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Wang S, Wu H, Zhang Y, Sun G, Qian W, Qu F, Zhang X, Hu J. Transcriptome Reveals the Regulation of Exogenous Auxin Inducing Rooting of Non-Rooting Callus of Tea Cuttings. Int J Mol Sci 2024; 25:8080. [PMID: 39125650 PMCID: PMC11311428 DOI: 10.3390/ijms25158080] [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: 05/28/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Cuttage is the main propagation method of tea plant cultivars in China. However, some tea softwood cuttings just form an expanded and loose callus at the base, without adventitious root (AR) formation during the propagation period. Meanwhile, exogenous auxin could promote the AR formation of tea plant cuttings, but the regulation mechanism has not yet explained clearly. We conducted this study to elucidate the regulatory mechanism of exogenous auxin-induced adventitious root (AR) formation of such cuttings. The transcriptional expression profile of non-rooting tea calluses in response to exogenous IBA and NAA was analyzed using ONT RNA Seq technology. In total, 56,178 differentially expressed genes (DEGs) were detected, and most of genes were significantly differentially expressed after 12 h of exogenous auxin treatment. Among these DEGs, we further identified 80 DEGs involved in the auxin induction pathway and AR formation. Specifically, 14 auxin respective genes (ARFs, GH3s, and AUX/IAAs), 3 auxin transporters (AUX22), 19 auxin synthesis- and homeostasis-related genes (cytochrome P450 (CYP450) and calmodulin-like protein (CML) genes), and 44 transcription factors (LOB domain-containing protein (LBDs), SCARECROW-LIKE (SCL), zinc finger protein, WRKY, MYB, and NAC) were identified from these DEGs. Moreover, we found most of these DEGs were highly up-regulated at some stage before AR formation, suggesting that they may play a potential role in the AR formation of tea plant cuttings. In summary, this study will provide a theoretical foundation to deepen our understanding of the molecular mechanism of AR formation in tea cuttings induced by auxin during propagation time.
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Affiliation(s)
| | | | | | | | | | | | | | - Jianhui Hu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (S.W.); (H.W.); (Y.Z.); (G.S.); (W.Q.); (F.Q.); (X.Z.)
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2
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Noureddine J, Mu B, Hamidzada H, Mok WL, Bonea D, Nambara E, Zhao R. Knockout of endoplasmic reticulum-localized molecular chaperone HSP90.7 impairs seedling development and cellular auxin homeostasis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:218-236. [PMID: 38565312 DOI: 10.1111/tpj.16754] [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: 02/24/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
The Arabidopsis endoplasmic reticulum-localized heat shock protein HSP90.7 modulates tissue differentiation and stress responses; however, complete knockout lines have not been previously reported. In this study, we identified and analyzed a mutant allele, hsp90.7-1, which was unable to accumulate the HSP90.7 full-length protein and showed seedling lethality. Microscopic analyses revealed its essential role in male and female fertility, trichomes and root hair development, proper chloroplast function, and apical meristem maintenance and differentiation. Comparative transcriptome and proteome analyses also revealed the role of the protein in a multitude of cellular processes. Particularly, the auxin-responsive pathway was specifically downregulated in the hsp90.7-1 mutant seedlings. We measured a much-reduced auxin content in both root and shoot tissues. Through comprehensive histological and molecular analyses, we confirmed PIN1 and PIN5 accumulations were dependent on the HSP90 function, and the TAA-YUCCA primary auxin biosynthesis pathway was also downregulated in the mutant seedlings. This study therefore not only fulfilled a gap in understanding the essential role of HSP90 paralogs in eukaryotes but also provided a mechanistic insight on the ER-localized chaperone in regulating plant growth and development via modulating cellular auxin homeostasis.
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Affiliation(s)
- Jenan Noureddine
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Bona Mu
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Homaira Hamidzada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Wai Lam Mok
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Diana Bonea
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eiji Nambara
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Rongmin Zhao
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
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Huang C, Wang D, Yang Y, Yang H, Zhang B, Li H, Zhang H, Li Y, Yuan W. SUPPRESSOR OF FRIGIDA 4 cooperates with the histone methylation reader EBS to positively regulate root development. PLANT PHYSIOLOGY 2024:kiae321. [PMID: 38875008 DOI: 10.1093/plphys/kiae321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/20/2024] [Indexed: 06/15/2024]
Abstract
Maintenance and homeostasis of the quiescent center (QC) in Arabidopsis (Arabidopsis thaliana) root apical meristems are critical for stem cell organization and root development. Despite great progress in relevant research, the molecular mechanisms that determine the root stem cell fate and QC still need further exploration. In Arabidopsis, SUPPRESSOR OF FRIGIDA 4 (SUF4) encodes a C2H2-type zinc finger protein that represses flowering by transcriptional activation of FLOWERING LOCUS C (FLC) through the FRIGIDA (FRI) pathway, and EARLY BOLTING IN SHORT DAYS (EBS) is a bivalent histone reader that prevents premature flowering. Here, we found that SUF4 directly interacts with EBS in vivo and in vitro. Loss of function of SUF4 and/or EBS resulted in disorganization of the QC, aberrant cell division, and stunted root growth. RNA-seq and reverse transcription quantitative real-time polymerase chain reaction analysis revealed that SUF4 and EBS coregulate many root development-related genes. A series of biochemical analyses demonstrated that SUF4 directly binds to the promoter of SCARECROW (SCR), which encodes a key regulator of root development. Chromatin immunoprecipitation assay indicated that both SUF4 and EBS are recruited to the SCR locus in an interdependent manner to promote H3K4me3 levels and suppress H3K27me3 levels, thereby activating the expression of SCR. These findings improve our understanding of the function of SUF4 and EBS and provide insights into the molecular mechanism that couples a transcription factor and a histone methylation reader to modulate QC specification and root development in Arabidopsis.
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Affiliation(s)
- Can Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Diao Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yanqi Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Hong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Biaoming Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Haitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Haitao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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Huang Y, Zheng Q, Zhang MM, He X, Zhao X, Wang L, Lan S, Liu ZJ. Genome-Wide Identification and Expression Analysis of the GRAS Gene Family and Their Responses to Heat Stress in Cymbidium goeringii. Int J Mol Sci 2024; 25:6363. [PMID: 38928070 PMCID: PMC11204107 DOI: 10.3390/ijms25126363] [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: 05/16/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The GRAS gene family, responsible for encoding transcription factors, serves pivotal functions in plant development, growth, and responses to stress. The exploration of the GRAS gene family within the Orchidaceae has been comparatively limited, despite its identification and functional description in various plant species. This study aimed to conduct a thorough examination of the GRAS gene family in Cymbidum goeringii, focusing on its physicochemical attributes, phylogenetic associations, gene structure, cis-acting elements, and expression profiles under heat stress. The results show that a total of 54 CgGRASs were pinpointed from the genome repository and categorized into ten subfamilies via phylogenetic associations. Assessment of gene sequence and structure disclosed the prevalent existence of the VHIID domain in most CgGRASs, with around 57.41% (31/54) CgGRASs lacking introns. The Ka/Ks ratios of all CgGRASs were below one, indicating purifying selection across all CgGRASs. Examination of cis-acting elements unveiled the presence of numerous elements linked to light response, plant hormone signaling, and stress responsiveness. Furthermore, CgGRAS5 contained the highest quantity of cis-acting elements linked to stress response. Experimental results from RT-qPCR demonstrated notable variations in the expression levels of eight CgGRASs after heat stress conditions, particularly within the LAS, HAM, and SCL4/7 subfamilies. In conclusion, this study revealed the expression pattern of CgGRASs under heat stress, providing reference for further exploration into the roles of CgGRAS transcription factors in stress adaptation.
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Affiliation(s)
- Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Linying Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
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5
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Song X, Yu Y, Zhu J, Li C. BRIP1 and BRIP2 maintain root meristem by affecting auxin-mediated regulation. PLANTA 2023; 259:8. [PMID: 38019301 DOI: 10.1007/s00425-023-04283-0] [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: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
MAIN CONCLUSION This study reveals that mutations in BRIP1/2 subunits of the BAS complex disrupt root meristem development by decreasing PIN genes expression, affecting auxin transport, and downregulating essential root genes PLT. Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes play vital roles in plant development. BRAHMA-interacting proteins1 (BRIP1) and BRIP2 are subunits of BRAHMA (BRM)-associated SWI/SNF complex (BAS) in plants; however, their role and underlying regulatory mechanism in root development are still unknown. Here, we show that brip1 brip2 double mutants have a significantly shortened root meristem and an irregular arrangement in a portion of the root stem cell niche. The mutations in BRIP1 and BRIP2 cause decreased expression of the PIN-FORMED (PIN) genes, which in turn reduces the transport of auxin at the root tip, leading to the disruption of the accurate establishment of normal auxin concentration gradients in the stem cells. Chromatin immunoprecipitation (ChIP) experiments indicated that BRIP1 and BRIP2 directly bind to the PINs. Furthermore, we found a significant down-regulation in the expression of key root development genes, PLETHORA (PLT), in brip1 brip2. The brip1 brip2 plt1 plt2 quadruple mutations do not show further exacerbation in the short-root phenotype compared to plt1 plt2 double mutants. Using a dexamethasone (DEX)-inducible PLT2 transgenic line, we showed that acute overexpression of PLT2 partially rescues root meristem defects of brip1 brip2, suggesting that BRIP1 and BRIP2 act in part through the PLT1/2 pathway. Taken together, our results identify the critical role and the underlying mechanism of BRIP1/2 in maintaining the development of root meristem through the regulation of auxin output and expression of PLTs.
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Affiliation(s)
- Xin Song
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiameng Zhu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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6
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Perez-Garcia P, Pucciariello O, Sanchez-Corrionero A, Cabrera J, Del Barrio C, Del Pozo JC, Perales M, Wabnik K, Moreno-Risueno MA. The cold-induced factor CBF3 mediates root stem cell activity, regeneration, and developmental responses to cold. PLANT COMMUNICATIONS 2023; 4:100737. [PMID: 37865820 PMCID: PMC10721530 DOI: 10.1016/j.xplc.2023.100737] [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: 01/13/2023] [Revised: 09/01/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Plant growth and development involve the specification and regeneration of stem cell niches (SCNs). Although plants are exposed to disparate environmental conditions, how environmental cues affect developmental programs and stem cells is not well understood. Root stem cells are accommodated in meristems in SCNs around the quiescent center (QC), which maintains their activity. Using a combination of genetics and confocal microscopy to trace morphological defects and correlate them with changes in gene expression and protein levels, we show that the cold-induced transcription factor (TF) C-REPEAT BINDING FACTOR 3 (CBF3), which has previously been associated with cold acclimation, regulates root development, stem cell activity, and regeneration. CBF3 is integrated into the SHORT-ROOT (SHR) regulatory network, forming a feedback loop that maintains SHR expression. CBF3 is primarily expressed in the root endodermis, whereas the CBF3 protein is localized to other meristematic tissues, including root SCNs. Complementation of cbf3-1 using a wild-type CBF3 gene and a CBF3 fusion with reduced mobility show that CBF3 movement capacity is required for SCN patterning and regulates root growth. Notably, cold induces CBF3, affecting QC activity. Furthermore, exposure to moderate cold around 10°C-12°C promotes root regeneration and QC respecification in a CBF3-dependent manner during the recuperation period. By contrast, CBF3 does not appear to regulate stem cell survival, which has been associated with recuperation from more acute cold (∼4°C). We propose a role for CBF3 in mediating the molecular interrelationships among the cold response, stem cell activity, and development.
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Affiliation(s)
- Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain.
| | - Ornella Pucciariello
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Cristina Del Barrio
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Juan Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain.
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7
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Liu Q, Teng S, Deng C, Wu S, Li H, Wang Y, Wu J, Cui X, Zhang Z, Quick WP, Brutnell TP, Sun X, Lu T. SHORT ROOT and INDETERMINATE DOMAIN family members govern PIN-FORMED expression to regulate minor vein differentiation in rice. THE PLANT CELL 2023; 35:2848-2870. [PMID: 37154077 PMCID: PMC10396363 DOI: 10.1093/plcell/koad125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/08/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023]
Abstract
C3 and C4 grasses directly and indirectly provide the vast majority of calories to the human diet, yet our understanding of the molecular mechanisms driving photosynthetic productivity in grasses is largely unexplored. Ground meristem cells divide to form mesophyll or vascular initial cells early in leaf development in C3 and C4 grasses. Here we define a genetic circuit composed of SHORT ROOT (SHR), INDETERMINATE DOMAIN (IDD), and PIN-FORMED (PIN) family members that specifies vascular identify and ground cell proliferation in leaves of both C3 and C4 grasses. Ectopic expression and loss-of-function mutant studies of SHR paralogs in the C3 plant Oryza sativa (rice) and the C4 plant Setaria viridis (green millet) revealed the roles of these genes in both minor vein formation and ground cell differentiation. Genetic and in vitro studies further suggested that SHR regulates this process through its interactions with IDD12 and 13. We also revealed direct interactions of these IDD proteins with a putative regulatory element within the auxin transporter gene PIN5c. Collectively, these findings indicate that a SHR-IDD regulatory circuit mediates auxin transport by negatively regulating PIN expression to modulate minor vein patterning in the grasses.
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Affiliation(s)
- Qiming Liu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Shouzhen Teng
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Chen Deng
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Suting Wu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Haoshu Li
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Yanwei Wang
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Jinxia Wu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Xuean Cui
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Zhiguo Zhang
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - William Paul Quick
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
- C4 Rice Centre, International Rice Research Institute, Los Banos, Laguna 4030, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Thomas P Brutnell
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Xuehui Sun
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Tiegang Lu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
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8
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Li Y, Luo J, Chen R, Zhou Y, Yu H, Chu Z, Lu Y, Gu X, Wu S, Wang P, Kuang H, Ouyang B. Folate shapes plant root architecture by affecting auxin distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:969-985. [PMID: 36587293 DOI: 10.1111/tpj.16093] [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: 07/21/2020] [Revised: 11/26/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.
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Affiliation(s)
- Ying Li
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Jinying Luo
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Rong Chen
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhuannan Chu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuang Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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9
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Wang M, Zhang H, Zhao X, Zhou J, Qin G, Liu Y, Kou X, Zhao Z, Wu T, Zhu JK, Feng X, Li L. SYNTAXIN OF PLANTS81 regulates root meristem activity and stem cell niche maintenance via ROS signaling. PLANT PHYSIOLOGY 2023; 191:1365-1382. [PMID: 36427205 PMCID: PMC9922426 DOI: 10.1093/plphys/kiac530] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Root growth and development depend on continuous cell division and differentiation in root tips. In these processes, reactive oxygen species (ROS) play a critical role as signaling molecules. However, few ROS signaling regulators have been identified. In this study, we found knockdown of a syntaxin gene, SYNTAXIN OF PLANTS81 in Arabidopsis thaliana (AtSYP81) resulted in a severe reduction in root meristem activity and disruption of root stem cell niche (SCN) identity. Subsequently, we found AtSYP81 was highly expressed in roots and localized on the endoplasmic reticulum (ER). Interestingly, the reduced expression of AtSYP81 conferred a decreased number of peroxisomes in root meristem cells, raising a possibility that AtSYP81 regulates root development through peroxisome-mediated ROS production. Further transcriptome analysis revealed that class III peroxidases, which are responsible for intracellular ROS homeostasis, showed significantly changed expression in the atsyp81 mutants and AtSYP81 overexpression lines, adding evidence of the regulatory role of AtSYP81 in ROS signaling. Accordingly, rescuing the decreased ROS level via applying ROS donors effectively restored the defects in root meristem activity and SCN identity in the atsyp81 mutants. APETALA2 (AP2) transcription factors PLETHORA1 and 2 (PLT1 and PLT2) were then established as the downstream effectors in this pathway, while potential crosstalk between ROS signaling and auxin signaling was also indicated. Taken together, our findings suggest that AtSYP81 regulates root meristem activity and maintains root SCN identity by controlling peroxisome- and peroxidase-mediated ROS homeostasis, thus both broadening and deepening our understanding of the biological roles of SNARE proteins and ROS signaling.
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Affiliation(s)
- Mingjing Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Hailong Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Xiaonan Zhao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Jingwen Zhou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Guochen Qin
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yuqi Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Xiaoyue Kou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Zhenjie Zhao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Tao Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lixin Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
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10
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Yoon EK, Oh J, Lim J. (Don't) Look Up!: Is short-root just a short-root plant? FRONTIERS IN PLANT SCIENCE 2022; 13:1069996. [PMID: 36466291 PMCID: PMC9712719 DOI: 10.3389/fpls.2022.1069996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
SHORT-ROOT (SHR) is a mobile transcription factor that plays important roles in ground tissue patterning, stem cell niche specification and maintenance, and vascular development in Arabidopsis roots. Although mRNA and protein of SHR are also found in hypocotyls, inflorescence stems, and leaves, its role in the above-ground organs has been less explored. In most developmental cases, SHR, together with its partner SCARECROW (SCR), regulates the expression of downstream target genes in controlling formative and proliferative cell divisions. Accumulating evidence on the regulatory role of SHR in shoots suggests that SHR may also play key roles in the above-ground organs. Interestingly, recent work has provided new evidence that SHR is also required for cell elongation in the hypocotyl of the etiolated seedling. This suggests that the novel roles of SHR and SHR-mediated regulatory networks can be found in shoots. Furthermore, comparative research on SHR function in roots and shoots will broaden and deepen our understanding of plant growth and development.
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11
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Ou X, Wang Y, Li J, Zhang J, Xie Z, He B, Jiang Z, Wang Y, Su W, Song S, Hao Y, Chen R. Genome-wide identification of the KNOTTED HOMEOBOX gene family and their involvement in stalk development in flowering Chinese cabbage. FRONTIERS IN PLANT SCIENCE 2022; 13:1019884. [PMID: 36438132 PMCID: PMC9686407 DOI: 10.3389/fpls.2022.1019884] [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: 09/20/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Gibberellin and cytokinin synergistically regulate the stalk development in flowering Chinese cabbage. KNOX proteins were reported to function as important regulators of the shoot apex to promote meristem activity by synchronously inducing CTK and suppressing GA biosynthesis, while their regulatory mechanism in the bolting and flowering is unknown. In this study, 9 BcKNOX genes were identified and mapped unevenly on 6 out of 10 flowering Chinese cabbage chromosomes. The BcKNOXs were divided into three subfamilies on the basis of sequences and gene structure. The proteins contain four conserved domains except for BcKNATM. Three BcKNOX TFs (BcKNOX1, BcKNOX3, and BcKNOX5) displayed high transcription levels on tested tissues at various stages. The major part of BcKNOX genes showed preferential expression patterns in response to low-temperature, zeatin (ZT), and GA3 treatment, indicating that they were involved in bud differentiation and bolting. BcKNOX1 and BcKNOX5 showed high correlation level with gibberellins synthetase, and CTK metabolic genes. BcKONX1 also showed high correlation coefficients within BcRGA1 and BcRGL1 which are negative regulators of GA signaling. In addition, BcKNOX1 interacted with BcRGA1 and BcRGL1, as confirmed by yeast two-hybrid (Y2H) and biomolecular fluorescence complementation assay (BiFC). This analysis has provided useful foundation for the future functional roles' analysis of flowering Chinese cabbage KNOX genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yanwei Hao
- *Correspondence: Yanwei Hao, ; Riyuan Chen,
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12
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Xie C, Ding Z. NAC1 Maintains Root Meristem Activity by Repressing the Transcription of E2Fa in Arabidopsis. Int J Mol Sci 2022; 23:ijms232012258. [PMID: 36293114 PMCID: PMC9603599 DOI: 10.3390/ijms232012258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Root meristem is a reserve of undifferentiated cells which guide root development. To maintain root meristem identity and therefore continuous root growth, the rate of cell differentiation must coordinate with the rate of generation of new cells. The E2 promoter-binding factor a (E2Fa) has been shown to regulate root growth through controlling G1/S cell cycle transitions in Arabidopsis thaliana. Here, we found that NAC1, a member of the NAM/ATAF/CUC family of transcription factors, regulated root growth by directly repressing the transcription of E2Fa. Loss of NAC1 triggers an up-regulation of the E2Fa expression and causes a reduced meristem size and short-root phenotype, which are largely rescued by mutation of E2Fa. Further analysis showed that NAC1 was shown to regulate root meristem by controlling endopolyploidy levels in an E2Fa-dependent manner. This study provides evidence to show that NAC1 maintains root meristem size and root growth by directly repressing the transcription of E2Fa in Arabidopsis.
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13
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A Comparative Transcriptome Analysis Reveals the Molecular Mechanisms That Underlie Somatic Embryogenesis in Peaonia ostii ‘Fengdan’. Int J Mol Sci 2022; 23:ijms231810595. [PMID: 36142512 PMCID: PMC9505998 DOI: 10.3390/ijms231810595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Low propagation rate is the primary problem that limits industry development of tree peony. In this study, a highly efficient regeneration system for tree peony using somatic embryogenesis (SE) was established. The transcriptomes of zygotic embryo explants (S0), non-embryonic callus (S1), embryonic callus (S2), somatic embryos (S3), and regenerated shoots (S4) were analyzed to determine the regulatory mechanisms that underlie SE in tree peony. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of S1-vs-S2 and S1-vs-S3, respectively. The enriched DEGs were primarily involved in hormone signal transduction, stress response and the nucleus (epigenetic modifications). The results indicated that cell division, particularly asymmetric cell division, was enhanced in S3. Moreover, the genes implicated in cell fate determination played central roles in S3. Hormone signal pathways work in concert with epigenetic modifications and stress responses to regulate SE. SERK, WOX9, BBM, FUS3, CUC, and WUS were characterized as the molecular markers for tree peony SE. To our knowledge, this is the first study of the SE of tree peony using transcriptome sequencing. These results will improve our understanding of the molecular mechanisms that underly SE in tree peony and will benefit the propagation and genetic engineering of this plant.
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14
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Ou Y, Tao B, Wu Y, Cai Z, Li H, Li M, He K, Gou X, Li J. Essential roles of SERKs in the ROOT MERISTEM GROWTH FACTOR-mediated signaling pathway. PLANT PHYSIOLOGY 2022; 189:165-177. [PMID: 35134233 PMCID: PMC9070818 DOI: 10.1093/plphys/kiac036] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/05/2022] [Indexed: 05/08/2023]
Abstract
ROOT MERISTEM GROWTH FACTORs (RGFs), a group of peptide hormones, play key roles in root apical meristem development. In Arabidopsis (Arabidopsis thaliana), there are 11 members of RGFs, in which at least RGF1, RGF2, and RGF3 are expressed at the root tip and are involved in root stem cell niche maintenance. RGFs are perceived by five functionally redundant receptor-like protein kinases, RGF1 INSENSITIVE 1 (RGI1) to RGI5, to maintain the expression of two downstream APETALA 2 (AP2) transcription factor genes, PLETHORA 1 (PLT1) and PLT2, and to stabilize PLT2. RGI1 to RGI3 were also named RGF RECEPTOR 1 (RGFR1) to RGFR3, respectively. Although previous studies have suggested that BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) and its paralogs, SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASEs (SERKs), may act as coreceptors of RGIs, comprehensive genetic and biochemical analyses have not been well documented. Here, we report that single, double, and triple mutants of SERKs show various degrees of short root phenotypes and insensitivity to exogenously applied RGF1. The interaction between RGIs and BAK1 and their mutual phosphorylation are RGF1 dependent. We also found that RGF1-induced MAPK activation relies on both RGIs and SERKs. We demonstrate that RGIs play redundant roles in regulating root apical meristem development. Therefore, we genetically and biochemically substantiated that SERKs, as coreceptors, play essential roles in the RGF1-mediated signaling pathway.
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Affiliation(s)
| | | | - Yujun Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zeping Cai
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Huiqiang Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Meizhen Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Kai He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Author for correspondence:
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15
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Dhar S, Kim J, Yoon EK, Jang S, Ko K, Lim J. SHORT-ROOT Controls Cell Elongation in the Etiolated Arabidopsis Hypocotyl. Mol Cells 2022; 45:243-256. [PMID: 35249891 PMCID: PMC9001151 DOI: 10.14348/molcells.2021.5008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 11/27/2022] Open
Abstract
Transcriptional regulation, a core component of gene regulatory networks, plays a key role in controlling individual organism's growth and development. To understand how plants modulate cellular processes for growth and development, the identification and characterization of gene regulatory networks are of importance. The SHORT-ROOT (SHR) transcription factor is known for its role in cell divisions in Arabidopsis (Arabidopsis thaliana). However, whether SHR is involved in hypocotyl cell elongation remains unknown. Here, we reveal that SHR controls hypocotyl cell elongation via the transcriptional regulation of XTH18, XTH22, and XTH24, which encode cell wall remodeling enzymes called xyloglucan endotransglucosylase/hydrolases (XTHs). Interestingly, SHR activates transcription of the XTH genes, independently of its partner SCARECROW (SCR), which is different from the known mode of action. In addition, overexpression of the XTH genes can promote cell elongation in the etiolated hypocotyl. Moreover, confinement of SHR protein in the stele still induces cell elongation, despite the aberrant organization in the hypocotyl ground tissue. Therefore, it is likely that SHR-mediated growth is uncoupled from SHR-mediated radial patterning in the etiolated hypocotyl. Our findings also suggest that intertissue communication between stele and endodermis plays a role in coordinating hypocotyl cell elongation of the Arabidopsis seedling. Taken together, our study identifies SHR as a new crucial regulator that is necessary for cell elongation in the etiolated hypocotyl.
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Affiliation(s)
- Souvik Dhar
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
- Present address: School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
| | - Jinkwon Kim
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Eun Kyung Yoon
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
- Present address: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Sejeong Jang
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Kangseok Ko
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Jun Lim
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
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16
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Shahan R, Hsu CW, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN, Ohler U. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Dev Cell 2022; 57:543-560.e9. [PMID: 35134336 DOI: 10.1101/2020.06.29.178863] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/27/2021] [Accepted: 01/13/2022] [Indexed: 05/22/2023]
Abstract
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.
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Affiliation(s)
- Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Che-Wei Hsu
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Benjamin J Cole
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Isaiah W Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Stephen Zhang
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anna Hendrika Cornelia Vlot
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany.
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17
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Shahan R, Hsu CW, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN, Ohler U. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Dev Cell 2022; 57:543-560.e9. [PMID: 35134336 PMCID: PMC9014886 DOI: 10.1016/j.devcel.2022.01.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/27/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022]
Abstract
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.
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Affiliation(s)
- Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Che-Wei Hsu
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Benjamin J Cole
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Isaiah W Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Stephen Zhang
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anna Hendrika Cornelia Vlot
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany.
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18
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Clark NM, Elmore JM, Walley JW. To the proteome and beyond: advances in single-cell omics profiling for plant systems. PLANT PHYSIOLOGY 2022; 188:726-737. [PMID: 35235661 PMCID: PMC8825333 DOI: 10.1093/plphys/kiab429] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 05/19/2023]
Abstract
Recent advances in single-cell proteomics for animal systems could be adapted for plants to increase our understanding of plant development, response to stimuli, and cell-to-cell signaling.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - James Mitch Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
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19
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Tang M, Li B, Zhou X, Bolt T, Li JJ, Cruz N, Gaudinier A, Ngo R, Clark‐Wiest C, Kliebenstein DJ, Brady SM. A genome-scale TF-DNA interaction network of transcriptional regulation of Arabidopsis primary and specialized metabolism. Mol Syst Biol 2021; 17:e10625. [PMID: 34816587 PMCID: PMC8611409 DOI: 10.15252/msb.202110625] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Plant metabolism is more complex relative to individual microbes. In single-celled microbes, transcriptional regulation by single transcription factors (TFs) is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Plant primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber, and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana TFs and gene promoters in primary and specialized metabolic pathways were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the tricarboxylic acid (TCA) cycle. The resulting network suggests that plant metabolic design principles are distinct from those of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.
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Affiliation(s)
- Michelle Tang
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
- Plant Biology Graduate GroupUniversity of California, DavisDavisCAUSA
| | - Baohua Li
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Xue Zhou
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Tayah Bolt
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Jia Jie Li
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Neiman Cruz
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Allison Gaudinier
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Plant Biology Graduate GroupUniversity of California, DavisDavisCAUSA
| | - Richard Ngo
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Caitlin Clark‐Wiest
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
| | - Daniel J Kliebenstein
- Department of Plant SciencesUniversity of California, DavisDavisCAUSA
- DynaMo Center of ExcellenceUniversity of CopenhagenFrederiksberg CDenmark
| | - Siobhan M Brady
- Department of Plant Biology and Genome CenterUniversity of California, DavisDavisCAUSA
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20
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Yang B, Minne M, Brunoni F, Plačková L, Petřík I, Sun Y, Nolf J, Smet W, Verstaen K, Wendrich JR, Eekhout T, Hoyerová K, Van Isterdael G, Haustraete J, Bishopp A, Farcot E, Novák O, Saeys Y, De Rybel B. Non-cell autonomous and spatiotemporal signalling from a tissue organizer orchestrates root vascular development. NATURE PLANTS 2021; 7:1485-1494. [PMID: 34782768 PMCID: PMC7612341 DOI: 10.1038/s41477-021-01017-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 10/06/2021] [Indexed: 05/28/2023]
Abstract
During plant development, a precise balance of cytokinin is crucial for correct growth and patterning, but it remains unclear how this is achieved across different cell types and in the context of a growing organ. Here we show that in the root apical meristem, the TMO5/LHW complex increases active cytokinin levels via two cooperatively acting enzymes. By profiling the transcriptomic changes of increased cytokinin at single-cell level, we further show that this effect is counteracted by a tissue-specific increase in CYTOKININ OXIDASE 3 expression via direct activation of the mobile transcription factor SHORTROOT. In summary, we show that within the root meristem, xylem cells act as a local organizer of vascular development by non-autonomously regulating cytokinin levels in neighbouring procambium cells via sequential induction and repression modules.
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Affiliation(s)
- BaoJun Yang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Max Minne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Federica Brunoni
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Lenka Plačková
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Ivan Petřík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Yanbiao Sun
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wouter Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kevin Verstaen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
| | - Jos R Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klára Hoyerová
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jurgen Haustraete
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Protein Service Facility, VIB Center for Inflammation Research, Ghent, Belgium
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Loughborough, UK
| | - Etienne Farcot
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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21
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The Overexpression of NUC Promotes Development and Increases Resistance to Nitrogen Deficiency in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms222111413. [PMID: 34768843 PMCID: PMC8583770 DOI: 10.3390/ijms222111413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
NUTCRACKER (NUC) is a transcription factor expressed in multiple tissues, but little is known about its physiological roles. In this study, we explored the physiological function of NUC with the Arabidopsis knockout, rescue, and overexpression lines. We found that NUC overexpression promoted development at the germination, seedling, and juvenile stages. NUC overexpression increased resistance to nitrogen (N) deficiency stress by increasing the chlorophyll content, suppressing anthocyanin accumulation, and increasing the biomass under N deficiency. In contrast, the absence of NUC did not affect such characteristics. N deficiency significantly increased the expression of NUC in leaves but did not affect the expression of NUC in roots. The overexpression of NUC promoted primary root length under both normal and N deficiency conditions. Furthermore, we found that the N-responsive and lateral-root-related genes TGA1 and NRT2.4 had NUC-binding sites in their promoter regions and that their expression was upregulated by NUC under N deficiency. The overexpression of the NUC increased the number and length of the lateral roots under N deficiency through inducible promotion. Multiple lines of investigation suggest that the regulatory function of the NUC could be bypassed through its redundant MAGPIE (MGP) when the NUC is absent. Our findings provide novel insight into NUC's functions and will assist efforts to improve plants' development and resistance to nutrient stresses.
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22
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Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification. Methods Mol Biol 2021. [PMID: 34251619 DOI: 10.1007/978-1-0716-1534-8_4] [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: 08/05/2023]
Abstract
Gene expression data analysis and the prediction of causal relationships within gene regulatory networks (GRNs) have guided the identification of key regulatory factors and unraveled the dynamic properties of biological systems. However, drawing accurate and unbiased conclusions requires a comprehensive understanding of relevant tools, computational methods, and their workflows. The topics covered in this chapter encompass the entire workflow for GRN inference including: (1) experimental design; (2) RNA sequencing data processing; (3) differentially expressed gene (DEG) selection; (4) clustering prior to inference; (5) network inference techniques; and (6) network visualization and analysis. Moreover, this chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background. To address this need, TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, is chosen for the purpose of providing a detailed tutorial.
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23
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Fu J, Zhang X, Liu J, Gao X, Bai J, Hao Y, Cui H. A mechanism coordinating root elongation, endodermal differentiation, redox homeostasis and stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1029-1039. [PMID: 34056773 DOI: 10.1111/tpj.15361] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Root growth relies on both cell division and cell elongation, which occur in the meristem and elongation zones, respectively. SCARECROW (SCR) and SHORT-ROOT (SHR) are GRAS family genes essential for root growth and radial patterning in the Arabidopsis root. Previous studies showed that SCR and SHR promote root growth by suppressing cytokinin response in the meristem, but there is evidence that SCR expressed beyond the meristem is also required for root growth. Here we report a previously unknown role for SCR in promoting cell elongation. Consistent with this, we found that the scr mutant accumulated a higher level of reactive oxygen species (ROS) in the elongation zone, which is probably due to decreased expression of peroxidase gene 3, which consumes hydrogen peroxide in a reaction leading to Casparian strip formation. When the oxidative stress response was blocked in the scr mutant by mutation in ABSCISIC ACID 2 (ABA2) or when the redox status was ameliorated by the upbeat 1 (upb1) mutant, the root became significantly longer, with longer cells and a larger and more mitotically active meristem. Remarkably, however, the stem cell and radial patterning defects in the double mutants still persisted. Since ROS and peroxidases are essential for endodermal differentiation, these results suggest that SCR plays a role in coordinating cell elongation, endodermal differentiation, redox homeostasis and oxidative stress response in the root. We also provide evidence that this role of SCR is independent of SHR, even though they function similarly in other aspects of root growth and development.
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Affiliation(s)
- Jing Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinglin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiaming Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xudong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Juan Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yueling Hao
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Hongchang Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
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24
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Huang X, Li W, Zhang X. Flavonoid scutellarin positively regulates root length through NUTCRACKER. PLANT DIVERSITY 2021; 43:248-254. [PMID: 34195510 PMCID: PMC8233521 DOI: 10.1016/j.pld.2020.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 06/13/2023]
Abstract
Exploring approaches to regulate meristem is of special importance and broad interest. In this study, we found that the flavonoid scutellarin, which has a 6-hydroxyl and a 7-glucoside, increased root length through the transcription factor NUTCRACKER (NUC). This root lengthening disappeared in NUC-knockout and reappeared in NUC-rescue plants. Scutellarin induced NUC expression and promoted the division of cortex/endodermal initials. In contrast, naringenin, which has same chemical backbone but without 6-hydroxyl and with 7-hydroxyl group, showed the opposite or no effects. Our results demonstrate that scutellarin promotes root length through NUC-mediated regulatory pathways and reveal that flavonoids with and without the 6-hydroxyl and 7-glucoside have positive and negative effects on meristem size, respectively.
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Affiliation(s)
- Xing Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiqi Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xudong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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25
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Verma S, Attuluri VPS, Robert HS. An Essential Function for Auxin in Embryo Development. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a039966. [PMID: 33431580 DOI: 10.1101/cshperspect.a039966] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Embryogenesis in seed plants is the process during which a single cell develops into a mature multicellular embryo that encloses all the modules and primary patterns necessary to build the architecture of the new plant after germination. This process involves a series of cell divisions and coordinated cell fate determinations resulting in the formation of an embryonic pattern with a shoot-root axis and cotyledon(s). The phytohormone auxin profoundly controls pattern formation during embryogenesis. Auxin functions in the embryo through its maxima/minima distribution, which acts as an instructive signal for tissue specification and organ initiation. In this review, we describe how disruptions of auxin biosynthesis, transport, and response severely affect embryo development. Also, the mechanism of auxin action in the development of the shoot-root axis and the three-tissue system is discussed with recent findings. Biological tools that can be implemented to study the auxin function during embryo development are presented, as they may be of interest to the reader.
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Affiliation(s)
- Subodh Verma
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Venkata Pardha Saradhi Attuluri
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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26
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Tomescu AMF. The stele - a developmental perspective on the diversity and evolution of primary vascular architecture. Biol Rev Camb Philos Soc 2021; 96:1263-1283. [PMID: 33655608 DOI: 10.1111/brv.12699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/15/2022]
Abstract
The stele concept is one of the oldest enduring concepts in plant biology. Here, I review the history of the concept and build an argument for an updated view of steles and their evolution. Studies of stelar organization have generated a widely ranging array of definitions that determine the way we classify steles and construct scenarios about the evolution of stelar architecture. Because at the organismal level biological evolution proceeds by changes in development, concepts of structure need to be grounded in development to be relevant in an evolutionary perspective. For the stele, most traditional definitions that incorporate development have viewed it as the totality of tissues that either originate from procambium - currently the prevailing view - or are bordered by a boundary layer (e.g. endodermis). Consensus between these two perspectives can be reached by recasting the stele as a structural entity of dual nature. Following a brief review of the history of the stele concept, basic terminology related to stelar organization, and traditional classifications of the steles, I revisit boundary layers from the perspective of histogenesis as a dynamic mosaic of developmental domains. I review anatomical and molecular data to explore and reaffirm the importance of boundary layers for stelar organization. Drawing on information from comparative anatomy, developmental regulation, and the fossil record, I propose a stele concept that integrates both the boundary layer and the procambial perspectives, consistent with a dual nature of the stele. This dual stele model posits that stelar architecture is determined at the apical meristem by two major cell fate specification events: a first one that specifies a provascular domain and its boundaries, and a second event that specifies a procambial domain (which will mature into conducting tissues) from cell subpopulations of the provascular domain. If the position and extent of the developmental domains defined by the two events are determined by different concentrations of the same morphogen (most likely auxin), then the distribution of this organizer factor in the shoot apical meristem, as modulated by changes in axis size and the effect of lateral organs, can explain the different stelar configurations documented among tracheophytes. This model provides working hypotheses that incorporate assumptions and generate implications that can be tested empirically. The model also offers criteria for an updated classification of steles in line with current understanding of plant development. In this classification, steles fall into two major categories determined by the configuration of boundary layers: boundary protosteles and boundary siphonosteles, each with subtypes defined by the architecture of the vascular tissues. Validation of the dual stele model and, more generally, in-depth understanding of the regulation of stelar architecture, will necessitate targeted efforts in two areas: (i) the regulation of procambium, vascular tissue, and boundary layer specification in all extant vascular plants, considering that most of the diversity in stelar architecture is hosted by seed-free plants, which are the least explored in terms of developmental regulation; (ii) the configuration of vascular tissues and, especially, boundary layers, in as many extinct lineages as possible.
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Affiliation(s)
- Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, U.S.A
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27
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Yang X, Zhang Y, Shan J, Sun J, Li D, Zhang X, Li W, Zhao L. GmIDD Is Induced by Short Days in Soybean and May Accelerate Flowering When Overexpressed in Arabidopsis via Inhibiting AGAMOUS-LIKE 18. FRONTIERS IN PLANT SCIENCE 2021; 12:629069. [PMID: 33841461 PMCID: PMC8029582 DOI: 10.3389/fpls.2021.629069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/22/2021] [Indexed: 05/31/2023]
Abstract
Photoperiod is one of the main climatic factors that determine flowering time and yield. Some members of the INDETERMINATE DOMAIN (IDD) transcription factor family have been reported to be involved in regulation of flowering time in Arabidopsis, maize, and rice. In this study, the domain analysis showed that GmIDD had a typical ID domain and was a member of the soybean IDD transcription factor family. Quantitative real-time PCR analysis showed that GmIDD was induced by short day conditions in leaves and regulated by circadian clock. Under long day conditions, transgenic Arabidopsis overexpressing GmIDD flowered earlier than wild-type, and idd mutants flowered later, while the overexpression of GmIDD rescued the late-flowering phenotype of idd mutants. Chromatin immunoprecipitation sequencing assays of GmIDD binding sites in GmIDD-overexpression (GmIDD-ox) Arabidopsis further identified potential direct targets, including a transcription factor, AGAMOUS-like 18 (AGL18). GmIDD might inhibit the transcriptional activity of flower repressor AGL18 by binding to the TTTTGGTCC motif of AGL18 promoter. Furthermore, the results also showed that GmIDD overexpression increased the transcription levels of flowering time-related genes FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), LEAFY (LFY) and APETALA1 (AP1) in Arabidopsis. Taken together, GmIDD appeared to inhibit the transcriptional activity of AGL18 and induced the expression of FT gene to promote Arabidopsis flowering.
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28
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Bertolotti G, Unterholzner SJ, Scintu D, Salvi E, Svolacchia N, Di Mambro R, Ruta V, Linhares Scaglia F, Vittorioso P, Sabatini S, Costantino P, Dello Ioio R. A PHABULOSA-Controlled Genetic Pathway Regulates Ground Tissue Patterning in the Arabidopsis Root. Curr Biol 2021; 31:420-426.e6. [PMID: 33176130 PMCID: PMC7846283 DOI: 10.1016/j.cub.2020.10.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/07/2020] [Accepted: 10/13/2020] [Indexed: 12/03/2022]
Abstract
In both animals and plants, development involves anatomical modifications. In the root of Arabidopsis thaliana, maturation of the ground tissue (GT)—a tissue comprising all cells between epidermal and vascular ones—is a paradigmatic example of these modifications, as it generates an additional tissue layer, the middle cortex (MC).1, 2, 3, 4 In early post-embryonic phases, the Arabidopsis root GT is composed of one layer of endodermis and one of cortex. A second cortex layer, the MC, is generated by asymmetric cell divisions in about 80% of Arabidopsis primary roots, in a time window spanning from 7 to 14 days post-germination (dpg). The cell cycle regulator CYCLIN D6;1 (CYCD6;1) plays a central role in this process, as its accumulation in the endodermis triggers the formation of MC.5 The phytohormone gibberellin (GA) is a key regulator of the timing of MC formation, as alterations in its signaling and homeostasis result in precocious endodermal asymmetric cell divisions.3,6,7 However, little is known on how GAs are regulated during GT maturation. Here, we show that the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) transcription factor PHABULOSA (PHB) is a master regulator of MC formation, controlling the accumulation of CYCD6;1 in the endodermis in a cell non-autonomous manner. We show that PHB activates the GA catabolic gene GIBBERELLIN 2 OXIDASE 2 (GA2ox2) in the vascular tissue, thus regulating the stability of the DELLA protein GIBBERELLIN INSENSITIVE (GAI)—a GA signaling repressor—in the root and, hence, CYCD6;1 expression in the endodermis. PHB regulates cell non-autonomously the timing of MC formation A time-dependent rise of PHB expression controls the CYCD6;1 switch in the GT PHB regulates GAI stability modulating GA levels PHB regulates root GA levels activating GA2ox2 expression in the vasculature
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Affiliation(s)
- Gaia Bertolotti
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | - Simon Josef Unterholzner
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazzale Università, 5, 39100 Bolzano, Italy
| | - Daria Scintu
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | - Elena Salvi
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | - Noemi Svolacchia
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | - Riccardo Di Mambro
- Department of Biology, University of Pisa, via L. Ghini, 13, 56126 Pisa, Italy
| | - Veronica Ruta
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | | | - Paola Vittorioso
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | - Sabrina Sabatini
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | - Paolo Costantino
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70, 00185 Rome, Italy.
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29
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García-Gómez ML, Garay-Arroyo A, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER. Hormonal Regulation of Stem Cell Proliferation at the Arabidopsis thaliana Root Stem Cell Niche. FRONTIERS IN PLANT SCIENCE 2021; 12:628491. [PMID: 33747009 PMCID: PMC7966715 DOI: 10.3389/fpls.2021.628491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/12/2021] [Indexed: 05/13/2023]
Abstract
The root stem cell niche (SCN) of Arabidopsis thaliana consists of the quiescent center (QC) cells and the surrounding initial stem cells that produce progeny to replenish all the tissues of the root. The QC cells divide rather slowly relative to the initials, yet most root tissues can be formed from these cells, depending on the requirements of the plant. Hormones are fundamental cues that link such needs with the cell proliferation and differentiation dynamics at the root SCN. Nonetheless, the crosstalk between hormone signaling and the mechanisms that regulate developmental adjustments is still not fully understood. Developmental transcriptional regulatory networks modulate hormone biosynthesis, metabolism, and signaling, and conversely, hormonal responses can affect the expression of transcription factors involved in the spatiotemporal patterning at the root SCN. Hence, a complex genetic-hormonal regulatory network underlies root patterning, growth, and plasticity in response to changing environmental conditions. In this review, we summarize the scientific literature regarding the role of hormones in the regulation of QC cell proliferation and discuss how hormonal signaling pathways may be integrated with the gene regulatory network that underlies cell fate in the root SCN. The conceptual framework we present aims to contribute to the understanding of the mechanisms by which hormonal pathways act as integrators of environmental cues to impact on SCN activity.
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Affiliation(s)
- Mónica L. García-Gómez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Elena R. Álvarez-Buylla,
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30
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Mase K, Tsukagoshi H. Reactive Oxygen Species Link Gene Regulatory Networks During Arabidopsis Root Development. FRONTIERS IN PLANT SCIENCE 2021; 12:660274. [PMID: 33986765 PMCID: PMC8110921 DOI: 10.3389/fpls.2021.660274] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/22/2021] [Indexed: 05/22/2023]
Abstract
Plant development under altered nutritional status and environmental conditions and during attack from invaders is highly regulated by plant hormones at the molecular level by various signaling pathways. Previously, reactive oxygen species (ROS) were believed to be harmful as they cause oxidative damage to cells; however, in the last decade, the essential role of ROS as signaling molecules regulating plant growth has been revealed. Plant roots accumulate relatively high levels of ROS, and thus, maintaining ROS homeostasis, which has been shown to regulate the balance between cell proliferation and differentiation at the root tip, is important for proper root growth. However, when the balance is disturbed, plants are unable to respond to the changes in the surrounding conditions and cannot grow and survive. Moreover, ROS control cell expansion and cell differentiation processes such as root hair formation and lateral root development. In these processes, the transcription factor-mediated gene expression network is important downstream of ROS. Although ROS can independently regulate root growth to some extent, a complex crosstalk occurs between ROS and other signaling molecules. Hormone signals are known to regulate root growth, and ROS are thought to merge with these signals. In fact, the crosstalk between ROS and these hormones has been elucidated, and the central transcription factors that act as a hub between these signals have been identified. In addition, ROS are known to act as important signaling factors in plant immune responses; however, how they also regulate plant growth is not clear. Recent studies have strongly indicated that ROS link these two events. In this review, we describe and discuss the role of ROS signaling in root development, with a particular focus on transcriptional regulation. We also summarize the crosstalk with other signals and discuss the importance of ROS as signaling molecules for plant root development.
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Harnvanichvech Y, Gorelova V, Sprakel J, Weijers D. The Arabidopsis embryo as a quantifiable model for studying pattern formation. QUANTITATIVE PLANT BIOLOGY 2021; 2:e3. [PMID: 37077211 PMCID: PMC10095805 DOI: 10.1017/qpb.2021.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 05/03/2023]
Abstract
Phenotypic diversity of flowering plants stems from common basic features of the plant body pattern with well-defined body axes, organs and tissue organisation. Cell division and cell specification are the two processes that underlie the formation of a body pattern. As plant cells are encased into their cellulosic walls, directional cell division through precise positioning of division plane is crucial for shaping plant morphology. Since many plant cells are pluripotent, their fate establishment is influenced by their cellular environment through cell-to-cell signaling. Recent studies show that apart from biochemical regulation, these two processes are also influenced by cell and tissue morphology and operate under mechanical control. Finding a proper model system that allows dissecting the relationship between these aspects is the key to our understanding of pattern establishment. In this review, we present the Arabidopsis embryo as a simple, yet comprehensive model of pattern formation compatible with high-throughput quantitative assays.
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Affiliation(s)
- Yosapol Harnvanichvech
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Vera Gorelova
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Author for correspondence: Dolf Weijers, E-mail:
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Seo M, Lee JY. Dissection of Functional Modules of AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 4 in the Development of the Root Xylem. FRONTIERS IN PLANT SCIENCE 2021; 12:632078. [PMID: 33889164 PMCID: PMC8056045 DOI: 10.3389/fpls.2021.632078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/25/2021] [Indexed: 05/13/2023]
Abstract
Xylem development in the Arabidopsis root apical meristem requires a complex cross talk between plant hormone signaling and transcriptional factors (TFs). The key processes involve fine-tuning between neighboring cells, mediated via the intercellular movement of signaling molecules. As an example, we previously reported that AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN (AHL) 4 (AHL4), a member of the 29 AT-hook family TFs in Arabidopsis, moves into xylem precursors from their neighbors to determine xylem differentiation. As part of the effort to understand the molecular functions of AHL4, we performed domain swapping analyses using AHL1 as a counterpart, finding that AHL4 has three functionally distinctive protein modules. The plant and prokaryotes conserved (PPC) domain of AHL4 acts as a mediator of protein-protein interactions with AHL members. The N-terminus of AHL4 is required for the regulation of xylem development likely via its unique DNA-binding activity. The C-terminus of AHL4 confers intercellular mobility. Our characterization of modules in the AHL4 protein will augment our understanding of the complexity of regulation and the evolution of intercellular mobility in AHL4 and its relatives.
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Affiliation(s)
- Minji Seo
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul, South Korea
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- *Correspondence: Ji-Young Lee,
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BAM1/2 receptor kinase signaling drives CLE peptide-mediated formative cell divisions in Arabidopsis roots. Proc Natl Acad Sci U S A 2020; 117:32750-32756. [PMID: 33288706 PMCID: PMC7768756 DOI: 10.1073/pnas.2018565117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proper elaboration of the plant body plan requires that cell division patterns are coordinated during development in complex tissues. Activation of cell cycle machinery is critical for this process, but it is not clear how or if this links to cell-to-cell communication networks that are important during development. Here we show that key cell divisions that generate the plant root are controlled by cell-to-cell signaling peptides which act through plant-specific receptor kinases to control expression of a specific cyclinD cell cycle regulatory gene. We show that cyclinD gene expression depends on both receptor signaling and the SHORT-ROOT transcription factor to ensure timely and robust cell division patterns. Cell division is often regulated by extracellular signaling networks to ensure correct patterning during development. In Arabidopsis, the SHORT-ROOT (SHR)/SCARECROW (SCR) transcription factor dimer activates CYCLIND6;1 (CYCD6;1) to drive formative divisions during root ground tissue development. Here, we show plasma-membrane-localized BARELY ANY MERISTEM1/2 (BAM1/2) family receptor kinases are required for SHR-dependent formative divisions and CYCD6;1 expression, but not SHR-dependent ground tissue specification. Root-enriched CLE ligands bind the BAM1 extracellular domain and are necessary and sufficient to activate SHR-mediated divisions and CYCD6;1 expression. Correspondingly, BAM-CLE signaling contributes to the restriction of formative divisions to the distal root region. Additionally, genetic analysis reveals that BAM-CLE and SHR converge to regulate additional cell divisions outside of the ground tissues. Our work identifies an extracellular signaling pathway regulating formative root divisions and provides a framework to explore this pathway in patterning and evolution.
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Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division. Proc Natl Acad Sci U S A 2020; 117:15332-15342. [PMID: 32541020 DOI: 10.1073/pnas.2002166117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In the Arabidopsis root, stem cells are maintained in an undifferentiated state by a less mitotically active population of cells called the quiescent center (QC). Determining how the QC regulates the surrounding stem cell initials, or what makes the QC fundamentally different from the actively dividing initials, is important for understanding how stem cell divisions are maintained. Here we gained insight into the differences between the QC and the cortex endodermis initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). We constructed an ordinary differential equation model of SHR and SCR in the QC and CEI which incorporated the stoichiometry of the SHR-SCR complex as well as upstream transcriptional regulation of SHR and SCR. Our model prediction, coupled with experimental validation, showed that high levels of the SHR-SCR complex are associated with more CEI division but less QC division. Furthermore, our model prediction allowed us to propose the putative upstream SHR regulators SEUSS and WUSCHEL-RELATED HOMEOBOX 5 and to experimentally validate their roles in QC and CEI division. In addition, our model established the timing of QC and CEI division and suggests that SHR repression of QC division depends on formation of the SHR homodimer. Thus, our results support that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.
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Gene Regulation via the Combination of Transcription Factors in the INDETERMINATE DOMAIN and GRAS Families. Genes (Basel) 2020; 11:genes11060613. [PMID: 32498388 PMCID: PMC7349898 DOI: 10.3390/genes11060613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/29/2022] Open
Abstract
INDETERMINATE DOMAIN (IDD) family proteins are plant-specific transcription factors. Some Arabidopsis IDD (AtIDD) proteins regulate the expression of SCARECROW (SCR) by interacting with GRAS family transcription factors SHORT-ROOT (SHR) and SCR, which are involved in root tissue formation. Some AtIDD proteins regulate genes involved in the synthesis (GA3ox1) or signaling (SCL3) of gibberellic acid (GA) by interacting with DELLA proteins, a subfamily of the GRAS family. We analyzed the DNA binding properties and protein–protein interactions of select AtIDD proteins. We also investigated the transcriptional activity of the combination of AtIDD and GRAS proteins (AtIDD proteins combined with SHR and SCR or with REPRESSOR of ga1-3 (RGA)) on the promoters of SCR,SCL3, and GA3ox1 by conducting a transient assay using Arabidopsis culture cells. Our results showed that the SCR promoter could be activated by the IDD and RGA complexes and that the SCL3 and GA3ox1 promoters could be activated by the IDD, SHR, and SCR complexes, indicating the possibility that these complexes regulate and consequently coordinate the expression of genes involved in GA synthesis (GA3ox1), GA signaling (SCL3), and root formation (SCR).
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Genome-Wide Analysis of the GRAS Gene Family in Barley ( Hordeum vulgare L.). Genes (Basel) 2020; 11:genes11050553. [PMID: 32423019 PMCID: PMC7290968 DOI: 10.3390/genes11050553] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 11/16/2022] Open
Abstract
The GRAS (named after first three identified proteins within this family, GAI, RGA, and SCR) family contains plant-specific genes encoding transcriptional regulators that play a key role in gibberellin (GA) signaling, which regulates plant growth and development. Even though GRAS genes have been characterized in some plant species, little research is known about the GRAS genes in barley (Hordeum vulgare L.). In this study, we observed 62 GRAS members from barley genome, which were grouped into 12 subgroups by using phylogenomic analysis together with the GRAS genes from Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). Chromosome localization and gene structure analysis suggested that duplication events and abundant presence of intronless genes might account for the massive expansion of GRAS gene family in barley. The analysis of RNA-seq data indicates the expression pattern of GRAS genes in various tissues at different stages in barley. Noteworthy, our qRT-PCR analysis showed the expression of 18 candidate GRAS genes abundantly in the developing inflorescence, indicating their potential roles in the barley inflorescence development and reproduction. Collectively, our evolutionary and expression analysis of GRAS family are useful for future functional characterization of GA signaling in barley and agricultural improvement.
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Kim H, Zhou J, Kumar D, Jang G, Ryu KH, Sebastian J, Miyashima S, Helariutta Y, Lee JY. SHORTROOT-Mediated Intercellular Signals Coordinate Phloem Development in Arabidopsis Roots. THE PLANT CELL 2020; 32:1519-1535. [PMID: 32111671 PMCID: PMC7203941 DOI: 10.1105/tpc.19.00455] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/06/2020] [Accepted: 02/25/2020] [Indexed: 05/19/2023]
Abstract
Asymmetric cell division (ACD) and positional signals play critical roles in the tissue patterning process. In the Arabidopsis (Arabidopsis thaliana) root meristem, two major phloem cell types arise via ACDs of distinct origins: one for companion cells (CCs) and the other for proto- and metaphloem sieve elements (SEs). The molecular mechanisms underlying each of these processes have been reported; however, how these are coordinated has remained elusive. Here, we report a new phloem development process coordinated via the SHORTROOT (SHR) transcription factor in Arabidopsis. The movement of SHR into the endodermis regulates the ACD for CC formation by activating microRNA165/6, while SHR moving into the phloem regulates the ACD generating the two phloem SEs. In the phloem, SHR sequentially activates NAC-REGULATED SEED MORPHOLOGY 1 (NARS1) and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN 2 (SND2), and these three together form a positive feedforward loop. Under this regulatory scheme, NARS1, generated in the CCs of the root differentiation zone, establishes a top-down signal that drives the ACD for phloem SEs in the meristem. SND2 appears to function downstream to amplify NARS1 via positive feedback. This new regulatory mechanism expands our understanding of the sophisticated vascular tissue patterning processes occurring during postembryonic root development.plantcell;32/5/1519/FX1F1fx1.
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Affiliation(s)
- Hyoujin Kim
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
| | - Jing Zhou
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
- Elo Life Systems, Durham, North Carolina 27709
| | - Deepak Kumar
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
| | - Geupil Jang
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Kook Hui Ryu
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
| | - Jose Sebastian
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur 760010, India
| | - Shunsuke Miyashima
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
| | - Ykä Helariutta
- Institute of Biotechnology, Department of Biological and Environmental Sciences, University of Helsinki, FIN-00014, Finland
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, United Kingdom
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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González-García MP, Bustillo-Avendaño E, Sanchez-Corrionero A, del Pozo JC, Moreno-Risueno MA. Fluorescence-Activated Cell Sorting Using the D-Root Device and Optimization for Scarce and/or Non-Accessible Root Cell Populations. PLANTS 2020; 9:plants9040499. [PMID: 32295129 PMCID: PMC7238278 DOI: 10.3390/plants9040499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/11/2020] [Indexed: 01/18/2023]
Abstract
Fluorescence-activated cell sorting (FACS) is a technique used to isolate specific cell populations based on characteristics detected by flow cytometry. FACS has been broadly used in transcriptomic analyses of individual cell types during development or under different environmental conditions. Different protoplast extraction protocols are available for plant roots; however, they were designed for accessible cell populations, which normally were grown in the presence of light, a non-natural and stressful environment for roots. Here, we report a protocol using FACS to isolate root protoplasts from Arabidopsis green fluorescent protein (GFP)-marked lines using the minimum number of enzymes necessary for an optimal yield, and with the root system grown in darkness in the D-Root device. This device mimics natural conditions as the shoot grows in the presence of light while the roots grow in darkness. In addition, we optimized this protocol for specific patterns of scarce cell types inside more differentiated tissues using the mCherry fluorescent protein. We provide detailed experimental protocols for effective protoplasting, subsequent purification through FACS, and RNA extraction. Using this RNA, we generated cDNA and sequencing libraries, proving that our methods can be used for genome-wide transcriptomic analyses of any cell-type from roots grown in darkness.
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A system-level mechanistic explanation for asymmetric stem cell fates: Arabidopsis thaliana root niche as a study system. Sci Rep 2020; 10:3525. [PMID: 32103059 PMCID: PMC7044435 DOI: 10.1038/s41598-020-60251-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/23/2019] [Indexed: 11/09/2022] Open
Abstract
Asymmetric divisions maintain long-term stem cell populations while producing new cells that proliferate and then differentiate. Recent reports in animal systems show that divisions of stem cells can be uncoupled from their progeny differentiation, and the outcome of a division could be influenced by microenvironmental signals. But the underlying system-level mechanisms, and whether this dynamics also occur in plant stem cell niches (SCN), remain elusive. This article presents a cell fate regulatory network model that contributes to understanding such mechanism and identify critical cues for cell fate transitions in the root SCN. Novel computational and experimental results show that the transcriptional regulator SHR is critical for the most frequent asymmetric division previously described for quiescent centre stem cells. A multi-scale model of the root tip that simulated each cell's intracellular regulatory network, and the dynamics of SHR intercellular transport as a cell-cell coupling mechanism, was developed. It revealed that quiescent centre cell divisions produce two identical cells, that may acquire different fates depending on the feedback between SHR's availability and the state of the regulatory network. Novel experimental data presented here validates our model, which in turn, constitutes the first proposed systemic mechanism for uncoupled SCN cell division and differentiation.
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40
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The Arabidopsis Hypoxia Inducible AtR8 Long Non-Coding RNA also Contributes to Plant Defense and Root Elongation Coordinating with WRKY Genes under Low Levels of Salicylic Acid. Noncoding RNA 2020; 6:ncrna6010008. [PMID: 32110879 PMCID: PMC7151572 DOI: 10.3390/ncrna6010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/22/2020] [Accepted: 02/23/2020] [Indexed: 12/13/2022] Open
Abstract
AtR8 lncRNA was previously identified in the flowering plant Arabidopsis thaliana as an abundant Pol III-transcribed long non-coding RNA (lncRNA) of approximately 260 nt. AtR8 lncRNA accumulation is responsive to hypoxic stress and salicylic acid (SA) treatment in roots, but its function has not yet been identified. In this study, microarray analysis of an atr8 mutant and wild-type Arabidopsis indicated a strong association of AtR8 lncRNA with the defense response. AtR8 accumulation exhibited an inverse correlation with an accumulation of two WRKY genes (WRKY53/WRKY70) when plants were exposed to exogenous low SA concentrations (20 µM), infected with Pseudomonas syringae, or in the early stage of development. The highest AtR8 accumulation was observed 5 days after germination, at which time no WRKY53 or WRKY70 mRNA was detectable. The presence of low levels of SA resulted in a significant reduction of root length in atr8 seedlings, whereas wrky53 and wrky70 mutants exhibited the opposite phenotype. Taken together, AtR8 lncRNA participates in Pathogenesis-Related Proteins 1 (PR-1)-independent defense and root elongation, which are related to the SA response. The mutual regulation of AtR8 lncRNA and WRKY53/WRKY70 is mediated by Nonexpressor of Pathogenesis-Related Gene 1 (NPR1).
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Singh S, Singh A, Singh A, Yadav S, Bajaj I, Kumar S, Jain A, Sarkar AK. Role of chromatin modification and remodeling in stem cell regulation and meristem maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:778-792. [PMID: 31793642 DOI: 10.1093/jxb/erz459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
In higher plants, pluripotent stem cells reside in the specialized microenvironment called stem cell niches (SCNs) harbored at the shoot apical meristem (SAM) and root apical meristem (RAM), which give rise to the aerial and underground parts of a plant, respectively. The model plant Arabidopsis thaliana (Arabidopsis) has been extensively studied to decipher the intricate regulatory mechanisms involving some key transcriptions factors and phytohormones that play pivotal roles in stem cell homeostasis, meristem maintenance, and organ formation. However, there is increasing evidence to show the epigenetic regulation of the chromatin architecture, gene expression exerting an influence on an innate balance between the self-renewal of stem cells, and differentiation of the progeny cells to a specific tissue type or organ. Post-translational histone modifications, ATP-dependent chromatin remodeling, and chromatin assembly/disassembly are some of the key features involved in the modulation of chromatin architecture. Here, we discuss the major epigenetic regulators and illustrate their roles in the regulation of stem cell activity, meristem maintenance, and related organ patterning in Arabidopsis.
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Affiliation(s)
- Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Alka Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ishita Bajaj
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shailendra Kumar
- Amity School of Architecture and Planning, Amity University, Kant Kalwar, Rajasthan, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University, Kant Kalwar, Rajasthan, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Campos R, Goff J, Rodriguez-Furlan C, Van Norman JM. The Arabidopsis Receptor Kinase IRK Is Polarized and Represses Specific Cell Divisions in Roots. Dev Cell 2020; 52:183-195.e4. [DOI: 10.1016/j.devcel.2019.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/30/2019] [Accepted: 11/25/2019] [Indexed: 01/05/2023]
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Zhang J, Eswaran G, Alonso-Serra J, Kucukoglu M, Xiang J, Yang W, Elo A, Nieminen K, Damén T, Joung JG, Yun JY, Lee JH, Ragni L, Barbier de Reuille P, Ahnert SE, Lee JY, Mähönen AP, Helariutta Y. Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. NATURE PLANTS 2019; 5:1033-1042. [PMID: 31595065 PMCID: PMC6795544 DOI: 10.1038/s41477-019-0522-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/19/2019] [Indexed: 05/18/2023]
Abstract
Vascular cambium, a lateral plant meristem, is a central producer of woody biomass. Although a few transcription factors have been shown to regulate cambial activity1, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we use cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses to identify 62 new transcription factor genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified transcription factors with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the transcription factor network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.
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Affiliation(s)
- Jing Zhang
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Gugan Eswaran
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Juan Alonso-Serra
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Melis Kucukoglu
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jiale Xiang
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Weibing Yang
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Annakaisa Elo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kaisa Nieminen
- Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Teddy Damén
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Jae-Young Yun
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Jung-Hun Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Laura Ragni
- ZMBP-Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | | | - Sebastian E Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ji-Young Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea.
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| | - Ykä Helariutta
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
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Sakamoto T, Sotta N, Suzuki T, Fujiwara T, Matsunaga S. The 26S Proteasome Is Required for the Maintenance of Root Apical Meristem by Modulating Auxin and Cytokinin Responses Under High-Boron Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:590. [PMID: 31156663 PMCID: PMC6530338 DOI: 10.3389/fpls.2019.00590] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/23/2019] [Indexed: 05/26/2023]
Abstract
Boron (B), an essential micronutrient, causes adverse effects on the growth and development of plants when highly accumulated. By the analysis of Arabidopsis mutants hypersensitive to high-boron (high-B) stress, we have shown that 26S proteasome (26SP) is required to maintain the morphology of the root apical meristem (RAM) under high-B stress. To further understand the molecular function of 26SP in tolerance to high-B stress in the RAM, in this study we investigated the pathways regulated by 26SP using a 26SP subunit mutant, rpt5a, which is hypersensitive to high-B stress. Expression of RPT5a was induced by high-B stress in the entire RAM accompanied by its strong expression in the stele, including the stem cells. Analysis of stele organization in the rpt5a mutant revealed that 26SP is especially important for maintenance of the stele under high-B stress condition (3 mM B treatment). Expression analyses of an auxin-response reporter revealed that auxin responses were enhanced in the stele and the stem cell niche by high-B stress, especially in the rpt5a mutant. In contrast, the expression of TCS::GFP representing cytokinin signaling in the stem cell niche was unchanged in the wild type and extremely weak in the rpt5a mutant, irrespective of B condition. The drastically aberrant auxin and cytokinin responses in the rpt5a mutant under high-B stress were supported by transcriptome analysis using root tips. These results suggest that the collapse of hormonal crosstalk in the stele including the stem cells occurred in the rpt5a mutant, especially under high-B stress. Treatment with the auxin signaling inhibitor α-(phenyl ethyl-2-one)-indole-3-acetic acid (PEO-IAA) reduced sensitivity to high-B stress in the wild type and restored the RAM morphology in the rpt5a mutant under the high-B stress condition. In addition, cytokinin treatment conferred the rpt5a mutant with tolerance to high-B stress in RAM morphology. It is concluded that 26SP containing RPT5a is required for maintenance of auxin/cytokinin balance in the stele, which is crucial for preventing defects in RAM morphology under high-B stress.
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Affiliation(s)
- Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Naoyuki Sotta
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyō, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyō, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
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Kumar M, Le DT, Hwang S, Seo PJ, Kim HU. Role of the INDETERMINATE DOMAIN Genes in Plants. Int J Mol Sci 2019; 20:ijms20092286. [PMID: 31075826 PMCID: PMC6539433 DOI: 10.3390/ijms20092286] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
The INDETERMINATE DOMAIN (IDD) genes comprise a conserved transcription factor family that regulates a variety of developmental and physiological processes in plants. Many recent studies have focused on the genetic characterization of IDD family members and revealed various biological functions, including modulation of sugar metabolism and floral transition, cold stress response, seed development, plant architecture, regulation of hormone signaling, and ammonium metabolism. In this review, we summarize the functions and working mechanisms of the IDD gene family in the regulatory network of metabolism and developmental processes.
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Affiliation(s)
- Manu Kumar
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Dung Thi Le
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
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Di Mambro R, Svolacchia N, Dello Ioio R, Pierdonati E, Salvi E, Pedrazzini E, Vitale A, Perilli S, Sozzani R, Benfey PN, Busch W, Costantino P, Sabatini S. The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size. Curr Biol 2019; 29:1199-1205.e4. [PMID: 30880016 DOI: 10.1016/j.cub.2019.02.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/27/2018] [Accepted: 02/06/2019] [Indexed: 12/28/2022]
Abstract
Plant developmental plasticity relies on the activities of meristems, regions where stem cells continuously produce new cells [1]. The lateral root cap (LRC) is the outermost tissue of the root meristem [1], and it is known to play an important role during root development [2-6]. In particular, it has been shown that mechanical or genetic ablation of LRC cells affect meristem size [7, 8]; however, the molecular mechanisms involved are unknown. Root meristem size and, consequently, root growth depend on the position of the transition zone (TZ), a boundary that separates dividing from differentiating cells [9, 10]. The interaction of two phytohormones, cytokinin and auxin, is fundamental in controlling the position of the TZ [9, 10]. Cytokinin via the ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) control auxin distribution within the meristem, generating an instructive auxin minimum that positions the TZ [10]. We identify a cytokinin-dependent molecular mechanism that acts in the LRC to control the position of the TZ and meristem size. We show that auxin levels within the LRC cells depends on PIN-FORMED 5 (PIN5), a cytokinin-activated intracellular transporter that pumps auxin from the cytoplasm into the endoplasmic reticulum, and on irreversible auxin conjugation mediated by the IAA-amino synthase GRETCHEN HAGEN 3.17 (GH3.17). By titrating auxin in the LRC, the PIN5 and the GH3.17 genes control auxin levels in the entire root meristem. Overall, our results indicate that the LRC serves as an auxin sink that, under the control of cytokinin, regulates meristem size and root growth.
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Affiliation(s)
- Riccardo Di Mambro
- Department of Biology, University of Pisa - via L. Ghini, 13 - 56126 Pisa, Italy.
| | - Noemi Svolacchia
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Emanuela Pierdonati
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Elena Salvi
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Emanuela Pedrazzini
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche - Via Alfonso Corti, 12 - 20133 Milano, Italy
| | - Alessandro Vitale
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche - Via Alfonso Corti, 12 - 20133 Milano, Italy
| | - Serena Perilli
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Paolo Costantino
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Sabrina Sabatini
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy.
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Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Proc Natl Acad Sci U S A 2019; 116:3091-3099. [PMID: 30718437 DOI: 10.1073/pnas.1817621116] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light-dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C4 plants. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade upstream of SHORTROOT1, a key Kranz anatomy regulator. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of maize C4 enzyme genes and RUBISCO SMALL SUBUNIT2 Our study provides not only a powerful method but also novel insights into the regulatory networks underlying Kranz anatomy development and C4 photosynthesis.
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Qi L, Zhang X, Zhai H, Liu J, Wu F, Li C, Chen Q. Elongator Is Required for Root Stem Cell Maintenance by Regulating SHORTROOT Transcription. PLANT PHYSIOLOGY 2019; 179:220-232. [PMID: 30401723 PMCID: PMC6324240 DOI: 10.1104/pp.18.00534] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/29/2018] [Indexed: 05/26/2023]
Abstract
SHORTROOT (SHR) is essential for stem cell maintenance and radial patterning in Arabidopsis (Arabidopsis thaliana) roots, but how its expression is regulated is unknown. Here, we report that the Elongator complex, which consists of six subunits (ELP1 to ELP6), regulates the transcription of SHR Depletion of Elongator drastically reduced SHR expression and led to defective root stem cell maintenance and radial patterning. The importance of the nuclear localization of Elongator for its functioning, together with the insensitivity of the elp1 mutant to the transcription elongation inhibitor 6-azauracil, and the direct interaction of the ELP4 subunit with the carboxyl-terminal domain of RNA polymerase II, support the notion that Elongator plays important roles in transcription elongation. Indeed, we found that ELP3 associates with the premessenger RNA of SHR and that mutation of Elongator reduces the enrichment of RNA polymerase II on the SHR gene body. Moreover, Elongator interacted in vivo with SUPPRESSOR OF Ty4, a well-established transcription elongation factor that is recruited to the SHR locus. Together, these results demonstrate that Elongator acts in concert with SUPPRESSOR OF Ty4 to regulate the transcription of SHR.
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Affiliation(s)
- Linlin Qi
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyue Zhang
- University of the Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huawei Zhai
- University of the Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Fangming Wu
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanyou Li
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
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Lai YS, Stefano G, Zemelis-Durfee S, Ruberti C, Gibbons L, Brandizzi F. Systemic signaling contributes to the unfolded protein response of the plant endoplasmic reticulum. Nat Commun 2018; 9:3918. [PMID: 30254194 PMCID: PMC6156401 DOI: 10.1038/s41467-018-06289-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 08/29/2018] [Indexed: 01/06/2023] Open
Abstract
The unfolded protein response (UPR) of the endoplasmic reticulum constitutes a conserved and essential cytoprotective pathway designed to survive biotic and abiotic stresses that alter the proteostasis of the endoplasmic reticulum. The UPR is typically considered cell-autonomous and it is yet unclear whether it can also act systemically through non-cell autonomous signaling. We have addressed this question using a genetic approach coupled with micro-grafting and a suite of molecular reporters in the model plant species Arabidopsis thaliana. We show that the UPR has a non-cell autonomous component, and we demonstrate that this is partially mediated by the intercellular movement of the UPR transcription factor bZIP60 facilitating systemic UPR signaling. Therefore, in multicellular eukaryotes such as plants, non-cell autonomous UPR signaling relies on the systemic movement of at least a UPR transcriptional modulator.
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Affiliation(s)
- Ya-Shiuan Lai
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Giovanni Stefano
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA
| | - Starla Zemelis-Durfee
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Cristina Ruberti
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
| | - Lizzie Gibbons
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
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50
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Sedelnikova OV, Hughes TE, Langdale JA. Understanding the Genetic Basis of C 4 Kranz Anatomy with a View to Engineering C 3 Crops. Annu Rev Genet 2018; 52:249-270. [PMID: 30208293 DOI: 10.1146/annurev-genet-120417-031217] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One of the most remarkable examples of convergent evolution is the transition from C3 to C4 photosynthesis, an event that occurred on over 60 independent occasions. The evolution of C4 is particularly noteworthy because of the complexity of the developmental and metabolic changes that took place. In most cases, compartmentalized metabolic reactions were facilitated by the development of a distinct leaf anatomy known as Kranz. C4 Kranz anatomy differs from ancestral C3 anatomy with respect to vein spacing patterns across the leaf, cell-type specification around veins, and cell-specific organelle function. Here we review our current understanding of how Kranz anatomy evolved and how it develops, with a focus on studies that are dissecting the underlying genetic mechanisms. This research field has gained prominence in recent years because understanding the genetic regulation of Kranz may enable the C3-to-C4 transition to be engineered, an endeavor that would significantly enhance crop productivity.
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Affiliation(s)
- Olga V Sedelnikova
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom; , ,
| | - Thomas E Hughes
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom; , ,
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom; , ,
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