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Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. Proc Natl Acad Sci U S A 2022; 119:2107879119. [PMID: 35046022 PMCID: PMC8794810 DOI: 10.1073/pnas.2107879119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.
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Jiang L, Wang Y, Xia A, Wang Q, Zhang X, Jez JM, Li Z, Tan W, He Y. A natural single-nucleotide polymorphism variant in sulfite reductase influences sulfur assimilation in maize. THE NEW PHYTOLOGIST 2021; 232:692-704. [PMID: 34254312 DOI: 10.1111/nph.17616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Plants absorb sulfur from the environment and assimilate it into suitable forms for the biosynthesis of a broad range of molecules. Although the biochemical pathway of sulfur assimilation is known, how genetic differences contribute to natural variation in sulfur assimilation remains poorly understood. Here, using a genome-wide association study, we uncovered a single-nucleotide polymorphism (SNP) variant in the sulfite reductase (SiR) gene that was significantly associated with SiR protein abundance in a maize natural association population. We also demonstrated that the synonymous C to G base change at SNP69 may repress translational activity by altering messenger RNA secondary structure, which leads to reduction in ZmSiR protein abundance and sulfur assimilation activity. Population genetic analyses showed that the SNP69C allele was likely a variant occurring after the initial maize domestication and accumulated with the spread of maize cultivation from tropical to temperate regions. This study provides the first evidence that genetic polymorphisms in the exon of ZmSiR could influence the protein abundance through a posttranscriptional mechanism and in part contribute to natural variation in sulfur assimilation. These findings provide a prospective target to improve maize varieties with proper sulfur nutrient levels assisted by molecular breeding and engineering.
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Affiliation(s)
- Luguang Jiang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Yan Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Aiai Xia
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Qi Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Xiaolei Zhang
- Safety and Quality Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Weiming Tan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Yan He
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
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Xiang T, Li J, Bao S, Xu Z, Wang L, Long F, He C. Digital RNA-seq transcriptome plus tissue anatomy analyses reveal the developmental mechanism of the calabash-shaped root in Tetrastigma hemsleyanum. TREE PHYSIOLOGY 2021; 41:1729-1748. [PMID: 33601408 DOI: 10.1093/treephys/tpab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Tetrastigma hemsleyanum Diels & Gilg ex Diels is a liana plant with promising medicinal and ornamental values. Its calabash-shaped roots (CRs) are served as a traditional Chinese herb. However, it takes a long growth period to form CRs. In this study, three types of architectural roots, including fibrous roots (FRs), bar-shaped roots (BRs) and CRs, were employed as materials, and the characteristics of histo-anatomy and digital RNA-seq transcriptome profiles were analyzed. Among the three types of roots, the vascular bundles in FRs were intact, while some of the vascular bundles degenerated in BRs, and only few traces of vascular bundles existed in CRs. Meanwhile, no obvious cell inclusions were found in the cytoplasm of FRs, while a few inclusions were found in BRs, and abundant inclusions were detected in CRs, which might be the main source of medicinal components in roots. The transcriptome profiles and qRT-PCR validation indicated that seven upregulated genes, encoding xyloglucan glycosyltransferase, ACC oxidase, CYP711A1, SHORT-ROOT transcript factor, galacturonosyltransferas, WAT1 and WRKY, and two downregulated genes, encoding LRR receptor-like serine/threonine-protein kinase and CYP83B1, were probably involved in the formation and development of CRs. In addition, Gene Ontology terms of intrinsic component of membrane, integral component of membrane, cell periphery, membrane part, plasma membrane, membrane, intrinsic component of plasma membrane, cellular chemical homeostasis and plasma membrane part were probably related to the formation of CRs. Kyoto Encyclopedia of Genes and Genomes pathways related to the development of CRs probably included MAPK signaling pathway-plant, plant hormone signal transduction and circadian rhythm-plant. Our finding suggested a probable mode for the formation of CRs.
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Affiliation(s)
- Taihe Xiang
- College of Life and Environmental Sciences, Hangzhou Normal University, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
| | - Jiangshan Li
- College of Life and Environmental Sciences, Hangzhou Normal University, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
| | - Shuying Bao
- College of Life and Environmental Sciences, Hangzhou Normal University, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
| | - Zhengxian Xu
- College of Life and Environmental Sciences, Hangzhou Normal University, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
| | - Leizhen Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
| | - Fazong Long
- College of Life and Environmental Sciences, Hangzhou Normal University, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
| | - Chenjing He
- College of Life and Environmental Sciences, Hangzhou Normal University, NO. 2318, Yuhangtang Road, Yuhang District, Hangzhou 311121, China
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The Recovery from Sulfur Starvation Is Independent from the mRNA Degradation Initiation Enzyme PARN in Arabidopsis. PLANTS 2019; 8:plants8100380. [PMID: 31569782 PMCID: PMC6843384 DOI: 10.3390/plants8100380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 11/23/2022]
Abstract
When plants are exposed to sulfur limitation, they upregulate the sulfate assimilation pathway at the expense of growth-promoting measures. Upon cessation of the stress, however, protective measures are deactivated, and growth is restored. In accordance with these findings, transcripts of sulfur-deficiency marker genes are rapidly degraded when starved plants are resupplied with sulfur. Yet it remains unclear which enzymes are responsible for the degradation of transcripts during the recovery from starvation. In eukaryotes, mRNA decay is often initiated by the cleavage of poly(A) tails via deadenylases. As mutations in the poly(A) ribonuclease PARN have been linked to altered abiotic stress responses in Arabidopsis thaliana, we investigated the role of PARN in the recovery from sulfur starvation. Despite the presence of putative PARN-recruiting AU-rich elements in sulfur-responsive transcripts, sulfur-depleted PARN hypomorphic mutants were able to reset their transcriptome to pre-starvation conditions just as readily as wildtype plants. Currently, the subcellular localization of PARN is disputed, with studies reporting both nuclear and cytosolic localization. We detected PARN in cytoplasmic speckles and reconciled the diverging views in literature by identifying two PARN splice variants whose predicted localization is in agreement with those observations.
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Sugiyama R, Hirai MY. Atypical Myrosinase as a Mediator of Glucosinolate Functions in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1008. [PMID: 31447873 PMCID: PMC6691170 DOI: 10.3389/fpls.2019.01008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/18/2019] [Indexed: 05/04/2023]
Abstract
Glucosinolates (GLSs) are a well-known class of specialized plant metabolites, distributed mostly in the order Brassicales. A vast research field in basic and applied sciences has grown up around GLSs owing to their presence in important agricultural crops and the model plant Arabidopsis thaliana, and their broad range of bioactivities beneficial to human health. The major purpose of GLSs in plants has been considered their function as a chemical defense against predators. GLSs are physically separated from a specialized class of beta-thioglucosidases called myrosinases, at the tissue level or at the single-cell level. They are brought together as a consequence of tissue damage, primarily triggered by herbivores, and their interaction results in the release of toxic volatile chemicals including isothiocyanates. In addition, recent studies have suggested that plants may adopt other strategies independent of tissue disruption for initiating GLS breakdown to cope with certain biotic/abiotic stresses. This hypothesis has been further supported by the discovery of an atypical class of GLS-hydrolyzing enzymes possessing features that are distinct from those of the classical myrosinases. Nevertheless, there is only little information on the physiological importance of atypical myrosinases. In this review, we focus on the broad diversity of the beta-glucosidase subclasses containing known atypical myrosinases in A. thaliana to discuss the hypothesis that numerous members of these subclasses can hydrolyze GLSs to regulate their diverse functions in plants. Also, the increasingly broadening functional repertoires of known atypical/classical myrosinases are described with reference to recent findings. Assessment of independent insights gained from A. thaliana with respect to (1) the phenotype of mutants lacking genes in the GLS metabolic/breakdown pathways, (2) fluctuation in GLS contents/metabolism under specific conditions, and (3) the response of plants to exogenous GLSs or their hydrolytic products, will enable us to reconsider the physiological importance of GLS breakdown in particular situations, which is likely to be regulated by specific beta-glucosidases.
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