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Mutanwad KV, Debreczeny M, Lucyshyn D. Root Hair Imaging Using Confocal Microscopy. Methods Mol Biol 2024; 2787:81-94. [PMID: 38656483 DOI: 10.1007/978-1-0716-3778-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Plant genetics plays a key role in determining root hair initiation and development. A complex network of genetic interactions therefore closely monitors and influences root hair phenotype and morphology. The significance of these genes can be studied by employing, for instance, loss-of-function mutants, overexpression plant lines, and fluorescently labeled constructs. Confocal laser scanning microscopy is a great tool to visually observe and document these morphological features. This chapter elaborates the techniques involved in handling of microscopic setup to acquire images displaying root hair distribution along the fully elongated zone of Arabidopsis thaliana roots. Additionally, we illustrate an approach to visualize early fate determination of epidermal cells in the root apical meristem, by describing a method for imaging YFP tagged transgenic plant lines.
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Affiliation(s)
- Krishna Vasant Mutanwad
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Monika Debreczeny
- Core Facility Multiscale Imaging, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Doris Lucyshyn
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
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2
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Ke S, Jiang Y, Zhou M, Li Y. Genome-Wide Identification, Evolution, and Expression Analysis of the WD40 Subfamily in Oryza Genus. Int J Mol Sci 2023; 24:15776. [PMID: 37958759 PMCID: PMC10648978 DOI: 10.3390/ijms242115776] [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: 09/12/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula, Oryza nivara, and Oryza longistaminata. In this study, 383 WD40 genes in the Oryza genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the Oryza genus, and all were segmental duplications. WD40s had similar expansion patterns in the Oryza genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the Oryza genus have similar evolutionary patterns, so Oryza sativa ssp. indica was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, OsiWD40-26/37/42 contained elements of flavonoid synthesis, and OsiWD40-15 had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most OsiWD40s were expressed in leaves, roots, and panicles. The expression of OsiWD40s was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. OsiWD40-24 was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many OsiWD40s might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development.
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Affiliation(s)
| | | | | | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.K.); (Y.J.); (M.Z.)
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3
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Hanlon MT, Vejchasarn P, Fonta JE, Schneider HM, McCouch SR, Brown KM. Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation. BMC PLANT BIOLOGY 2023; 23:6. [PMID: 36597029 PMCID: PMC9811729 DOI: 10.1186/s12870-022-04026-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus, indica, temperate japonica, and tropical japonica). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets. RESULTS We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice and Arabidopsis. CONCLUSIONS Root hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.
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Affiliation(s)
- Meredith T Hanlon
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, Huck Institutes of the Life Sciences, Penn State University, University Park, PA, 16802, USA
| | - Phanchita Vejchasarn
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Rice Department, Ministry of Agriculture, Ubon Ratchathani Rice Research Center, Ubon Ratchathani, 34000, Thailand
| | - Jenna E Fonta
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, Huck Institutes of the Life Sciences, Penn State University, University Park, PA, 16802, USA
| | - Hannah M Schneider
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, the Netherlands
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853-1901, USA
- Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Kathleen M Brown
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA.
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Lim SH, Kim DH, Lee JY. RsTTG1, a WD40 Protein, Interacts with the bHLH Transcription Factor RsTT8 to Regulate Anthocyanin and Proanthocyanidin Biosynthesis in Raphanus sativus. Int J Mol Sci 2022; 23:ijms231911973. [PMID: 36233274 PMCID: PMC9570178 DOI: 10.3390/ijms231911973] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
MBW complexes, consisting of MYB, basic helix–loop–helix (bHLH), and WD40 proteins, regulate multiple traits in plants, including anthocyanin and proanthocyanidin (PA) biosynthesis and the determination of epidermal cell fate. Here, a WD40 gene from Raphanus sativus, designated TRANSPARENT TESTA GLABRA 1 (RsTTG1), was cloned and functionally characterized. Heterologous expression of RsTTG1 in the Arabidopsis thaliana mutant ttg1-22 background restored accumulation of anthocyanin and PA in the mutant and rescued trichome development. In radish, RsTTG1 was abundantly expressed in all root and leaf tissues, independently of anthocyanin accumulation, while its MBW partners RsMYB1 and TRANSPARENT TESTA 8 (RsTT8) were expressed at higher levels in pigment-accumulating tissues. In yeast two-hybrid analysis, the full-length RsTTG1 protein interacted with RsTT8. Moreover, transient protoplast co-expression assays demonstrated that RsTTG1, which localized to both the cytoplasm and nucleus, moves from the cytoplasm to the nucleus in the presence of RsTT8. When co-expressed with RsMYB1 and RsTT8, RsTTG1 stably activated the promoters of the anthocyanin biosynthesis genes CHALCONE SYNTHASE (RsCHS) and DIHYDROFLAVONOL 4-REDUCTASE (RsDFR). Transient expression of RsTTG1 in tobacco leaves exhibited an increase in anthocyanin accumulation due to activation of the expression of anthocyanin biosynthesis genes when simultaneously expressed with RsMYB1 and RsTT8. These results indicate that RsTTG1 is a vital regulator of pigmentation and trichome development as a functional homolog of AtTTG1.
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Affiliation(s)
- Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea
- Research Institute of International Technology and Information, Hankyong National University, Anseong 17579, Korea
- Correspondence: ; Tel.: +82-31-670-5105
| | - Da-Hye Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea
- Research Institute of International Technology and Information, Hankyong National University, Anseong 17579, Korea
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
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Huang X, Yi P, Liu Y, Li Q, Jiang Y, Yi Y, Yan H. RrTTG1 promotes fruit prickle development through an MBW complex in Rosa roxburghii. FRONTIERS IN PLANT SCIENCE 2022; 13:939270. [PMID: 36105707 PMCID: PMC9465040 DOI: 10.3389/fpls.2022.939270] [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: 05/09/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Fruit prickles are widely distributed on the pericarp and exhibit polymorphic traits at different developmental stages. Although they are multicellular appendages that are well-known for helping plants defend against biotic and abiotic stresses, their origination and molecular mechanism are still less known. Here, we studied the origination and molecular mechanism of fruit prickles in Rosa roxburghii. Using morphological and histological observations, we found that the fruit prickle primordium of R. roxburghii originated from the ground meristem that underwent cell division to form flagelliform prickles, continued to enlarge, and finally lignified to form mature fruit prickles. We amplified a homolog of candidate gene TRANSPARENT TESTA GLABRA1 (TTG1) from R. roxburghii, named RrTTG1. RrTTG1 harbored four conserved WD-repeat domains and was exclusively nuclear-localized. Using qRT-PCR and in situ hybridization, we found that RrTTG1 was constitutively expressed and highly expressed during the initiation and cell expansion phases of fruit prickles. Ectopic expression analysis in Arabidopsis proved that RrTTG1 substantially enhanced the number of trichome and pigmentation production and inhibited root hair formation. Besides, RrTTG1 complemented the phenotypes of the ttg1 mutant in Arabidopsis, thus indicating that RrTTG1 played pleiotropic roles akin to AtTTG1. We demonstrated that the RrTTG1 only interacted with RrEGL3, a homolog of ENHANCER OF GLABRA3 (EGL3), via yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Briefly, RrTTG1 might positively regulate the initiation of fruit prickle primordium and cell enlargement by forming the RrTTG1-RrEGL3-RrGL1 complex in R. roxburghii. Therefore, our results help characterize the RrTTG1 in R. roxburghii and also elucidate the establishment of the prickles regulatory system in the Rosaceae plants.
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Affiliation(s)
- Xiaolong Huang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
| | - Peipei Yi
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
| | - Yanjing Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
| | - Qiaohong Li
- Sichuan Provincial Academy of Natural Resource Science, Chengdu, China
| | - Yu Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yin Yi
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Guiyang, China
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Vincent C, Ebert R, Hermans C. Root hair quantification is an accessible approach to phenotyping important functional traits. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3304-3307. [PMID: 35290442 DOI: 10.1093/jxb/erac102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Christopher Vincent
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Rebecca Ebert
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, B-1050 Brussels, Belgium
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Shao C, Cai F, Bao Z, Zhang Y, Shi G, Zhou Z, Chen X, Li Y, Bao M, Zhang J. PaNAC089 is a membrane-tethered transcription factor (MTTF) that modulates flowering, chlorophyll breakdown and trichome initiation. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:392-404. [PMID: 35209991 DOI: 10.1071/fp21320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Flowering and senescence are essential developmental stages of green plants, which are governed by complex molecular regulatory networks. However, the connection between flowering regulation and senescence regulation in London plane tree (Platanus acerifolia ) remains unknown. In this study, we identified a gene PaNAC089 from London plane tree, which encodes a membrane-tethered transcription factor (MTTF) belonging to the NAC (NAM, ATAF1/2, CUC2) transcription factor family. We investigated the functions of PaNAC089 in the regulation of flowering and senescence through the analysis of expression profiles and transgenic phenotypes. Heterologous overexpression of ΔPaNAC089 delayed flowering and inhibited chlorophyll breakdown to produce dark green rosette leaves in Arabidopsis . In addition, the trichome density of rosette leaves was decreased in transgenic lines. In ΔPaNAC089 overexpression plants, a series of functional genes with inhibited expression were identified by quantitative real-time polymerase chain reaction (qRT-PCR), including genes that regulate flowering, chlorophyll decomposition, and trichome initiation. Furthermore, Δ PaNAC089 directly binds to the promoter of CONSTANS (CO ) and NON-YELLOWING2 (NYE2 ) in the yeast one-hybrid assay. Consistent with this, luciferase (LUC) transient expression assays also showed that Δ PaNAC089 could inhibit the activity of NYE2 . To summarise, our data suggests that PaNAC089 is an MTTF that modulates flowering, chlorophyll breakdown and trichome initiation.
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Affiliation(s)
- Changsheng Shao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Fangfang Cai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China; and Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, Zhejiang, China
| | - Zhiru Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yanping Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Gehui Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zheng Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiyan Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yangyang Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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8
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Mohammed HA, Khan RA. Anthocyanins: Traditional Uses, Structural and Functional Variations, Approaches to Increase Yields and Products' Quality, Hepatoprotection, Liver Longevity, and Commercial Products. Int J Mol Sci 2022; 23:2149. [PMID: 35216263 PMCID: PMC8875224 DOI: 10.3390/ijms23042149] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
Anthocyanins are water-soluble, colored compounds of the flavonoid class, abundantly found in the fruits, leaves, roots, and other parts of the plants. The fruit berries are prime sources and exhibit different colors. The anthocyanins utility as traditional medicament for liver protection and cure, and importance as strongest plants-based anti-oxidants have conferred these plants products different biological activities. These activities include anti-inflammation, liver protective, analgesic, and anti-cancers, which have provided the anthocyanins an immense commercial value, and has impelled their chemistry, biological activity, isolation, and quality investigations as prime focus. Methods in extraction and production of anthocyanin-based products have assumed vital economic importance. Different extraction techniques in aquatic solvents mixtures, eutectic solvents, and other chemically reactive extractions including low acid concentrations-based extractions have been developed. The prophylactic and curative therapy roles of the anthocyanins, together with no reported toxicity has offered much-needed impetus and economic benefits to these classes of compounds which are commercially available. Information retrieval from various search engines, including the PubMed®, ScienceDirect®, Scopus®, and Google Scholar®, were used in the review preparation. This imparted an outlook on the anthocyanins occurrence, roles in plants, isolation-extraction, structures, biosynthetic as well as semi- and total-synthetic pathways, product quality and yields enhancements, including uses as part of traditional medicines, and uses in liver disorders, prophylactic and therapeutic applications in liver protection and longevity, liver cancer and hepatocellular carcinoma. The review also highlights the integrated approach to yields maximizations to meet the regular demands of the anthocyanins products, also as part of the extract-rich preparations together with a listing of marketed products available for human consumption as nutraceuticals/food supplements.
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Affiliation(s)
- Hamdoon A. Mohammed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo 11371, Egypt
| | - Riaz A. Khan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia
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Sepulveda-Garcia E, Fulton EC, Parlan EV, O’Connor LE, Fleming AA, Replogle AJ, Rocha-Sosa M, Gendron JM, Thines B. Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2021; 10:2228. [PMID: 34686037 PMCID: PMC8537223 DOI: 10.3390/plants10102228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022]
Abstract
SCF-type E3 ubiquitin ligases provide specificity to numerous selective protein degradation events in plants, including those that enable survival under environmental stress. SCF complexes use F-box (FBX) proteins as interchangeable substrate adaptors to recruit protein targets for ubiquitylation. FBX proteins almost universally have structure with two domains: A conserved N-terminal F-box domain interacts with a SKP protein and connects the FBX protein to the core SCF complex, while a C-terminal domain interacts with the protein target and facilitates recruitment. The F-BOX STRESS INDUCED (FBS) subfamily of plant FBX proteins has an atypical structure, however, with a centrally located F-box domain and additional conserved regions at both the N- and C-termini. FBS proteins have been linked to environmental stress networks, but no ubiquitylation target(s) or biological function has been established for this subfamily. We have identified two WD40 repeat-like proteins in Arabidopsis that are highly conserved in plants and interact with FBS proteins, which we have named FBS INTERACTING PROTEINs (FBIPs). FBIPs interact exclusively with the N-terminus of FBS proteins, and this interaction occurs in the nucleus. FBS1 destabilizes FBIP1, consistent with FBIPs being ubiquitylation targets SCFFBS1 complexes. This work indicates that FBS proteins may function in stress-responsive nuclear events, and it identifies two WD40 repeat-like proteins as new tools with which to probe how an atypical SCF complex, SCFFBS, functions via FBX protein N-terminal interaction events.
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Affiliation(s)
- Edgar Sepulveda-Garcia
- Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Mexico;
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico;
| | - Elena C. Fulton
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Emily V. Parlan
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Lily E. O’Connor
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Anneke A. Fleming
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Amy J. Replogle
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Mario Rocha-Sosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico;
| | - Joshua M. Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA;
| | - Bryan Thines
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
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10
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Shao C, Cai F, Zhang J, Zhang Y, Bao Z, Bao M. A Class II TCP Transcription Factor PaTCP4 from Platanus acerifolia Regulates Trichome Formation in Arabidopsis. DNA Cell Biol 2021; 40:1235-1250. [PMID: 34558965 DOI: 10.1089/dna.2021.0300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
London plane tree is widely grown as a landscaping and street tree, but the release of its trichomes creates a serious air-borne pollution problem. Identifying the key genes that regulate the development of trichomes is, therefore, an important tool for the molecular breeding of Platanus acerifolia. In this study, a sequence homologous with the Arabidopsis Class II TCP subfamily was identified from London plane, and named PaTCP4. The expression of PaTCP4 was detected in various organs of London plane trees, significantly in the trichomes. Overexpression of PaTCP4 in Arabidopsis reduced the trichome density on the first pair of true leaves, and atypical 5-branched trichomes were also detected on those leaves. The expression of endogenous AtCPC and AtTCL2 was significantly increased in PaTCP4 transgenic lines, and was associated with a decrease in the expression of endogenous AtGL2. Furthermore, the expression of endogenous AtGL3 was significantly increased. In addition, the protein product of PaTCP4 was shown to directly activate AtCPC, AtTCL2, AtGL3, AtGIS, PaGIS, and PaGL3 in yeast one-hybrid assays and in the dual-luciferase reporter system. Taken together, these results identify a role for PaTCP4 in trichome initiation and branching in Arabidopsis. Thus, PaTCP4 represents a strong candidate gene for regulating the development of trichomes in London plane trees.
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Affiliation(s)
- Changsheng Shao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fangfang Cai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China.,Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanping Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhiru Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
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11
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Wang Y, Tian H, Wang W, Wang X, Zheng K, Hussain S, Lin R, Wang T, Wang S. The Carboxyl-Terminus of TRANSPARENT TESTA GLABRA1 Is Critical for Its Functions in Arabidopsis. Int J Mol Sci 2021; 22:ijms221810039. [PMID: 34576199 PMCID: PMC8467004 DOI: 10.3390/ijms221810039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
The Arabidopsis WD40 repeat protein TRANSPARENT TESTA GLABRA1 (TTG1) regulates cell fate determination, including trichome initiation and root hair formation, as well as secondary metabolism such as flavonoid biosynthesis and seed coat mucilage production. TTG1 regulates different processes via regulating the expression of its downstream target genes by forming MYB-bHLH-WD40 (MBW) activator complexes with different R2R3 MYB and bHLH transcription factors. Here, we report the identification of the carboxyl (C)-terminus as a critical domain for TTG1′s functions in Arabidopsis. We found that the ttg1Δ15aa mutant shows pleiotropic phenotypes identical to a TTG1 loss-of-function mutant. Gene sequencing indicates that a single nucleotide substitution in TTG1 led to a premature stop at the W327 residue, leading to the production of a truncated TTG1 protein with a deletion of the last 15 C-terminal amino acids. The expression of TTG1 under the control of its native promoter fully restored the ttg1Δ15aa mutant phenotypes. Consistent with these observations, the expression levels of TTG1 downstream genes such as GLABRA2 (GL2) and CAPRICE (CPC) were reduced in the ttg1Δ15aa mutant. Assays in Arabidopsis protoplast show that TTG1Δ15aa failed to interact with the bHLH transcription factor GL3, and the deletion of the last 3 C-terminal amino acids or the 339L amino acid alone fully abolished the interaction of TTG1 with GL3. Furthermore, the expression of TTG1Δ3aa under the control of TTG1 native promoter failed to restore the ttg1Δ15aa mutant phenotypes. Taken together, our results suggest that the C-terminal domain of TTG1 is required for its proper function in Arabidopsis.
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Affiliation(s)
- Yating Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China; (Y.W.); (W.W.); (X.W.)
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (H.T.); (K.Z.); (S.H.); (R.L.); (T.W.)
| | - Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (H.T.); (K.Z.); (S.H.); (R.L.); (T.W.)
| | - Wei Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China; (Y.W.); (W.W.); (X.W.)
| | - Xutong Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China; (Y.W.); (W.W.); (X.W.)
| | - Kaijie Zheng
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (H.T.); (K.Z.); (S.H.); (R.L.); (T.W.)
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Saddam Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (H.T.); (K.Z.); (S.H.); (R.L.); (T.W.)
| | - Rao Lin
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (H.T.); (K.Z.); (S.H.); (R.L.); (T.W.)
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China; (H.T.); (K.Z.); (S.H.); (R.L.); (T.W.)
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China; (Y.W.); (W.W.); (X.W.)
- Correspondence:
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12
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Dorrity MW, Alexandre CM, Hamm MO, Vigil AL, Fields S, Queitsch C, Cuperus JT. The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Nat Commun 2021; 12:3334. [PMID: 34099698 PMCID: PMC8184767 DOI: 10.1038/s41467-021-23675-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023] Open
Abstract
The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to Arabidopsis thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. We find that the entirety of a cell's regulatory landscape and its transcriptome independently capture cell type identity. We leverage this shared information on cell identity to integrate accessibility and transcriptome data to characterize developmental progression, endoreduplication and cell division. We further use the combined data to characterize cell type-specific motif enrichments of transcription factor families and link the expression of family members to changing accessibility at specific loci, resolving direct and indirect effects that shape expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
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Affiliation(s)
- Michael W. Dorrity
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Cristina M. Alexandre
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Morgan O. Hamm
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Anna-Lena Vigil
- grid.272362.00000 0001 0806 6926School of Life Sciences, University of Nevada, Las Vegas, NV USA
| | - Stanley Fields
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA ,grid.34477.330000000122986657Department of Medicine, University of Washington, Seattle, WA USA
| | - Christine Queitsch
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Josh T. Cuperus
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
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13
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Balkunde R, Deneer A, Bechtel H, Zhang B, Herberth S, Pesch M, Jaegle B, Fleck C, Hülskamp M. Identification of the Trichome Patterning Core Network Using Data from Weak ttg1 Alleles to Constrain the Model Space. Cell Rep 2020; 33:108497. [PMID: 33326794 DOI: 10.1016/j.celrep.2020.108497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 09/02/2020] [Accepted: 11/18/2020] [Indexed: 11/28/2022] Open
Abstract
The regular distribution of trichomes on leaves in Arabidopsis is a well-understood model system for two-dimensional pattern formation. It involves more than 10 genes and is governed by two patterning principles, the activator-inhibitor (AI) and the activator-depletion (AD) mechanisms, though their relative contributions are unknown. The complexity of gene interactions, protein interactions, and intra- and intercellular mobility of proteins makes it very challenging to understand which aspects are relevant for pattern formation. In this study, we use global mathematical methods combined with a constraining of data to identify the structure of the underlying network. To constrain the model, we perform a genetic, cell biological, and biochemical study of weak ttg1 alleles. We find that the core of trichome patterning is a combination of AI and AD mechanisms differentiating between two pathways activating the long-range inhibitor CPC and the short-range inhibitor TRY.
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Affiliation(s)
- Rachappa Balkunde
- Botanical Institute, Biocenter, Cologne University, 50674 Cologne, Germany
| | - Anna Deneer
- Lab for Systems and Synthetic Biology and Biometrics, Department of Mathematical and Statistical Methods, Wageningen University, 6700 HB, Wageningen, The Netherlands
| | - Hanna Bechtel
- Botanical Institute, Biocenter, Cologne University, 50674 Cologne, Germany
| | - Bipei Zhang
- Botanical Institute, Biocenter, Cologne University, 50674 Cologne, Germany
| | - Stefanie Herberth
- Botanical Institute, Biocenter, Cologne University, 50674 Cologne, Germany
| | - Martina Pesch
- Botanical Institute, Biocenter, Cologne University, 50674 Cologne, Germany
| | - Benjamin Jaegle
- Botanical Institute, Biocenter, Cologne University, 50674 Cologne, Germany
| | - Christian Fleck
- Lab for Systems and Synthetic Biology and Biometrics, Department of Mathematical and Statistical Methods, Wageningen University, 6700 HB, Wageningen, The Netherlands.
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, 50674 Cologne, Germany.
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14
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Mattioli R, Francioso A, Mosca L, Silva P. Anthocyanins: A Comprehensive Review of Their Chemical Properties and Health Effects on Cardiovascular and Neurodegenerative Diseases. Molecules 2020; 25:E3809. [PMID: 32825684 PMCID: PMC7504512 DOI: 10.3390/molecules25173809] [Citation(s) in RCA: 257] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetables. Dietary sources of anthocyanins include red and purple berries, grapes, apples, plums, cabbage, or foods containing high levels of natural colorants. Cyanidin, delphinidin, malvidin, peonidin, petunidin, and pelargonidin are the six common anthocyanidins. Following consumption, anthocyanin, absorption occurs along the gastrointestinal tract, the distal lower bowel being the place where most of the absorption and metabolism occurs. In the intestine, anthocyanins first undergo extensive microbial catabolism followed by absorption and human phase II metabolism. This produces hybrid microbial-human metabolites which are absorbed and subsequently increase the bioavailability of anthocyanins. Health benefits of anthocyanins have been widely described, especially in the prevention of diseases associated with oxidative stress, such as cardiovascular and neurodegenerative diseases. Furthermore, recent evidence suggests that health-promoting effects attributed to anthocyanins may also be related to modulation of gut microbiota. In this paper we attempt to provide a comprehensive view of the state-of-the-art literature on anthocyanins, summarizing recent findings on their chemistry, biosynthesis, nutritional value and on their effects on human health.
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Affiliation(s)
- Roberto Mattioli
- Department of Sciences, RomaTre University, v.le G. Marconi 446, 00146 Rome, Italy;
| | - Antonio Francioso
- Department of Biochemical Sciences, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy;
| | - Luciana Mosca
- Department of Biochemical Sciences, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy;
| | - Paula Silva
- Laboratory of Histology and Embryology, Institute of Biomedical Sciences Abel Salazar (ICBAS), Rua de Jorge Viterbo Ferreira n°228, 4050-313 Porto, Portugal
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15
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Iorizzo M, Curaba J, Pottorff M, Ferruzzi MG, Simon P, Cavagnaro PF. Carrot Anthocyanins Genetics and Genomics: Status and Perspectives to Improve Its Application for the Food Colorant Industry. Genes (Basel) 2020; 11:E906. [PMID: 32784714 PMCID: PMC7465225 DOI: 10.3390/genes11080906] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/11/2022] Open
Abstract
Purple or black carrots (Daucus carota ssp. sativus var. atrorubens Alef) are characterized by their dark purple- to black-colored roots, owing their appearance to high anthocyanin concentrations. In recent years, there has been increasing interest in the use of black carrot anthocyanins as natural food dyes. Black carrot roots contain large quantities of mono-acylated anthocyanins, which impart a measure of heat-, light- and pH-stability, enhancing the color-stability of food products over their shelf-life. The genetic pathway controlling anthocyanin biosynthesis appears well conserved among land plants; however, different variants of anthocyanin-related genes between cultivars results in tissue-specific accumulations of purple pigments. Thus, broad genetic variations of anthocyanin profile, and tissue-specific distributions in carrot tissues and organs, can be observed, and the ratio of acylated to non-acylated anthocyanins varies significantly in the purple carrot germplasm. Additionally, anthocyanins synthesis can also be influenced by a wide range of external factors, such as abiotic stressors and/or chemical elicitors, directly affecting the anthocyanin yield and stability potential in food and beverage applications. In this study, we critically review and discuss the current knowledge on anthocyanin diversity, genetics and the molecular mechanisms controlling anthocyanin accumulation in carrots. We also provide a view of the current knowledge gaps and advancement needs as regards developing and applying innovative molecular tools to improve the yield, product performance and stability of carrot anthocyanin for use as a natural food colorant.
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Affiliation(s)
- Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (J.C.); (M.P.); (M.G.F.)
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Julien Curaba
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (J.C.); (M.P.); (M.G.F.)
| | - Marti Pottorff
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (J.C.); (M.P.); (M.G.F.)
| | - Mario G. Ferruzzi
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (J.C.); (M.P.); (M.G.F.)
| | - Philipp Simon
- Department of Horticulture, University of Wisconsin–Madison, Madison, WI 53706, USA;
- Vegetable Crops Research Unit, US Department of Agriculture–Agricultural Research Service, Madison, WI 53706, USA
| | - Pablo F. Cavagnaro
- National Scientific and Technical Research Council (CONICET), National Agricultural Technology Institute (INTA) E.E.A. La Consulta, Mendoza 5567, Argentina;
- Faculty of Agricultural Sciences, National University of Cuyo, Mendoza 5505, Argentina
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16
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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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