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Long Y, Zeng J, Liu X, Wang Z, Tong Q, Zhou R, Liu X. Transcriptomic and metabolomic profiling reveals molecular regulatory network involved in flower development and phenotypic changes in two Lonicera macranthoides varieties. 3 Biotech 2024; 14:174. [PMID: 38855147 PMCID: PMC11153451 DOI: 10.1007/s13205-024-04019-1] [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: 01/23/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024] Open
Abstract
Due to the medicinal importance of the flowers of Xianglei type (XL) Lonicera macranthoides, it is important to understand the molecular mechanisms that underlie their development. In this study, we elucidated the transcriptomic and metabolomic mechanisms that underlie the flower development mechanism of two L. macranthoides varieties. In this study, 3435 common differentially expressed unigenes (DEGs) and 1138 metabolites were identified. These common DEGs were mainly enriched in plant hormone signal transduction pathways. Metabolomic analysis showed that amino acids were the main metabolites of differential accumulation in wild-type (WT) L. macranthoides, whereas in XL, they were flavonoids and phenylalanine metabolites. Genes and transcription factors (TFs), such as MYB340, histone deacetylase 1 (HDT1), small auxin-up RNA 32 (SAUR32), auxin response factor 6 (ARF6), PIN-LIKES 7 (PILS7), and WRKY6, likely drive metabolite accumulation. Plant hormone signals, especially auxin signals, and various TFs induce downstream flower organ recognition genes, resulting in a differentiation of the two L. macranthoides varieties in terms of their developmental trajectories. In addition, photoperiodic, autonomous, and plant hormone pathways jointly regulated the L. macranthoides corolla opening. SAUR32, Arabidopsis response regulator 9 (ARR9), Gibberellin receptor (GID1B), and Constans-like 10 (COL10) were closely related to the unfolding of the L. macranthoides corolla. These findings offer valuable understanding of the flower growth process of L. macranthoides and the excellent XL phenotypes at the molecular level. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04019-1.
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Affiliation(s)
- YuQing Long
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - Juan Zeng
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - XiaoRong Liu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - ZhiHui Wang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - QiaoZhen Tong
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
| | - RiBao Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
| | - XiangDan Liu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
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Yu L, Xia J, Jiang R, Wang J, Yuan X, Dong X, Chen Z, Zhao Z, Wu B, Zhan L, Zhang R, Tang K, Li J, Xu X. Genome-Wide Identification and Characterization of the CCT Gene Family in Rapeseed ( Brassica napus L.). Int J Mol Sci 2024; 25:5301. [PMID: 38791340 PMCID: PMC11121423 DOI: 10.3390/ijms25105301] [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: 02/29/2024] [Revised: 05/01/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
The CCT gene family is present in plants and is involved in biological processes such as flowering, circadian rhythm regulation, plant growth and development, and stress resistance. We identified 87, 62, 46, and 40 CCTs at the whole-genome level in B. napus, B. rapa, B. oleracea, and A. thaliana, respectively. The CCTs can be classified into five groups based on evolutionary relationships, and each of these groups can be further subdivided into three subfamilies (COL, CMF, and PRR) based on function. Our analysis of chromosome localization, gene structure, collinearity, cis-acting elements, and expression patterns in B. napus revealed that the distribution of the 87 BnaCCTs on the chromosomes of B. napus was uneven. Analysis of gene structure and conserved motifs revealed that, with the exception of a few genes that may have lost structural domains, the majority of genes within the same group exhibited similar structures and conserved domains. The gene collinearity analysis identified 72 orthologous genes, indicating gene duplication and expansion during the evolution of BnaCCTs. Analysis of cis-acting elements identified several elements related to abiotic and biotic stress, plant hormone response, and plant growth and development in the promoter regions of BnaCCTs. Expression pattern and protein interaction network analysis showed that BnaCCTs are differentially expressed in various tissues and under stress conditions. The PRR subfamily genes have the highest number of interacting proteins, indicating their significant role in the growth, development, and response to abiotic stress of B. napus.
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Affiliation(s)
- Liyiqi Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Jichun Xia
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Rujiao Jiang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Jiajia Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Xiaolong Yuan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Xinchao Dong
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Zhenjie Chen
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Zizheng Zhao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Boen Wu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Lanlan Zhan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Ranfeng Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Kang Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (L.Y.); (J.X.); (R.J.); (J.W.); (X.Y.); (X.D.); (Z.C.); (Z.Z.); (B.W.); (L.Z.); (R.Z.); (K.T.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
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Yang W, Zhou C, Guo Y, Niu S, El-Kassaby YA, Li W. Genome-wide identification of the Pinus tabuliformis CONSTANS-like gene family and their potential roles in reproductive cone development. Int J Biol Macromol 2024; 254:127621. [PMID: 37890750 DOI: 10.1016/j.ijbiomac.2023.127621] [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: 07/19/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023]
Abstract
The CONSTANS-like (COL) genes, as a core transcription factor in the photoperiod regulation pathway, play a key role in plant reproduction development. However, their molecular characterization has rarely been studied in Pinus tabuliformis. Here, 10 PtCOL genes were identified in the P. tabuliformis genome and multiple sequence alignments have indicated that the PtCOL proteins contained highly conserved B-BOX1 and CCT domains. Sequence similarity analysis showed that PtCOL1 and PtCOL3 had the higher similarity with Norway spruce COLs (PaCOL2 and PaCOL1) and Arabidopsis COLs (AtCOL3, 4 and 5), respectively. Phylogeny and gene structure analyses revealed that PtCOLs were divided into three subgroups, each with identical or similar distributions of exons, introns, and motifs. Moreover, 10 PtCOLs were distributed on 6 chromosomes and PtCOL9 has syntenic gene pairs in both Ginkgo biloba and Sequoiadendron giganteum. Interestingly, in transcriptome profiles, most PtCOLs exhibited a diurnal oscillation pattern under both long (LD) and short (SD) day conditions. Additionally, PtCOLs were highly expressed in needles and female cones, and showed different spatial expression patterns. Among the ten PtCOLs, PtCOL1/3 heterologous overexpression Arabidopsis displayed a delayed-flowering phenotype under SD, indicating that they are likely to play a crucial role in the reproductive development. Additionally, PtCOL1 and PtCOL3 were not only capable of interacting with each other, but they were each capable of interacting with themselves. Furthermore, PtCOL1 and PtCOL3 were also involved in the MADS-box protein-protein interaction (PPI) network in P. tabuliformis cone development. Direct interactions of PtDAL11 with PtCOL1/3 impeded PtCOL1/3 translocation into the nucleus. In summary, this study provided comprehensive understanding for the functions of the PtCOL gene family and revealed their biological roles in the photoperiod-dependent P. tabuliformis cone development.
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Affiliation(s)
- Wenbin Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Chengcheng Zhou
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yingtian Guo
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shihui Niu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Mishra AK, Kocábek T, Nath VS, Khan A, Matoušek J, Hazzouri KM, Sudalaimuthuasari N, Krofta K, Ludwig-Müller J, Amiri KMA. The multifaceted roles of R2R3 transcription factor HlMYB7 in the regulation of flavonoid and bitter acids biosynthesis, development and biotic stress tolerance in hop (Humulus lupulus L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107636. [PMID: 36958151 DOI: 10.1016/j.plaphy.2023.03.013] [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: 12/07/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Hop (Humulus lupulus) biosynthesizes the highly economically valuable secondary metabolites, which include flavonoids, bitter acids, polyphenols and essential oils. These compounds have important pharmacological properties and are widely implicated in the brewing industry owing to bittering flavor, floral aroma and preservative activity. Our previous studies documented that ternary MYB-bHLH-WD40 (MBW) and binary WRKY1-WD40 (WW) protein complexes transcriptionally regulate the accumulation of bitter acid (BA) and prenylflavonoids (PF). In the present study, we investigated the regulatory functions of the R2R3-MYB repressor HlMYB7 transcription factor, which contains a conserved N-terminal domain along with the repressive motif EAR, in regulating the PF- and BA-biosynthetic pathway and their accumulation in hop. Constitutive expression of HlMYB7 resulted in transcriptional repression of structural genes involved in the terminal steps of biosynthesis of PF and BA, as well as stunted growth, delayed flowering, and reduced tolerance to viroid infection in hop. Furthermore, yeast two-hybrid and transient reporter assays revealed that HlMYB7 targets both PF and BA pathway genes and suppresses MBW and WW protein complexes. Heterologous expression of HlMYB7 leads to down-regulation of structural genes of flavonoid pathway in Arabidopsis thaliana, including a decrease in anthocyanin content in Nicotiana tabacum. The combined results from functional and transcriptomic analyses highlight the important role of HlMYB7 in fine-tuning and balancing the accumulation of secondary metabolites at the transcriptional level, thus offer a plausible target for metabolic engineering in hop.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Vishnu Sukumari Nath
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Ahamed Khan
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Khaled M Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Karel Krofta
- Hop Research Institute, Co. Ltd, Kadaňská 2525, 438 46, Žatec, Czech Republic
| | | | - Khaled M A Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
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Liang RZ, Luo C, Liu Y, Hu WL, Guo YH, Yu HX, Lu TT, Chen SQ, Zhang XJ, He XH. Overexpression of two CONSTANS-like 2 (MiCOL2) genes from mango delays flowering and enhances tolerance to abiotic stress in transgenic Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111541. [PMID: 36417961 DOI: 10.1016/j.plantsci.2022.111541] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
The CO/COL gene family plays an important role in regulating photoperiod-dependent flowering time in plants. In this study, two COL2 gene homologs, MiCOL2A and MiCOL2B, were isolated from 'SiJiMi' mango, and their expression patterns and functions were characterized. The MiCOL2A and MiCOL2B genes both belonged to the group Ⅰ of CO/COL gene family. MiCOL2A and MiCOL2B exhibited distinct circadian rhythms and were highly expressed in leaves during the flowering induction period. Subcellular localization analysis revealed that MiCOL2A and MiCOL2B are localized in the nucleus. The overexpression of MiCOL2A and MiCOL2B significantly delayed flowering time in Arabidopsis under both long-day (LD) and short-day (SD) conditions. The MiCOL2A and MiCOL2B overexpression Arabidopsis plants exhibited more tolerance to slat and drought stress after abiotic stress treatments, with greater ROS scavenging capacity and protective enzyme activity, less cell damage and death and higher expression of stress response genes than wild type plants. Bimolecular fluorescence complementation (BiFC) analysis showed that MiCOL2A and MiCOL2B interacted with several stress-related proteins, including zinc finger protein 4 (MiZFP4), MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1) and RING zinc finger protein 34 (MiRZFP34). The results indicate that MiCOL2A and MiCOL2B are not only involved in flowering time but also play a positive role in abiotic stress responses in plants.
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Affiliation(s)
- Rong-Zhen Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Yuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Wan-Li Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Yi-Hang Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Hai-Xia Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Ting-Ting Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Shu-Quan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Xiu-Juan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Xin-Hua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China.
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Lee A, Jung H, Park HJ, Jo SH, Jung M, Kim YS, Cho HS. Their C-termini divide Brassica rapa FT-like proteins into FD-interacting and FD-independent proteins that have different effects on the floral transition. FRONTIERS IN PLANT SCIENCE 2023; 13:1091563. [PMID: 36714709 PMCID: PMC9878124 DOI: 10.3389/fpls.2022.1091563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Members of the FLOWERING LOCUS T (FT)-like clade of phosphatidylethanolamine-binding proteins (PEBPs) induce flowering by associating with the basic leucine zipper (bZIP) transcription factor FD and forming regulatory complexes in angiosperm species. However, the molecular mechanism of the FT-FD heterocomplex in Chinese cabbage (Brassica rapa ssp. pekinensis) is unknown. In this study, we identified 12 BrPEBP genes and focused our functional analysis on four BrFT-like genes by overexpressing them individually in an FT loss-of-function mutant in Arabidopsis thaliana. We determined that BrFT1 and BrFT2 promote flowering by upregulating the expression of floral meristem identity genes, whereas BrTSF and BrBFT, although close in sequence to their Arabidopsis counterparts, had no clear effect on flowering in either long- or short-day photoperiods. We also simultaneously genetically inactivated BrFT1 and BrFT2 in Chinese cabbage using CRISPR/Cas9-mediated genome editing, which revealed that BrFT1 and BrFT2 may play key roles in inflorescence organogenesis as well as in the transition to flowering. We show that BrFT-like proteins, except for BrTSF, are functionally divided into FD interactors and non-interactors based on the presence of three specific amino acids in their C termini, as evidenced by the observed interconversion when these amino acids are mutated. Overall, this study reveals that although BrFT-like homologs are conserved, they may have evolved to exert functionally diverse functions in flowering via their potential to be associated with FD or independently from FD in Brassica rapa.
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Affiliation(s)
- Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Min Jung
- Department of Biotechnology, NongWoo Bio, Anseong, Republic of Korea
| | - Youn-Sung Kim
- Department of Biotechnology, Jenong S&T, Anseong, Republic of Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
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Wang L, Yang C, Shan Q, Zhao M, Yu J, Li YF. Transcriptome-wide profiling of mRNA N 6-methyladenosine modification in rice panicles and flag leaves. Genomics 2023; 115:110542. [PMID: 36535337 DOI: 10.1016/j.ygeno.2022.110542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
N6-methyladenosine (m6A) modification is essential for plant growth and development. Exploring m6A methylation patterns in rice tissues is fundamental to understanding the regulatory effects of this modification. Here, we profiled the transcriptome-wide m6A landscapes of rice panicles at the booting stage (PB) and flowering stage (PF), and of flag leaves at the flowering stage (LF). The global m6A level differed significantly among the three tissues and was closely associated with the expression of writer and eraser genes. The methylated gene ratio was higher in the flag leaves than in the panicles. Compared with commonly methylated genes, tissue-specific methylated genes showed lower levels of both m6A modification and expression, and a preference for m6A deposition in the coding sequence region. The m6A profiles of the two organs had more distinct differences than the profiles of the same organ at different stages. A negative correlation between m6A levels and gene expression was observed in PF vs. PB but not in PF vs. LF, indicting the complicated regulatory effect of m6A on gene expression. The distinct expression patterns of m6A reader genes in different tissues indicate that readers may affect gene stability through binding. Overall, our findings demonstrated that m6A modification influences tissue function by regulating gene expression. Our findings provide valuable insights on the regulation and biological functions of m6A modifications in rice.
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Affiliation(s)
- Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China.
| | - Chenhui Yang
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Qianru Shan
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China.
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Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut ( Juglans mandshurica Maxim.). Int J Mol Sci 2022; 23:ijms23105433. [PMID: 35628244 PMCID: PMC9143237 DOI: 10.3390/ijms23105433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 12/18/2022] Open
Abstract
Flowers are imperative reproductive organs and play a key role in the propagation of offspring, along with the generation of several metabolic products in flowering plants. In Juglans mandshurica, the number and development of flowers directly affect the fruit yield and subsequently its commercial value. However, owing to the lack of genetic information, there are few studies on the reproductive biology of Juglans mandshurica, and the molecular regulatory mechanisms underlying the development of female and male inflorescence remain unclear. In this study, phytohormones and transcriptomic sequencing analyses at the three stages of female and male inflorescence growth were performed to understand the regulatory functions underlying flower development. Gibberellin is the most dominant phytohormone that regulates flower development. In total, 14,579 and 7188 differentially expressed genes were identified after analyzing the development of male and female flowers, respectively, wherein, 3241 were commonly expressed. Enrichment analysis for significantly enriched pathways suggested the roles of MAPK signaling, phytohormone signal transduction, and sugar metabolism. Genes involved in floral organ transition and flowering were obtained and analyzed; these mainly belonged to the M-type MADS-box gene family. Three flowering-related genes (SOC1/AGL20, ANT, and SVP) strongly interacted with transcription factors in the co-expression network. Two key CO genes (CO3 and CO1) were identified in the photoperiod pathway. We also identified two GA20xs genes, one SVP gene, and five AGL genes (AGL8, AGL9, AGL15, AGL19, and AGL42) that contributed to flower development. The findings are expected to provide a genetic basis for the studies on the regulatory networks and reproductive biology in inflorescence development for J. mandshurica.
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