, Munich, Germany
| | | | - Maria Albani
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
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Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F. Arabis alpina: A perennial model plant for ecological genomics and life-history evolution. Mol Ecol Resour 2021; 22:468-486. [PMID: 34415668 PMCID: PMC9293087 DOI: 10.1111/1755-0998.13490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 01/03/2023]
Abstract
Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.
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Affiliation(s)
- Stefan Wötzel
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS, Rome, Italy
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - George Coupland
- Department of Plant Development Biology, MPI for Plant Breeding Research, Cologne, Germany
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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Viudes S, Burlat V, Dunand C. Seed mucilage evolution: Diverse molecular mechanisms generate versatile ecological functions for particular environments. PLANT, CELL & ENVIRONMENT 2020; 43:2857-2870. [PMID: 32557703 DOI: 10.1111/pce.13827] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Plant myxodiasporous species have the ability to release a polysaccharidic mucilage upon imbibition of the seed (myxospermy) or the fruit (myxocarpy). This is a widespread capacity in angiosperms providing multiple ecological functions including higher germination efficiency under environmental stresses. It is unclear whether myxodiaspory has one or multiple evolutionary origins and why it was supposedly lost in several species. Here, we summarize recent advances on three main aspects of myxodiaspory. (a) It represents a combination of highly diverse traits at different levels of observation, ranging from the dual tissular origin of mucilage secretory cells to diverse mucilage polysaccharidic composition and ultrastructural organization. (b) An asymmetrical selection pressure is exerted on myxospermy-related genes that were first identified in Arabidopsis thaliana. The A. thaliana and the flax intra-species mucilage variants show that myxospermy is a fast-evolving trait due to high polymorphism in a few genes directly acting on mucilage establishment. In A. thaliana, these actors are downstream of a master regulatory complex and an original phylogenetic overview provided here illustrates that this complex has sequentially evolved after the common ancestor of seed plants and was fully established in the common ancestor of the rosid clade. (c) Newly identified myxodiaspory ecological functions indicate new perspectives such as soil microorganism control and plant establishment support.
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Affiliation(s)
- Sébastien Viudes
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, Castanet-Tolosan, France
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, Castanet-Tolosan, France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, Castanet-Tolosan, France
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TRANSPARENT TESTA GLABRA1, a Key Regulator in Plants with Multiple Roles and Multiple Function Mechanisms. Int J Mol Sci 2020; 21:ijms21144881. [PMID: 32664363 PMCID: PMC7402295 DOI: 10.3390/ijms21144881] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 01/01/2023] Open
Abstract
TRANSPARENT TESTA GLABRA1 (TTG1) is a WD40 repeat protein. The phenotypes caused by loss-of-function of TTG1 were observed about half a century ago, but the TTG1 gene was identified only about twenty years ago. Since then, TTG1 has been found to be a plant-specific regulator with multiple roles and multiple functional mechanisms. TTG1 is involved in the regulation of cell fate determination, secondary metabolisms, accumulation of seed storage reserves, plant responses to biotic and abiotic stresses, and flowering time in plants. In some processes, TTG1 may directly or indirectly regulate the expression of downstream target genes via forming transcription activator complexes with R2R3 MYB and bHLH transcription factors. Whereas in other processes, TTG1 may function alone or interact with other proteins to regulate downstream target genes. On the other hand, the studies on the regulation of TTG1 are very limited. So far, only the B3-domain family transcription factor FUSCA3 (FUS3) has been found to regulate the expression of TTG1, phosphorylation of TTG1 affects its interaction with bHLH transcription factor TT2, and TTG1 proteins can be targeted for degradation by the 26S proteasome. Here, we provide an overview of TTG1, including the identification of TTG1, the functions of TTG1, the possible function mechanisms of TTG1, and the regulation of TTG1. We also proposed potential research directions that may shed new light on the regulation and functional mechanisms of TTG1 in plants.
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Zhang B, Chopra D, Schrader A, Hülskamp M. Evolutionary comparison of competitive protein-complex formation of MYB, bHLH, and WDR proteins in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3197-3209. [PMID: 31071215 PMCID: PMC6598095 DOI: 10.1093/jxb/erz155] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/25/2019] [Indexed: 05/20/2023]
Abstract
A protein complex consisting of a MYB, basic Helix-Loop-Helix, and a WDR protein, the MBW complex, regulates five traits, namely the production of anthocyanidin, proanthocyanidin, and seed-coat mucilage, and the development of trichomes and root hairs. For complexes involved in trichome and root hair development it has been shown that the interaction of two MBW proteins can be counteracted by the respective third protein (called competitive complex formation). We examined competitive complex formation for selected MBW proteins from Arabidopsis thaliana, Arabis alpina, Gossypium hirsutum, Petunia hybrida, and Zea mays. Quantitative analyses of the competitive binding of MYBs and WDRs to bHLHs were done by pull-down assays using ProtA- and luciferase-tagged proteins expressed in human HEC cells. We found that some bHLHs show competitive complex formation whilst others do not. Competitive complex formation strongly correlated with a phylogenetic tree constructed with the bHLH proteins under investigation, suggesting a functional relevance. We demonstrate that this different behavior can be explained by changes in one amino acid and that this position is functionally relevant in trichome development but not in anthocyanidin regulation.
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Affiliation(s)
- Bipei Zhang
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Divykriti Chopra
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Andrea Schrader
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- Correspondence:
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Genetic and molecular analysis of trichome development in Arabis alpina. Proc Natl Acad Sci U S A 2019; 116:12078-12083. [PMID: 31123146 DOI: 10.1073/pnas.1819440116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic and molecular analysis of trichome development in Arabidopsis thaliana has generated a detailed knowledge about the underlying regulatory genes and networks. However, how rapidly these mechanisms diverge during evolution is unknown. To address this problem, we used an unbiased forward genetic approach to identify most genes involved in trichome development in the related crucifer species Arabis alpina In general, we found most trichome mutant classes known in A. thaliana We identified orthologous genes of the relevant A. thaliana genes by sequence similarity and synteny and sequenced candidate genes in the A. alpina mutants. While in most cases we found a highly similar gene-phenotype relationship as known from Arabidopsis, there were also striking differences in the regulation of trichome patterning, differentiation, and morphogenesis. Our analysis of trichome patterning suggests that the formation of two classes of trichomes is regulated differentially by the homeodomain transcription factor AaGL2 Moreover, we show that overexpression of the GL3 basic helix-loop-helix transcription factor in A. alpina leads to the opposite phenotype as described in A. thaliana Mathematical modeling helps to explain how this nonintuitive behavior can be explained by different ratios of GL3 and GL1 in the two species.
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Stephan L, Tilmes V, Hülskamp M. Selection and validation of reference genes for quantitative Real-Time PCR in Arabis alpina. PLoS One 2019; 14:e0211172. [PMID: 30830921 PMCID: PMC6398851 DOI: 10.1371/journal.pone.0211172] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/19/2019] [Indexed: 11/25/2022] Open
Abstract
Arabis alpina is a perennial arctic-alpine plant and an upcoming model organism for genetics and molecular biology for the Brassicaceae family. One essential method for most molecular approaches is the analysis of gene expression by reverse-transcription quantitative Real-Time PCR (RT-qPCR). For the normalisation of expression data in RT-qPCR experiments, it is essential to use reliable reference genes that are not affected under a wide range of conditions. In this study we establish a set of 15 A. alpina reference genes that were tested under different conditions including cold, drought, heat, salt and gibberellic acid treatments. Data analyses with geNORM, BestKeeper and NormFinder revealed the most stable reference genes for the tested conditions: RAN3, HCF and PSB33 are most suitable for cold treatments; UBQ10 and TUA5 for drought; RAN3, PSB33 and EIF4a for heat; CAC, TUA5, ACTIN 2 and PSB33 for salt and PSB33 and TUA5 for gibberellic acid treatments. CAC and ACTIN 2 showed the least variation over all tested samples. In addition, we show that two reference genes are sufficient to normalize RT-qPCR data under our treatment conditions. In future studies, these reference genes can be used for an adequate normalisation and thus help to generate high quality RT-qPCR data in A. alpina.
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Affiliation(s)
- Lisa Stephan
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Vicky Tilmes
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- * E-mail:
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Zhang B, Hülskamp M. Evolutionary Analysis of MBW Function by Phenotypic Rescue in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:375. [PMID: 30984225 PMCID: PMC6449874 DOI: 10.3389/fpls.2019.00375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/12/2019] [Indexed: 05/07/2023]
Abstract
The MBW complex consisting of the three proteins R2R3MYB, bHLH and WDR regulates five traits in Arabidopsis thaliana including trichome and root hair patterning, seed coat color, anthocyanidin production and seed coat mucilage release. The WDR gene TTG1 regulates each trait in specific combinations with different bHLH and R2R3MYB proteins. In this study we analyze to what extent the biochemical properties of the MBW proteins contribute to trait specificity by expressing them in appropriate A. thaliana mutants. We show that the rescue behavior of A. thaliana bHLH and R2R3MYB protein is sufficient to explain the function as derived previously from mutant analysis. When extending this rescue approach using MBW proteins from other species we find that proteins involved in anthocyanidin regulation typically show a rescue of the anthocyanidin phenotype but not of the other traits. Finally, we correlate the rescue abilities of MBW protein from different species with the A. thaliana proteins.
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Li S, Wu Y, Kuang J, Wang H, Du T, Huang Y, Zhang Y, Cao X, Wang Z. SmMYB111 Is a Key Factor to Phenolic Acid Biosynthesis and Interacts with Both SmTTG1 and SmbHLH51 in Salvia miltiorrhiza. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8069-8078. [PMID: 30001627 DOI: 10.1021/acs.jafc.8b02548] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription factors that include myeloblastosis (MYB), basic helix-loop-helix (bHLH), and tryptophan-aspartic acid (WD)-repeat protein often form a ternary complex to regulate the phenylpropanoid pathway. However, only a few MYB and bHLH members involved in the biosynthesis of salvianolic acid B (Sal B) have been reported, and little is known about Sal B pathway regulation by the WD40 protein transparent testa glabra 1 (TTG1)-dependent transcriptional complexes in Salvia miltiorrhiza. We isolated SmTTG1 from that species for detailed functional characterization. Enhanced or reduced expression of SmTTG1 was achieved by gain- or loss-of-function assays, respectively, revealing that SmTTG1 is necessary for Sal B biosynthesis. Interaction partners of the SmTTG1 protein were screened by yeast two-hybrid (Y2H) assays with the cDNA library of S. miltiorrhiza. A new R2R3-MYB transcription factor, SmMYB111, was found through this screening. Transgenic plants overexpressing or showing reduced expression of SmMYB111 upregulated or deregulated, respectively, the yields of Sal B. Both Y2H and bimolecular fluorescent complementation experiments demonstrated that SmMYB111 interacts with SmTTG1 and SmbHLH51, a positive regulator of the phenolic acid pathway. Our data verified the function of SmTTG1 and SmMYB111 in regulating phenolic acid biosynthesis in S. miltiorrhiza. Furthermore, ours is the first report of the potential ternary transcription complex SmTTG1-SmMYB111-SmbHLH51, which is involved in the production of Sal B in that species.
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Affiliation(s)
- Shasha Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China
| | - Yucui Wu
- School of Landscape and Ecological Engineering , Hebei University of Engineering , Handan , Hebei 056038 , People's Republic of China
| | - Jing Kuang
- Ningxia Polytechnic , Yinchuan , Ningxia 750001 , People's Republic of China
| | - Huaiqin Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China
| | - Tangzhi Du
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China
| | - Yaya Huang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China
| | - Yuan Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China
| | - Xiaoyan Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China
| | - Zhezhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry , Shaanxi Normal University , Xi'an , Shaanxi 710062 , People's Republic of China
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Gao Y, Liu J, Chen Y, Tang H, Wang Y, He Y, Ou Y, Sun X, Wang S, Yao Y. Tomato SlAN11 regulates flavonoid biosynthesis and seed dormancy by interaction with bHLH proteins but not with MYB proteins. HORTICULTURE RESEARCH 2018; 5:27. [PMID: 29872532 PMCID: PMC5981465 DOI: 10.1038/s41438-018-0032-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/03/2018] [Accepted: 03/11/2018] [Indexed: 05/18/2023]
Abstract
The flavonoid compounds are important secondary metabolites with versatile human nutritive benefits and fulfill a multitude of functions during plant growth and development. The abundance of different flavonoid compounds are finely tuned with species-specific pattern by a ternary MBW complex, which consists of a MYB, a bHLH, and a WD40 protein, but the essential role of SlAN11, which is a WD40 protein, is not fully understood in tomato until now. In this study, a tomato WD40 protein named as SlAN11 was characterized as an effective transcription regulator to promote plant anthocyanin and seed proanthocyanidin (PA) contents, with late flavonoid biosynthetic genes activated in 35S::SlAN11 transgenic lines, while the dihydroflavonol flow to the accumulation of flavonols or their glycosylated derivatives was reduced by repressing the expression of SlFLS in this SlAN11-overexpressed lines. The above changes were reversed in 35S::SlAN11-RNAi transgenic lines except remained levels of flavonol compounds and SlFLS expression. Interestingly, our data revealed that SlAN11 gene could affect seed dormancy by regulating the expressions of abscisic acid (ABA) signaling-related genes SlABI3 and SlABI5, and the sensitivity to ABA treatment in seed germination is conversely changed by SlAN11-overexpressed or -downregulated lines. Yeast two-hybrid assays demonstrated that SlAN11 interacted with bHLH but not with MYB proteins in the ternary MBW complex, whereas bHLH interacted with MYB in tomato. Our results indicated that low level of anthocyanins in tomato fruits, with low expression of bHLH (SlTT8) and MYB (SlANT1 and SlAN2) genes, remain unchanged upon modification of SlAN11 gene alone in the transgenic lines. These results suggest that the tomato WD40 protein SlAN11, coordinating with bHLH and MYB proteins, plays a crucial role in the fine adjustment of the flavonoid biosynthesis and seed dormancy in tomato.
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Affiliation(s)
- Yongfeng Gao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 China
| | - Jikai Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 China
| | - Yongfu Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 China
| | - Hai Tang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 China
| | - Yang Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 China
| | - Yongmei He
- Yunnan Engineering Laboratory for Agro-environment Pollution Control and Eco-remediation, The Innovation Team for Farmland Non-pollution Production of Yunnan Province, Kunming, 650201 China
| | - Yongbin Ou
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 China
| | - Xiaochun Sun
- Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, 712046 China
| | - Songhu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Yinan Yao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010 China
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Zhang B, Schrader A. TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2017; 6:E65. [PMID: 29261137 PMCID: PMC5750641 DOI: 10.3390/plants6040065] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/02/2017] [Accepted: 12/16/2017] [Indexed: 12/25/2022]
Abstract
The flavonoid composition of various tissues throughout plant development is of biological relevance and particular interest for breeding. Arabidopsis thaliana TRANSPARENT TESTA GLABRA 1 (AtTTG1) is an essential regulator of late structural genes in flavonoid biosynthesis. Here, we provide a review of the regulation of the pathway's core enzymes through AtTTG1-containing R2R3-MYELOBLASTOSIS-basic HELIX-LOOP-HELIX-WD40 repeat (MBW(AtTTG1)) complexes embedded in an evolutionary context. We present a comprehensive collection of A. thalianattg1 mutants and AtTTG1 orthologs. A plethora of MBW(AtTTG1) mechanisms in regulating the five major TTG1-dependent traits is highlighted.
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Affiliation(s)
- Bipei Zhang
- Botanical Institute, University of Cologne, Zuelpicher Str 47B, 50674 Cologne, Germany.
| | - Andrea Schrader
- Botanical Institute, University of Cologne, Zuelpicher Str 47B, 50674 Cologne, Germany.
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Miller JC, Chezem WR, Clay NK. Ternary WD40 Repeat-Containing Protein Complexes: Evolution, Composition and Roles in Plant Immunity. FRONTIERS IN PLANT SCIENCE 2016; 6:1108. [PMID: 26779203 PMCID: PMC4703829 DOI: 10.3389/fpls.2015.01108] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/23/2015] [Indexed: 05/18/2023]
Abstract
Plants, like mammals, rely on their innate immune system to perceive and discriminate among the majority of their microbial pathogens. Unlike mammals, plants respond to this molecular dialog by unleashing a complex chemical arsenal of defense metabolites to resist or evade pathogen infection. In basal or non-host resistance, plants utilize signal transduction pathways to detect "non-self," "damaged-self," and "altered-self"- associated molecular patterns and translate these "danger" signals into largely inducible chemical defenses. The WD40 repeat (WDR)-containing proteins Gβ and TTG1 are constituents of two independent ternary protein complexes functioning at opposite ends of a plant immune signaling pathway. They are also encoded by single-copy genes that are ubiquitous in higher plants, implying the limited diversity and functional conservation of their respective complexes. In this review, we summarize what is currently known about the evolutionary history of these WDR-containing ternary complexes, their repertoire and combinatorial interactions, and their downstream effectors and pathways in plant defense.
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Affiliation(s)
- Jimi C. Miller
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT, USA
| | - William R. Chezem
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew Haven, CT, USA
| | - Nicole K. Clay
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew Haven, CT, USA
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