1
|
Godbole RC, Kadam SB, Pable AA, Singh S, Barvkar VT. Phylogenomics of transcriptionally active AP2/ERF and bHLH transcription factors and study of their promoter regions in Nothapodytes nimmoniana (J.Graham) Mabb. Genome 2023; 66:235-250. [PMID: 37163758 DOI: 10.1139/gen-2023-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nothapodytes nimmoniana is a medicinally important plant producing anticancer monoterpene indole alkaloid (MIA), camptothecin (CPT). The CPT is synthesised through the strictosidine intermediate following the MIA pathway; however, transcriptional regulation of CPT pathway is still elusive in N. nimmoniana. Biosynthesis of MIA is regulated by various transcription factors (TFs) belonging to AP2/ERF, bHLH, MYB, and WRKY families. The present study identified transcriptionally active full-length 105 AP2/ERF and 68 bHLH family TFs from the N. nimmoniana. AP2/ERF TFs were divided into three subfamilies along with a soloist, while bHLH TFs were divided into 10 subfamilies according to their phylogenetic similarities. Three group IXa ERFs, Nn-ERF22, Nn-ERF29, and Nn-ERF41, one subfamily IVa TF Nn-bHLH7, and three subfamilies IIIe Nn-bHLH33, Nn-bHLH51, and Nn-bHLH52 clustered with the TFs regulating alkaloid biosynthesis in Catharanthus roseus, tomato, tobacco, and Artemisia annua. Expression of these TFs in N. nimmoniana was higher in roots, which is a primary CPT accumulating tissue. Moreover, genome skimming approach was used to reconstruct the promoter regions of candidate ERF genes to identify the cis-regulatory elements. The presence of G-boxes and other jasmonic acid-responsive elements in the promoter suggests the regulation of ERFs by bHLHs. The present study effectively generated and used genomics resource for characterisation of regulatory TFs from non-model medicinal plant.
Collapse
Affiliation(s)
- Rucha C Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Swapnil B Kadam
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Sudhir Singh
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| |
Collapse
|
2
|
Hao X, Wang C, Zhou W, Ruan Q, Xie C, Yang Y, Xiao C, Cai Y, Wang J, Wang Y, Zhang X, Maoz I, Kai G. OpNAC1 transcription factor regulates the biosynthesis of the anticancer drug camptothecin by targeting loganic acid O-methyltransferase in Ophiorrhiza pumila. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:133-149. [PMID: 36194508 DOI: 10.1111/jipb.13377] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Camptothecin (CPT) is an anticancer pentacyclic quinoline alkaloid widely used to treat cancer patients worldwide. However, the biosynthetic pathway and transcriptional regulation of camptothecin are largely unknown. Ophiorrhiza pumila, the herbaceous plant from the Rubiaceae family, has emerged as a model plant for studying camptothecin biosynthesis and regulation. In this study, a high-quality reference genome of O. pumila with estimated size of ~456.90 Mb was reported, and the accumulation level of camptothecin in roots was higher than that in stems and leaves. Based on its spatial distribution in the plant, we examined gene functions and expression by combining genomics with transcriptomic analysis. Two loganic acid O-methyltransferase (OpLAMTs) were identified in strictosidine-producing plant O. pumila, and enzyme catalysis assays showed that OpLAMT1 and not OpLAMT2 could convert loganic acid into loganin. Further knock-out of OpLAMT1 expression led to the elimination of loganin and camptothecin accumulation in O. pumila hairy roots. Four key residues were identified in OpLAMT1 protein crucial for the catalytic activity of loganic acid to loganin. By co-expression network, we identified a NAC transcription factor, OpNAC1, as a candidate gene for regulating camptothecin biosynthesis. Transgenic hairy roots and biochemical assays demonstrated that OpNAC1 suppressed OpLAMT1 expression. Here, we reported on two camptothecin metabolic engineering strategies paving the road for industrial-scale production of camptothecin in CPT-producing plants.
Collapse
Affiliation(s)
- Xiaolong Hao
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Can Wang
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Wei Zhou
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Qingyan Ruan
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chenhong Xie
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yinkai Yang
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chengyu Xiao
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yan Cai
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jingyi Wang
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yao Wang
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Itay Maoz
- Department of Postharvest Science, ARO, The Volcani Center, HaMaccabim Rd 68, POB 15159, Rishon LeZion, 7528809, Israel
| | - Guoyin Kai
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| |
Collapse
|
3
|
Godbole RC, Pable AA, Singh S, Barvkar VT. Interplay of transcription factors orchestrating the biosynthesis of plant alkaloids. 3 Biotech 2022; 12:250. [PMID: 36051988 PMCID: PMC9424429 DOI: 10.1007/s13205-022-03316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Plants produce a range of secondary metabolites primarily as defence molecules. A plant has to invest considerable energy to synthesise alkaloids, and sometimes they are even toxic to themselves. Hence, the biosynthesis of alkaloids is a spatiotemporally regulated process under quantitative feedback regulation which is accomplished by the signal reception, transcriptional/translational regulation, transport, storage and accumulation. The transcription factors (TFs) initiate the biosynthesis of alkaloids after appropriate cues. The present study recapitulates last decade understanding of the role of TFs in alkaloid biosynthesis. The present review discusses TF families, viz. AP2/ERF, bHLH, WRKY, MYB involved in the biosynthesis of various types of alkaloids. It also highlights the role of the jasmonic acid cascade and post-translational modifications of TF proteins. A thorough understanding of TFs will help us to decide a strategy to facilitate successful pathway manipulation and in vitro production.
Collapse
Affiliation(s)
- Rucha C. Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007 India
| | - Anupama A. Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007 India
| | - Sudhir Singh
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai, 400085 India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094 India
| | - Vitthal T. Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007 India
| |
Collapse
|
4
|
Wang H, Ni D, Shen J, Deng S, Xuan H, Wang C, Xu J, Zhou L, Guo N, Zhao J, Xing H. Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of GmAP2/ERF144 for Drought Tolerance in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:848766. [PMID: 35419020 PMCID: PMC8996232 DOI: 10.3389/fpls.2022.848766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/08/2022] [Indexed: 05/31/2023]
Abstract
Drought is a major environmental constraint that causes substantial reductions in plant growth and yield. Expression of stress-related genes is largely regulated by transcription factors (TFs), including in soybean [Glycine max (L.) Merr.]. In this study, 301 GmAP2/ERF genes that encode TFs were identified in the soybean genome. The TFs were divided into five categories according to their homology. Results of previous studies were then used to select the target gene GmAP2/ERF144 from among those up-regulated by drought and salt stress in the transcriptome. According to respective tissue expression analysis and subcellular determination, the gene was highly expressed in leaves and encoded a nuclear-localized protein. To validate the function of GmAP2/ERF144, the gene was overexpressed in soybean using Agrobacterium-mediated transformation. Compared with wild-type soybean, drought resistance of overexpression lines increased significantly. Under drought treatment, leaf relative water content was significantly higher in overexpressed lines than in the wild-type genotype, whereas malondialdehyde content and electrical conductivity were significantly lower than those in the wild type. Thus, drought resistance of transgenic soybean increased with overexpression of GmAP2/ERF144. To understand overall function of the gene, network analysis was used to predict the genes that interacted with GmAP2/ERF144. Reverse-transcription quantitative PCR showed that expression of those interacting genes in two transgenic lines was 3 to 30 times higher than that in the wild type. Therefore, GmAP2/ERF144 likely interacted with those genes; however, that conclusion needs to be verified in further specific experiments.
Collapse
|
5
|
Wen J, Lv J, Zhao K, Zhang X, Li Z, Zhang H, Huo J, Wan H, Wang Z, Zhu H, Deng M. Ethylene-Inducible AP2/ERF Transcription Factor Involved in the Capsaicinoid Biosynthesis in Capsicum. FRONTIERS IN PLANT SCIENCE 2022; 13:832669. [PMID: 35310674 PMCID: PMC8928445 DOI: 10.3389/fpls.2022.832669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/14/2022] [Indexed: 05/17/2023]
Abstract
Ethylene is very important in the process of plant development and regulates the biosynthesis of many secondary metabolites. In these regulatory mechanisms, transcription factors (TFs) that mediate ethylene signals play a very important role. Capsaicinoids (CAPs) are only synthesized and accumulated in Capsicum species, causing their fruit to have a special pungent taste, which can protect against attack from herbivores and pathogens. In this study, we identified the TF CcERF2, which is induced by ethylene, and demonstrated its regulatory effect on CAPs biosynthesis. Transcriptome sequencing analysis revealed that the expression patterns of CcERF2 and multiple genes associated with CAPs biosynthesis were basically the same. The spatiotemporal expression results showed CcERF2 was preferentially expressed in the placenta of the spicy fruit. Ethylene can induce the expression of CcERF2 and CAPs biosynthesis genes (CBGs). CcERF2 gene silencing and 1-methylcyclopropene (1-MCP) and pyrazinamide (PZA) treatments caused a decrease in expression of CBGs and a sharp decrease in content of CAPs. The results indicated that CcERF2 was indeed involved in the regulation of structural genes of the CAPs biosynthetic pathway.
Collapse
Affiliation(s)
- Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming, China
| | - Junheng Lv
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Kai Zhao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Xiang Zhang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Zuosen Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Hong Zhang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Jinlong Huo
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Hongjian Wan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ziran Wang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Haishan Zhu
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Minghua Deng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
- *Correspondence: Minghua Deng, , orcid.org/0000-0001-8293-9035
| |
Collapse
|
6
|
The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses. Genes (Basel) 2020; 11:genes11121464. [PMID: 33297327 PMCID: PMC7762271 DOI: 10.3390/genes11121464] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022] Open
Abstract
Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.
Collapse
|