1
|
Orduña L, Li M, Navarro-Payá D, Zhang C, Santiago A, Romero P, Ramšak Ž, Magon G, Höll J, Merz P, Gruden K, Vannozzi A, Cantu D, Bogs J, Wong DCJ, Huang SSC, Matus JT. Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine. Plant J 2022; 110:529-547. [PMID: 35092714 DOI: 10.1111/tpj.15686] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 05/08/2023]
Abstract
The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.
Collapse
Affiliation(s)
- Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA
| | - David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Pablo Romero
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Gabriele Magon
- Department of Agronomy, Food, Natural resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, 35020, Italy
| | - Janine Höll
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Patrick Merz
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, 35020, Italy
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Jochen Bogs
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| |
Collapse
|
2
|
Li M, Hou L, Zhang C, Yang W, Liu X, Zhao H, Pang X, Li Y. Genome-Wide Identification of Direct Targets of ZjVND7 Reveals the Putative Roles of Whole-Genome Duplication in Sour Jujube in Regulating Xylem Vessel Differentiation and Drought Tolerance. Front Plant Sci 2022; 13:829765. [PMID: 35185994 PMCID: PMC8854171 DOI: 10.3389/fpls.2022.829765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/12/2022] [Indexed: 06/02/2023]
Abstract
The effects of whole-genome duplication span multiple levels. Previous study reported that the autotetraploid sour jujube exhibited superior drought tolerance than diploid. However, the difference in water transport system between diploids and autotetraploids and its mechanism remain unclear. Here, we found the number of xylem vessels and parenchyma cells in autotetraploid sour jujube increased to nearly twice that of diploid sour jujube, which may be closely related to the differences in xylem vessel differentiation-related ZjVND7 targets between the two ploidy types. Although the five enriched binding motifs are different, the most reliable motif in both diploid and autotetraploid sour jujube was CTTNAAG. Additionally, ZjVND7 targeted 236 and 321 genes in diploids and autotetraploids, respectively. More identified targeted genes of ZjVND7 were annotated to xylem development, secondary wall synthesis, cell death, cell division, and DNA endoreplication in autotetraploids than in diploids. SMR1 plays distinct roles in both proliferating and differentiated cells. Under drought stress, the binding signal of ZjVND7 to ZjSMR1 was stronger in autotetraploids than in diploids, and the fold-changes in the expression of ZjVND7 and ZjSMR1 were larger in the autotetraploids than in the diploids. These results suggested that the targeted regulation of ZjVND7 on ZjSMR1 may play valuable roles in autotetraploids in the response to drought stress. We hypothesized that the binding of ZjVND7 to ZjSMR1 might play a role in cell division and transdifferentiation from parenchyma cells to vessels in the xylem. This regulation could prolong the cell cycle and regulate endoreplication in response to drought stress and abscisic acid, which may be stronger in polyploids.
Collapse
Affiliation(s)
- Meng Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chenxing Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Weicong Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Xinru Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| |
Collapse
|
3
|
Yao J, Shen Z, Zhang Y, Wu X, Wang J, Sa G, Zhang Y, Zhang H, Deng C, Liu J, Hou S, Zhang Y, Zhang Y, Zhao N, Deng S, Lin S, Zhao R, Chen S. Populus euphratica WRKY1 binds the promoter of H+-ATPase gene to enhance gene expression and salt tolerance. J Exp Bot 2020. [PMID: 31680166 DOI: 10.5061/dryad.83ng085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plasma membrane proton pumps play a crucial role in maintaining ionic homeostasis in salt-resistant Populus euphratica under saline conditions. High levels of NaCl (200 mM) induced PeHA1 expression in P. euphratica roots and leaves. We isolated a 2022 bp promoter fragment upstream of the translational start of PeHA1 from P. euphratica. The promoter-reporter construct PeHA1-pro::GUS was transferred to tobacco plants, demonstrating that β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. DNA affinity purification sequencing revealed that PeWRKY1 protein targeted the PeHA1 gene. We assessed the salt-induced transcriptional response of PeWRKY1 and its interaction with PeHA1 in P. euphratica. PeWRKY1 binding to the PeHA1 W-box in the promoter region was verified by a yeast one-hybrid assay, EMSA, luciferase reporter assay, and virus-induced gene silencing. Transgenic tobacco plants overexpressing PeWRKY1 had improved expression of NtHA4, which has a cis-acting W-box in the regulatory region, and improved H+ pumping activity in both in vivo and in vitro assays. We conclude that salt stress up-regulated PeHA1 transcription due to the binding of PeWRKY1 to the W-box in the promoter region of PeHA1. Thus, we conclude that enhanced H+ pumping activity enabled salt-stressed plants to retain Na+ homeostasis.
Collapse
Affiliation(s)
- Jun Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Zedan Shen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yanli Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Xia Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Jianhui Wang
- Bluescape Hebei Biotech Co., Ltd, Baoding, PR China
| | - Gang Sa
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- Gansu Provincial Key Laboratory of Aridland Crop Sciences, Gansu Agricultural University, Lanzhou, PR China
| | - Yuhong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, PR China
| | - Huilong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Chen Deng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Jian Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Siyuan Hou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Ying Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Yinan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- Forestry Institute of New Technology, Chinese Academy of Forestry, Beijing, PR China
| | - Nan Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Shurong Deng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, PR China
| | - Shanzhi Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Rui Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Shaoliang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| |
Collapse
|
4
|
Yao J, Shen Z, Zhang Y, Wu X, Wang J, Sa G, Zhang Y, Zhang H, Deng C, Liu J, Hou S, Zhang Y, Zhang Y, Zhao N, Deng S, Lin S, Zhao R, Chen S. Populus euphratica WRKY1 binds the promoter of H+-ATPase gene to enhance gene expression and salt tolerance. J Exp Bot 2020; 71:1527-1539. [PMID: 31680166 PMCID: PMC7031066 DOI: 10.1093/jxb/erz493] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/06/2019] [Indexed: 05/22/2023]
Abstract
Plasma membrane proton pumps play a crucial role in maintaining ionic homeostasis in salt-resistant Populus euphratica under saline conditions. High levels of NaCl (200 mM) induced PeHA1 expression in P. euphratica roots and leaves. We isolated a 2022 bp promoter fragment upstream of the translational start of PeHA1 from P. euphratica. The promoter-reporter construct PeHA1-pro::GUS was transferred to tobacco plants, demonstrating that β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. DNA affinity purification sequencing revealed that PeWRKY1 protein targeted the PeHA1 gene. We assessed the salt-induced transcriptional response of PeWRKY1 and its interaction with PeHA1 in P. euphratica. PeWRKY1 binding to the PeHA1 W-box in the promoter region was verified by a yeast one-hybrid assay, EMSA, luciferase reporter assay, and virus-induced gene silencing. Transgenic tobacco plants overexpressing PeWRKY1 had improved expression of NtHA4, which has a cis-acting W-box in the regulatory region, and improved H+ pumping activity in both in vivo and in vitro assays. We conclude that salt stress up-regulated PeHA1 transcription due to the binding of PeWRKY1 to the W-box in the promoter region of PeHA1. Thus, we conclude that enhanced H+ pumping activity enabled salt-stressed plants to retain Na+ homeostasis.
Collapse
Affiliation(s)
- Jun Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Zedan Shen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yanli Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Xia Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Jianhui Wang
- Bluescape Hebei Biotech Co., Ltd, Baoding, PR China
| | - Gang Sa
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- Gansu Provincial Key Laboratory of Aridland Crop Sciences, Gansu Agricultural University, Lanzhou, PR China
| | - Yuhong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, PR China
| | - Huilong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Chen Deng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Jian Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Siyuan Hou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Ying Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Yinan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- Forestry Institute of New Technology, Chinese Academy of Forestry, Beijing, PR China
| | - Nan Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Shurong Deng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, PR China
| | - Shanzhi Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
| | - Rui Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- Correspondence: or
| | - Shaoliang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology (Box 162), Beijing Forestry University, Beijing, PR China
- Correspondence: or
| |
Collapse
|