1
|
Guan J, Zhu J, Liu H, Yang H, Zhong S, Chen W, Yi X, Chen C, Tan F, Shen J, Luo P. Arogenate dehydratase isoforms strategically deregulate phenylalanine biosynthesis in Akebia trifoliata. Int J Biol Macromol 2024; 271:132587. [PMID: 38788880 DOI: 10.1016/j.ijbiomac.2024.132587] [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] [Received: 11/10/2023] [Revised: 05/01/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Arogenate dehydratase (ADT) is key for phenylalanine (Phe) biosynthesis in plants. To examine ADT components and function in Akebia trifoliata, a representative of Ranunculaceae, we first identified eight ADTs (AktADT1-8, encoding sequences varying from 1032 to 1962 bp) in the A. trifoliata reference genome and five proteins (AktADT1, AktADT4, AktADT7, AktADT8 and AktADT8s) with moonlighting prephenate dehydratase (PDT) activity and Km values varying from 0.43 to 2.17 mM. Structurally, two basic residue combinations (Val314/Ala317 and Ala314/Val317) in the PAC domain are essential for the moonlighting PDT activity of ADTs. Functionally, AktADT4 and AktADT8 successfully restored the wild-type phenotype of pha2, a knockout mutant of Saccharomyces cerevisiae. In addition, AktADTs are ubiquitously expressed, but their expression levels are tissue specific, and the half maximal inhibitory concentration (IC50) of Phe for AktADTs ranged from 49.81 to 331.17 μM. Both AktADT4 and AktADT8 and AktADT8s localized to chloroplast stromules and the cytosol, respectively, while the remaining AktADTs localized to the chloroplast stroma. These findings suggest that various strategies exist for regulating Phe biosynthesis in A. trifoliata. This provides a reasonable explanation for the high Phe content and insights for further genetic improvement of the edible fruits of A. trifoliata.
Collapse
Affiliation(s)
- Ju Guan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China; Cuisine Science Key Laboratory of Sichuan Province, Sichuan Tourism University, Chengdu 611130, China
| | - Jun Zhu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Hao Liu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China; Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu 611130, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Wei Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China; Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu 611130, China
| | - Xiaoxiao Yi
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Jinliang Shen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China.
| |
Collapse
|
2
|
Zhang Q, Zhong S, Dong Q, Yang H, Yang H, Tan F, Chen C, Ren T, Shen J, Cao G, Luo P. Identification of Photoperiod- and Phytohormone-Responsive DNA-Binding One Zinc Finger (Dof) Transcription Factors in Akebia trifoliata via Genome-Wide Expression Analysis. Int J Mol Sci 2023; 24:ijms24054973. [PMID: 36902404 PMCID: PMC10002981 DOI: 10.3390/ijms24054973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
As a kind of plant-specific transcription factor (TF), DNA-Binding One Zinc Finger (Dof) is widely involved in the response to environmental change, and as an evolutionarily important perennial plant species, Akebia trifoliata is ideal for studying environmental adaptation. In this study, a total of 41 AktDofs were identified in the A. trifoliata genome. First, the characteristics, including the length, exon number, and chromosomal distribution of the AktDofs and the isoelectric point (PI), amino acid number, molecular weight (MW), and conserved motifs of their putative proteins, were reported. Second, we found that all AktDofs evolutionarily underwent strong purifying selection, and many (33, 80.5%) of them were generated by whole-genome duplication (WGD). Third, we outlined their expression profiles by the use of available transcriptomic data and RT-qPCR analysis. Finally, we identified four candidate genes (AktDof21, AktDof20, AktDof36, and AktDof17) and three other candidate genes (AktDof26, AktDof16, and AktDof12) that respond to long day (LD) and darkness, respectively, and that are closely associated with phytohormone-regulating pathways. Overall, this research is the first to identify and characterize the AktDofs family and is very helpful for further research on A. trifoliata adaptation to environmental factors, especially photoperiod changes.
Collapse
Affiliation(s)
- Qiuyi Zhang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Qing Dong
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoxing Cao
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
- Correspondence:
| |
Collapse
|
3
|
Liu C, Zhang M, Zhao X. Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae). BMC PLANT BIOLOGY 2023; 23:87. [PMID: 36759771 PMCID: PMC9912670 DOI: 10.1186/s12870-023-04086-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Uraria Desv. belongs to the tribe Desmodieae (Fabaceae), a group of legume plants, some of which have medicinal properties. However, due to a lack of genomic information, the interspecific relationships, genetic diversity, population genetics, and identification of functional genes within Uraria species are still unclear. RESULTS Using RNA-Seq, a total of 66,026 Uraria lagopodioides unigenes with a total sequence content of 52,171,904 bp were obtained via de novo assembly and annotated using GO, KEGG, and KOG databases. 17,740 SSRs were identified from a set of 66,026 unigenes. Cross-species amplification showed that 54 out of 150 potential unigene-derived SSRs were transferable in Uraria, of which 19 polymorphic SSRs were developed. Cluster analysis based on polymorphisms successfully distinguished seven Uraria species and revealed their interspecific relationships. Seventeen samples of seven Uraria species were clustered into two monophyletic clades, and phylogenetic relationships of Uraria species based on unigene-derived SSRs were consistent with classifications based on morphological characteristics. CONCLUSIONS Unigenes annotated in the present study will provide new insights into the functional genomics of Uraria species. Meanwhile, the unigene-derived SSR markers developed here will be invaluable for assessing the genetic diversity and evolutionary history of Uraria and relatives.
Collapse
Affiliation(s)
- Chaoyu Liu
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Maomao Zhang
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Xueli Zhao
- College of Forestry, Southwest Forestry University, Kunming, 650224, China.
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650224, China.
| |
Collapse
|
4
|
Zhong S, Li B, Chen W, Wang L, Guan J, Wang Q, Yang Z, Yang H, Wang X, Yu X, Fu P, Liu H, Chen C, Tan F, Ren T, Shen J, Luo P. The chromosome-level genome of Akebia trifoliata as an important resource to study plant evolution and environmental adaptation in the Cretaceous. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1316-1330. [PMID: 36305286 DOI: 10.1111/tpj.16011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
The environmental adaptation of eudicots is the most reasonable explanation for why they compose the largest clade of modern plants (>70% of angiosperms), which indicates that the basal eudicots would be valuable and helpful to study their survival and ability to thrive throughout evolutionary processes. Here, we detected two whole-genome duplication (WGD) events in the high-quality assembled Akebia trifoliata genome (652.73 Mb) with 24 138 protein-coding genes based on the evidence of intragenomic and intergenomic collinearity, synonymous substitution rate (KS ) values and polyploidization and diploidization traces; these events putatively occurred at 85.15 and 146.43 million years ago (Mya). The integrated analysis of 16 species consisting of eight basal and eight core eudicots further revealed that there was a putative ancient WGD at the early stage of eudicots (temporarily designated θ) at 142.72 Mya, similar to the older WGD of Akebia trifoliata, and a putative core eudicot-specific WGD (temporarily designated ω). Functional enrichment analysis of retained duplicate genes following the θ event is suggestive of adaptation to the extreme environment change in both the carbon dioxide concentration and desiccation around the Jurassic-Cretaceous boundary, while the retained duplicate genes following the ω event is suggestive of adaptation to the extreme droughts, possibly leading to the rapid spread of eudicots in the mid-Cretaceous. Collectively, the A. trifoliata genome experienced two WGD events, and the older event may have occurred at the early stage of eudicots, which likely increased plant environmental adaptability and helped them survive in ancient extreme environments.
Collapse
Affiliation(s)
- Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road in Haidian District, 100193, Beijing, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Bin Li
- State Key Laboratory of Tree Breeding and Forest Genetics, Research Institute of Forestry, Chinese Academy of Forestry, 1 Dongxiaofu Xiangshan Road in Haidian District, 100091, Beijing, China
| | - Wei Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Lili Wang
- Biomarker Technologies Co., Ltd, 12 Fuqian Street in Shunyi District, 101300, Beijing, China
| | - Ju Guan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Zujun Yang
- Center for Information in Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 2006 Xiyuan Avenue in West Hi-Tech Zone, 611731, Chengdu, Sichuan Province, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Xianshu Wang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Xiaojiao Yu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Peng Fu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Hongchang Liu
- Guizhou Key Laboratory for Propagation and Cultivation of Medicinal Plants, Guizhou University, 2708 Huaxi South Avenue in Huaxi District, 550025, Guiyang, Guizhou province, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road in Wenjiang District, 611130, Chengdu, Sichuan Province, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road in Haidian District, 100193, Beijing, China
| |
Collapse
|
5
|
Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Akebiatrifoliata: A Bioinformatics Study. Genes (Basel) 2022; 13:genes13091540. [PMID: 36140708 PMCID: PMC9498614 DOI: 10.3390/genes13091540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
WRKY transcription factors have been found in most plants and play an important role in regulating organ growth and disease response. Outlining the profile of WRKY genes is a very useful project for studying morphogenesis and resistance formation. In the present study, a total of 63 WRKY genes consisting of 13 class I, 41 class II, and 9 class III genes were identified from the newly published A. trifoliata genome, of which 62 were physically distributed on all 16 chromosomes. Structurally, two AkWRKY genes (AkWRKY6 and AkWRKY52) contained four domains, and AkWRKY17 lacked the typical heptapeptide structure. Evolutionarily, 42, 16, and 5 AkWRKY genes experienced whole genome duplication (WGD) or fragmentation, dispersed duplication, and tandem duplication, respectively; 28 Ka/Ks values of 30 pairs of homologous genes were far lower than 1, while those of orthologous gene pairs between AkWRKY41 and AkWRKY52 reached up to 2.07. Transcriptome analysis showed that many of the genes were generally expressed at a low level in 12 fruit samples consisting of three tissues, including rind, flesh, and seeds, at four developmental stages, and interaction analysis between AkWRKY and AkNBS genes containing W-boxes suggested that AkWRKY24 could play a role in plant disease resistance by positively regulating AkNBS18. In summary, the WRKY gene family of A. trifoliata was systemically characterized for the first time, and the data and information obtained regarding AkWRKY could be very useful in further theoretically elucidating the molecular mechanisms of plant development and response to pathogens and practically improving favorable traits such as disease resistance.
Collapse
|