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Singh S, Praveen A, Bhadrecha P. Genome-wide identification and analysis of SPL gene family in chickpea (Cicer arietinum L.). PROTOPLASMA 2024:10.1007/s00709-024-01936-z. [PMID: 38378886 DOI: 10.1007/s00709-024-01936-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
A transcription factor in plants encodes SQUAMOSA promoter binding protein-like (SPL) serves a broad spectrum of important roles for the plant, like, growth, flowering, and signal transduction. A gene family that encodes SPL proteins is documented in various model plant species, including Arabidopsis thaliana and Oryza sativa. Chickpea (Cicer arietinum), a leguminous crop, has not been thoroughly explored with regard to the SPL protein-encoding gene family. Chickpea SPL family genes were located and characterized computationally using a genomic database. Gene data of chickpea were obtained from the phytozome repository and was examined using bioinformatics methods. For investigating the possible roles of SPLs in chickpea, genome-wide characterization, expression, as well as structural analyses of this SPL gene family were performed. Cicer arietinum genome had 19 SPL genes, whereas, according to phylogenetic analysis, the SPLs in chickpea are segregated among four categories: Group-I has 2 introns, Group-II and IV have 1-2 introns (except CaSPL13 and CaSPL15 having 3 introns), and Group-III has 9 introns (except CaSPL1 and CaSPL11 with 1 and 8 introns, respectively). The SBP domain revealed that SPL proteins featured two zinc-binding sites, i.e., C3H and C2HC and one nuclear localization signal. All CaSPL proteins are found to contain highly conserved motifs, i.e., Motifs 1, 2, and 4, except CaSPL10 in which Motifs 1 and 4 were absent. Following analysis, it was found that Motifs 1 and 2 of the chickpea SBP domain are Zinc finger motifs, and Motif 4 includes a nuclear localization signal. All pairs of CaSPL paralogs developed by purifying selection. The CaSPL promoter investigation discovered cis-elements that are responsive to stress, light, and phytohormones. Examination of their expression patterns highlighted major CaSPLs to be evinced primarily among younger pods and flowers. Indicating their involvement in the plant's growth as well as development, along with their capacity to react as per different situations by handling the regulation of target gene's expression, several CaSPL genes are also expressed under certain stress conditions, namely, cold, salt, and drought. The majority of the CaSPL genes are widely expressed and play crucial roles in terms of the plant's growth, development, and responses to the environmental-stress conditions. Our work provides extensive insight into the gene family CaSPL, which might facilitate further studies related to the evolution and functions of the SPL genes for chickpea and other plant species.
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Affiliation(s)
- Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, 203201, U.P., India.
| | - Afsana Praveen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 67, India
| | - Pooja Bhadrecha
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
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Li X, Wang Z, Sun S, Dai Z, Zhang J, Wang W, Peng K, Geng W, Xia S, Liu Q, Zhai H, Gao S, Zhao N, Tian F, Zhang H, He S. IbNIEL-mediated degradation of IbNAC087 regulates jasmonic acid-dependent salt and drought tolerance in sweet potato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:176-195. [PMID: 38294064 DOI: 10.1111/jipb.13612] [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: 08/12/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
Sweet potato (Ipomoea batatas [L.] Lam.) is a crucial staple and bioenergy crop. Its abiotic stress tolerance holds significant importance in fully utilizing marginal lands. Transcriptional processes regulate abiotic stress responses, yet the molecular regulatory mechanisms in sweet potato remain unclear. In this study, a NAC (NAM, ATAF1/2, and CUC2) transcription factor, IbNAC087, was identified, which is commonly upregulated in salt- and drought-tolerant germplasms. Overexpression of IbNAC087 increased salt and drought tolerance by increasing jasmonic acid (JA) accumulation and activating reactive oxygen species (ROS) scavenging, whereas silencing this gene resulted in opposite phenotypes. JA-rich IbNAC087-OE (overexpression) plants exhibited more stomatal closure than wild-type (WT) and IbNAC087-Ri plants under NaCl, polyethylene glycol, and methyl jasmonate treatments. IbNAC087 functions as a nuclear transcriptional activator and directly activates the expression of the key JA biosynthesis-related genes lipoxygenase (IbLOX) and allene oxide synthase (IbAOS). Moreover, IbNAC087 physically interacted with a RING-type E3 ubiquitin ligase NAC087-INTERACTING E3 LIGASE (IbNIEL), negatively regulating salt and drought tolerance in sweet potato. IbNIEL ubiquitinated IbNAC087 to promote 26S proteasome degradation, which weakened its activation on IbLOX and IbAOS. The findings provide insights into the mechanism underlying the IbNIEL-IbNAC087 module regulation of JA-dependent salt and drought response in sweet potato and provide candidate genes for improving abiotic stress tolerance in crops.
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Affiliation(s)
- Xu Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Zhen Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Sifan Sun
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhuoru Dai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Wenbin Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Kui Peng
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wenhao Geng
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Shuanghong Xia
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
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Tang H, Jing D, Liu C, Xie X, Zhang L, Chen X, Li C. Genome-Wide Identification and Expression Analyses of the FAR1/FHY3 Gene Family Provide Insight into Inflorescence Development in Maize. Curr Issues Mol Biol 2024; 46:430-449. [PMID: 38248329 PMCID: PMC10814199 DOI: 10.3390/cimb46010027] [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: 12/04/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in Arabidopsis thaliana and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 ZmFAR1 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 ZmFAR1 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these ZmFAR1 genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six ZmFAR1 genes (ZmFAR1-1, ZmFAR1-10, ZmFAR1-11, ZmFAR1-12, ZmFAR1-14, and ZmFAR1-15) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in ZmFAR1-14 and ZmFAR1-9, which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding.
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Affiliation(s)
- Huaijun Tang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - De Jing
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Lei Zhang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Xunji Chen
- Institute of Nuclear and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Changyu Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
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Yan Z, Li K, Li Y, Wang W, Leng B, Yao G, Zhang F, Mu C, Liu X. The ZmbHLH32-ZmIAA9-ZmARF1 module regulates salt tolerance in maize. Int J Biol Macromol 2023; 253:126978. [PMID: 37741480 DOI: 10.1016/j.ijbiomac.2023.126978] [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: 06/29/2023] [Revised: 09/02/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
The growth and productivity of maize (Zea mays), along with other crop plants, can be significantly hindered by salt stress. Nevertheless, the precise molecular mechanism underlying salt tolerance in maize has yet to be fully elucidated. Hence, it was attempted to identify ZmIAA9, a member of the maize Aux/IAA gene family, as a positive regulator of salt tolerance in maize, which was accompanied by the increased ROS detoxification and elevated transcript abundances of ROS scavenging genes. Molecular and biochemical assays have provided compelling evidence that ZmbHLH32, a transcription factor belonging to the bHLH family, was capable of binding directly to the promoter region of ZmIAA9, thereby activating its expression. This interaction between ZmbHLH32 and ZmIAA9 could be critical for the regulation of salt tolerance in maize. As expected, overexpression of ZmbHLH32 led to the enhanced salt tolerance. In contrast, decreased salt tolerance was attained after application of knockout mutants of ZmbHLH32. Furthermore, ZmARF1, which could act as a downstream of ZmIAA9, was found to physically interact with ZmIAA9 and repress the expression levels of ROS scavenging genes. Thus, our work uncovers a novel mechanism of ZmbHLH32-ZmIAA9-ZmARF1 module-mediated salt tolerance in maize, which can be exploited for breeding salt-tolerant maize varieties.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Ke Li
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Yanli Li
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Wenli Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
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5
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Yang X, Hu R, Sun F, Shen S, Zhang M, Liu Y, Zhang Y, Du H, Lu K, Qu C, Yin N. Identification of the High-Affinity Potassium Transporter Gene Family (HKT) in Brassica U-Triangle Species and Its Potential Roles in Abiotic Stress in Brassica napus L. PLANTS (BASEL, SWITZERLAND) 2023; 12:3768. [PMID: 37960124 PMCID: PMC10649870 DOI: 10.3390/plants12213768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
Members of the high-affinity potassium transporter (HKT) protein family regulate the uptake and homeostasis of sodium and potassium ions, but little research describes their roles in response to abiotic stresses in rapeseed (Brassica napus L.). In this study, we identified and characterized a total of 36 HKT genes from the species comprising the triangle of U model (U-triangle species): B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinata. We analyzed the phylogenetic relationships, gene structures, motif compositions, and chromosomal distributions of the HKT family members of rapeseed. Based on their phylogenetic relationships and assemblage of functional domains, we classified the HKT members into four subgroups, HKT1;1 to HKT1;4. Analysis of the nonsynonymous substitutions (Ka), synonymous substitutions (Ks), and the Ka/Ks ratios of HKT gene pairs suggested that these genes have experienced strong purifying selective pressure after duplication, with their evolutionary relationships supporting the U-triangle theory. Furthermore, the expression profiles of BnaHKT genes varies among potassium, phytohormone and heavy-metal treatment. Their repression provides resistance to heavy-metal stress, possibly by limiting uptake. Our results systematically reveal the characteristics of HKT family proteins and their encoding genes in six Brassica species and lay a foundation for further exploration of the role of HKT family genes in heavy-metal tolerance.
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Affiliation(s)
- Xiaoran Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Ran Hu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Fujun Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Shulin Shen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Mengzhen Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Yiwei Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Yi Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Hai Du
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Nengwen Yin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (X.Y.); (R.H.); (F.S.); (S.S.); (M.Z.); (Y.L.); (Y.Z.); (H.D.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Nawade B, Bosamia TC, Lee JH, Jang JH, Lee OR. Genome-wide characterization of the soybean DOMAIN OF UNKNOWN FUNCTION 679 membrane protein gene family highlights their potential involvement in growth and stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1216082. [PMID: 37745995 PMCID: PMC10514519 DOI: 10.3389/fpls.2023.1216082] [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: 05/03/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023]
Abstract
The DMP (DUF679 membrane proteins) family is a plant-specific gene family that encodes membrane proteins. The DMP family genes are suggested to be involved in various programmed cell death processes and gamete fusion during double fertilization in Arabidopsis. However, their functional relevance in other crops remains unknown. This study identified 14 genes from the DMP family in soybean (Glycine max) and characterized their physiochemical properties, subcellular location, gene structure, and promoter regions using bioinformatics tools. Additionally, their tissue-specific and stress-responsive expressions were analyzed using publicly available transcriptome data. Phylogenetic analysis of 198 DMPs from monocots and dicots revealed six clades, with clade-I encoding senescence-related AtDMP1/2 orthologues and clade-II including pollen-specific AtDMP8/9 orthologues. The largest clade, clade-III, predominantly included monocot DMPs, while monocot- and dicot-specific DMPs were assembled in clade-IV and clade-VI, respectively. Evolutionary analysis suggests that soybean GmDMPs underwent purifying selection during evolution. Using 68 transcriptome datasets, expression profiling revealed expression in diverse tissues and distinct responses to abiotic and biotic stresses. The genes Glyma.09G237500 and Glyma.18G098300 showed pistil-abundant expression by qPCR, suggesting they could be potential targets for female organ-mediated haploid induction. Furthermore, cis-acting regulatory elements primarily related to stress-, hormone-, and light-induced pathways regulate GmDMPs, which is consistent with their divergent expression and suggests involvement in growth and stress responses. Overall, our study provides a comprehensive report on the soybean GmDMP family and a framework for further biological functional analysis of DMP genes in soybean or other crops.
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Affiliation(s)
- Bhagwat Nawade
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Tejas C. Bosamia
- Plant Omics Division, Council of Scientific and Industrial Research-Central Salt and Marine Chemical Research Institute (CSIR-CSMCRI), Bhavnagar, Gujarat, India
| | - Jae Hyun Lee
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Jin Hoon Jang
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
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Nguyen TT, Pham DT, Nguyen NH, Do PT, To HTM. The Germin-like protein gene OsGER4 is involved in heat stress response in rice root development. Funct Integr Genomics 2023; 23:271. [PMID: 37561192 DOI: 10.1007/s10142-023-01201-1] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important dietary carbohydrate sources for half of the world's population. However, it is not well adapted to environmental stress conditions, necessitating to create new and improved varieties to help ensure sufficient rice production in the face of rising populations and shrinking arable land. Recently, the development of the CRISPR/Cas9 gene editing system has allowed researchers to study functional genomics and engineer new rice varieties with great efficiency compared to conventional methods. In this study, we investigate the involvement of OsGER4, a germin-like protein identified by a genome-wide association study that is associated with rice root development under a stress hormone jasmonic acids treatment. Analysis of the OsGER4 promoter region revealed a series of regulatory elements that connect this gene to ABA signaling and water stress response. Under heat stress, osger4 mutant lines produce a significantly lower crown root than wild-type Kitaake rice. The loss of OsGER4 also led to the reduction of lateral root development. Using the GUS promoter line, OsGER4 expression was detected in the epidermis of the crown root primordial, in the stele of the crown root, and subsequently in the primordial of the lateral root. Taken together, these results illustrated the involvement of OsGER4 in root development under heat stress by regulating auxin transport through plasmodesmata, under control by both ABA and auxin signaling.
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Affiliation(s)
- Trang Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Dan The Pham
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Nhung Hong Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam.
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8
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Yan C, Yang T, Wang B, Yang H, Wang J, Yu Q. Genome-Wide Identification of the WD40 Gene Family in Tomato ( Solanum lycopersicum L.). Genes (Basel) 2023; 14:1273. [PMID: 37372453 DOI: 10.3390/genes14061273] [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: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
WD40 proteins are a superfamily of regulatory proteins widely found in eukaryotes that play an important role in regulating plant growth and development. However, the systematic identification and characterization of WD40 proteins in tomato (Solanum lycopersicum L.) have not been reported. In the present study, we identified 207 WD40 genes in the tomatoes genome and analyzed their chromosomal location, gene structure and evolutionary relationships. A total of 207 tomato WD40 genes were classified by structural domain and phylogenetic tree analyses into five clusters and 12 subfamilies and were found to be unevenly distributed across the 12 tomato chromosomes. We identified six tandem duplication gene pairs and 24 segmental duplication pairs in the WD40 gene family, with segmental duplication being the major mode of expansion in tomatoes. Ka/Ks analysis revealed that paralogs and orthologs of WD40 family genes underwent mainly purifying selection during the evolutionary process. RNA-seq data from different tissues and developmental periods of tomato fruit development showed tissue-specific expression of WD40 genes. In addition, we constructed four coexpression networks according to the transcriptome and metabolome data for WD40 proteins involved in fruit development that may be related to total soluble solid formation. The results provide a comprehensive overview of the tomato WD40 gene family and will provide valuable information for the validation of the function of tomato WD40 genes in fruit development.
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Affiliation(s)
- Cunyao Yan
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Haitao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830000, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830000, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830000, China
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9
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Kapoor P, Rakhra G, Kumar V, Joshi R, Gupta M, Rakhra G. Insights into the functional characterization of DIR proteins through genome-wide in silico and evolutionary studies: a systematic review. Funct Integr Genomics 2023; 23:166. [PMID: 37202648 DOI: 10.1007/s10142-023-01095-z] [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: 03/22/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Dirigent proteins (DIRs) are a new class of proteins that were identified during the 8-8' lignan biosynthetic pathway and involves the formation of ( +) or ( -)-pinoresinol through stereoselective coupling from E-coniferyl alcohol. These proteins are known to play a vital role in the development and stress response in plants. Various studies have reported the functional and structural characterization of dirigent gene family in different plants using in silico approaches. Here, we have summarized the importance of dirigent proteins in plants and their role in plant stress tolerance by analyzing the genome-wide analysis including gene structure, mapping of chromosomes, phylogenetic evolution, conserved motifs, gene structure, and gene duplications in important plants. Overall, this review would help to compare and clarify the molecular and evolutionary characteristics of dirigent gene family in different plants.
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Affiliation(s)
- Preedhi Kapoor
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Gurseen Rakhra
- Department of Nutrition and Dietetics, Faculty of Allied Health Sciences, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Vineet Kumar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Ridhi Joshi
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Mahiti Gupta
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, India
| | - Gurmeen Rakhra
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India.
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, India.
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10
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Welling MT, Deseo MA, O’Brien M, Clifton J, Bacic A, Doblin MS. Metabolomic analysis of methyl jasmonate treatment on phytocannabinoid production in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1110144. [PMID: 37025140 PMCID: PMC10070988 DOI: 10.3389/fpls.2023.1110144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Cannabis sativa is a multi-use and chemically complex plant which is utilized for food, fiber, and medicine. Plants produce a class of psychoactive and medicinally important specialized metabolites referred to as phytocannabinoids (PCs). The phytohormone methyl jasmonate (MeJA) is a naturally occurring methyl ester of jasmonic acid and a product of oxylipin biosynthesis which initiates and regulates the biosynthesis of a broad range of specialized metabolites across a number of diverse plant lineages. While the effects of exogenous MeJA application on PC production has been reported, treatments have been constrained to a narrow molar range and to the targeted analysis of a small number of compounds. Using high-resolution mass spectrometry with data-dependent acquisition, we examined the global metabolomic effects of MeJA in C. sativa to explore oxylipin-mediated regulation of PC biosynthesis and accumulation. A dose-response relationship was observed, with an almost two-fold increase in PC content found in inflorescences of female clones treated with 15 mM MeJA compared to the control group. Comparison of the inflorescence metabolome across MeJA treatments coupled with targeted transcript analysis was used to elucidate key regulatory components contributing to PC production and metabolism more broadly. Revealing these biological signatures improves our understanding of the role of the oxylipin pathway in C. sativa and provides putative molecular targets for the metabolic engineering and optimization of chemical phenotype for medicinal and industrial end-uses.
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11
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Guo X, Li Q, Yan B, Wang Y, Wang S, Xiong F, Zhang C, Zhang Y, Guo L. Mild shading promotes sesquiterpenoid synthesis and accumulation in Atractylodes lancea by regulating photosynthesis and phytohormones. Sci Rep 2022; 12:21648. [PMID: 36522369 PMCID: PMC9755305 DOI: 10.1038/s41598-022-25494-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Atractylodes lancea rhizome (AR) has high medicinal and economic value. A previous study has reported that the accumulation of sesquiterpenoids in AR has obvious advantages under bamboo canopy. A concrete shade value to promote the cultivation of high-quality AR has not been established. In this study, 80% shading was screened at six different light intensities (100%, 80%, 60%, 40%, 20%, 7%), and the mechanism was explored in terms of photosynthetic efficiency and phytohormones levels. The results indicated that the total sesquiterpenoid content of 80% mild shading increased by 58%, 52%, and 35%, respectively, compared to 100% strong light in seedling, expansion, and harvest stages and increased by 144%, 178%, and 94%, respectively, compared with 7% low light. The sesquiterpenoids hinesol and β-eudesmol contributed approximately 70% to the differential contribution ratio between mild shading and strong light (100%) or between mild shading and low light (7%). Furthermore, HMGR, DXR, and FPPS genes, which regulate sesquiterpenoid synthesis, were significantly upregulated in 80% mild shading. Transpiration rate; the intercellular CO2 concentration; net photosynthetic rate; and levels of jasmonic acid, abscisic acid, and gibberellin were strongly correlated (r > 0.85) with sesquiterpenoid accumulation. Cis-acting elements responding to light and phytohormones were present within the promoter regions of HMGR, DXR, and FPPS. Therefore, 80% shading promotes the synthesis and accumulation of sesquiterpenoids in AR by regulating photosynthetic efficiency and phytohormone production, thereby promoting transcriptional expression.
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Affiliation(s)
- Xiuzhi Guo
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Qiang Li
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Binbin Yan
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Yuefeng Wang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Sheng Wang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Feng Xiong
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Chengcai Zhang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Yan Zhang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Lanping Guo
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
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12
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Sultana MS, Mazarei M, Millwood RJ, Liu W, Hewezi T, Stewart CN. Functional analysis of soybean cyst nematode-inducible synthetic promoters and their regulation by biotic and abiotic stimuli in transgenic soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2022; 13:988048. [PMID: 36160998 PMCID: PMC9501883 DOI: 10.3389/fpls.2022.988048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
We previously identified cis-regulatory motifs in the soybean (Glycine max) genome during interaction between soybean and soybean cyst nematode (SCN), Heterodera glycines. The regulatory motifs were used to develop synthetic promoters, and their inducibility in response to SCN infection was shown in transgenic soybean hairy roots. Here, we studied the functionality of two SCN-inducible synthetic promoters; 4 × M1.1 (TAAAATAAAGTTCTTTAATT) and 4 × M2.3 (ATATAATTAAGT) each fused to the -46 CaMV35S core sequence in transgenic soybean. Histochemical GUS analyses of transgenic soybean plants containing the individual synthetic promoter::GUS construct revealed that under unstressed condition, no GUS activity is present in leaves and roots. While upon nematode infection, the synthetic promoters direct GUS expression to roots predominantly in the nematode feeding structures induced by the SCN and by the root-knot nematode (RKN), Meloidogyne incognita. There were no differences in GUS activity in leaves between nematode-infected and non-infected plants. Furthermore, we examined the specificity of the synthetic promoters in response to various biotic (insect: fall armyworm, Spodoptera frugiperda; and bacteria: Pseudomonas syringe pv. glycinea, P. syringe pv. tomato, and P. marginalis) stresses. Additionally, we examined the specificity to various abiotic (dehydration, salt, cold, wounding) as well as to the signal molecules salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid (ABA) in the transgenic plants. Our wide-range analyses provide insights into the potential applications of synthetic promoter engineering for conditional expression of transgenes leading to transgenic crop development for resistance improvement in plant.
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Affiliation(s)
- Mst Shamira Sultana
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Reginald J. Millwood
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
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Genome-wide analysis of the CAD gene family reveals two bona fide CAD genes in oil palm. 3 Biotech 2022; 12:149. [PMID: 35747504 PMCID: PMC9209623 DOI: 10.1007/s13205-022-03208-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/21/2022] [Indexed: 11/01/2022] Open
Abstract
Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis in plants. In this study, genome-wide analysis was performed to identify CAD genes in oil palm (Elaeis guineensis). Phylogenetic analysis was then conducted to select the bona fide EgCADs. The bona fide EgCAD genes and their respective 5' flanking regions were cloned and analysed. Their expression profiles were evaluated in various organs using RT-PCR. Seven EgCAD genes (EgCAD1-7) were identified and divided into four phylogenetic groups. EgCAD1 and EgCAD2 display high sequence similarities with other bona fide CADs and possess all the signature motifs of the bona fide CAD. They also display similar 3D protein structures. Gene expression analysis showed that EgCAD1 was expressed most abundantly in the root tissues, while EgCAD2 was expressed constitutively in all the tissues studied. EgCAD1 possesses only one transcription start site, while EgCAD2 has five. Interestingly, a TC microsatellite was found in the 5' flanking region of EgCAD2. The 5' flanking regions of EgCAD1 and EgCAD2 contain lignin-associated regulatory elements i.e. AC-elements, and other defence-related motifs, including W-box, GT-1 motif and CGTCA-motif. Altogether, these results imply that EgCAD1 and EgCAD2 are bona fide CAD involved in lignin biosynthesis during the normal development of oil palm and in response to stresses. Our findings shed some light on the roles of the bona fide CAD genes in oil palm and pave the way for manipulating lignin content in oil palm through a genetic approach. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03208-0.
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Mishra DK, Srivastava R, Pandey BK, Verma PC, Sawant SV. Identification and validation of the wound and insect bite early inducible promoter from Arabidopsis thaliana. 3 Biotech 2022; 12:74. [PMID: 35251877 PMCID: PMC8861216 DOI: 10.1007/s13205-022-03143-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/07/2022] [Indexed: 11/01/2022] Open
Abstract
A wound-inducible promoter facilitates the regulated gene expression at the targeted site during the time of mechanical stress or infestation by the pathogen. The present work has aimed to identify a wound-inducible promoter that expresses at early time points preceding wound-stress treatment in Arabidopsis thaliana. The computational analysis of microarray data (GSE5627) resulted in the identification of five early inducible genes, viz., AT1G17380, AT1G80440, AT2G43530, AT3G48360, and AT5G13220. The RT-PCR analysis showed AT5G13220 (JASMONATE-ASSOCIATED 1) gene induced at a significantly higher level post 30 min of wounding. Thus, the promoter of the highly induced and early expressed wound-inducible gene, AT5G13220 (named PW220), was characterized by fusing with β-glucuronidase (gusA) reporter or Cry1EC genes. The fluorometric analysis and histochemical staining of the gusA gene and quantitative estimation of Cry1EC protein in Nicotiana tabacum transgenic lines confirmed wound-induced expression characteristic of the selected promoter. Insect bioassay suggested that wound-inducible and constitutive expression of Cry1EC protein in transgenic lines showed a similar level of protection against different instar Spodoptera litura larvae. Furthermore, we identified that abscisic acid influenced the wound-specific expression of the selected PW220 promoter in the transgenic lines, which correlates with the presence of conserved cis-regulatory elements associated with dehydration and abscisic acid responses. Altogether, our results suggested that the wound-inducible promoter PW220 provides an excellent alternative for developing insect-tolerant transgenic crops in the future. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03143-0.
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Affiliation(s)
- Devesh Kumar Mishra
- grid.417642.20000 0000 9068 0476Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India ,grid.469887.c0000 0004 7744 2771AcSIR-Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India ,Present Address: Department of Botany. School of Applied Sciences, Om Sterling Global University, Hisar, Haryana 125001 India
| | - Rakesh Srivastava
- grid.417642.20000 0000 9068 0476Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India
| | - Bhoopendra K. Pandey
- grid.417642.20000 0000 9068 0476Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India ,grid.469887.c0000 0004 7744 2771AcSIR-Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
| | - Praveen Chandra Verma
- grid.417642.20000 0000 9068 0476Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India ,grid.469887.c0000 0004 7744 2771AcSIR-Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
| | - Samir Vishwanath Sawant
- grid.417642.20000 0000 9068 0476Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India ,grid.469887.c0000 0004 7744 2771AcSIR-Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
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15
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Chen H, Ge W. Identification, Molecular Characteristics, and Evolution of GRF Gene Family in Foxtail Millet (Setaria italica L.). Front Genet 2022; 12:727674. [PMID: 35185998 PMCID: PMC8851420 DOI: 10.3389/fgene.2021.727674] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Growth-regulating factor (GRF) is a multigene family that plays a vital role in the growth and development of plants. In the past, the GRF family of many plants has been studied. However, there is not a report about identification and evolution of GRF in foxtail millet (Setaria italia). Here, we identified 10 GRF genes in foxtail millet. Seven (70.00%) were regulated by Sit-miR396, and there were 19 optimal codons in GRFs of foxtail millet. Additionally, we found that WGD or segmental duplication have affected GRFs in foxtail millet between 15.07 and 45.97 million years ago. Regarding the GRF gene family of land plants, we identified a total of 157 GRF genes in 15 representative land plants. We found that GRF gene family originated from Group E, and the GRF gene family in monocots was gradually shrinking. Also, more loss resulted from the small number of GRF genes in lower plants. Exploring the evolution of GRF and functional analysis in the foxtail millet help us to understand GRF better and make a further study about the mechanism of GRF. These results provide a basis for the genetic improvement of foxtail millet and indicate an improvement of the yield.
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Dong D, Zhao Y, Teng K, Tan P, Liu Z, Yang Z, Han L, Chao Y. Expression of ZjPSY, a Phytoene Synthase Gene from Zoysia japonica Affects Plant Height and Photosynthetic Pigment Contents. PLANTS (BASEL, SWITZERLAND) 2022; 11:395. [PMID: 35161377 PMCID: PMC8840084 DOI: 10.3390/plants11030395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Phytoene synthase (PSY) is a key limiting enzyme in the carotenoid biosynthesis pathway for regulating phytoene synthesis. In this study, ZjPSY was isolated and identified from Zoysia japonica, an important lawn grass species. ZjPSY cDNA was 1230 bp in length, corresponding to 409 amino acids. ZjPSY showed higher expression in young leaves and was downregulated after GA3, ABA, SA, and MeJA treatments, exhibiting a sensitivity to plant hormones. Regulatory elements of light and plant hormone were found in the upstream of ZjPSY CDS. Expression of ZjPSY in Arabidopsis thaliana protein led to carotenoid accumulation and altered expression of genes involved in the carotenoid pathway. Under no-treatment condition, salt treatment, and drought treatment, transgenic plants exhibited yellowing, dwarfing phenotypes. The carotenoid content of transgenic plants was significantly higher than that of wild-type under salt stress and no-treatment condition. Yeast two-hybrid screening identified a novel interacting partner ZjJ2 (DNAJ homologue 2), which encodes heat-shock protein 40 (HSP40). Taken together, this study suggested that ZjPSY may affect plant height and play an important role in carotenoid synthesis. These results broadened the understanding of carotenoid synthesis pathways and laid a foundation for the exploration and utilization of the PSY gene.
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Affiliation(s)
- Di Dong
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Yuhong Zhao
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China;
| | - Ke Teng
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100083, China
| | - Penghui Tan
- Beijing Chaoyang Foreign Language School, Beijing 100101, China;
| | - Zhuocheng Liu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Zhuoxiong Yang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
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Wang H, Bi Y, Gao Y, Yan Y, Yuan X, Xiong X, Wang J, Liang J, Li D, Song F. A Pathogen-Inducible Rice NAC Transcription Factor ONAC096 Contributes to Immunity Against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae by Direct Binding to the Promoters of OsRap2.6, OsWRKY62, and OsPAL1. FRONTIERS IN PLANT SCIENCE 2021; 12:802758. [PMID: 34956298 PMCID: PMC8702954 DOI: 10.3389/fpls.2021.802758] [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: 10/27/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The rice NAC transcriptional factor family harbors 151 members, and some of them play important roles in rice immunity. Here, we report the function and molecular mechanism of a pathogen-inducible NAC transcription factor, ONAC096, in rice immunity against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae. Expression of ONAC096 was induced by M. oryzae and by abscisic acid and methyl jasmonate. ONAC096 had the DNA binding ability to NAC recognition sequence and was found to be a nucleus-localized transcriptional activator whose activity depended on its C-terminal. CRISPR/Cas9-mediated knockout of ONAC096 attenuated rice immunity against M. oryzae and X. oryzae pv. oryzae as well as suppressed chitin- and flg22-induced reactive oxygen species burst and expression of PTI marker genes OsWRKY45 and OsPAL4; by contrast, overexpression of ONAC096 enhanced rice immunity against these two pathogens and strengthened chitin- or flg22-induced PTI. RNA-seq transcriptomic profiling and qRT-PCR analysis identified a small set of defense and signaling genes that are putatively regulated by ONAC096, and further biochemical analysis validated that ONAC096 could directly bind to the promoters of OsRap2.6, OsWRKY62, and OsPAL1, three known defense and signaling genes that regulate rice immunity. ONAC096 interacts with ONAC066, which is a positive regulator of rice immunity. These results demonstrate that ONAC096 positively contributes to rice immunity against M. oryzae and X. oryzae pv. oryzae through direct binding to the promoters of downstream target genes including OsRap2.6, OsWRKY62, and OsPAL1.
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Affiliation(s)
- Hui Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Bi
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yizhou Gao
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuqing Yan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xi Yuan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Xiaohui Xiong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiajing Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiayu Liang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Iqbal Z, Iqbal MS, Sangpong L, Khaksar G, Sirikantaramas S, Buaboocha T. Comprehensive genome-wide analysis of calmodulin-binding transcription activator (CAMTA) in Durio zibethinus and identification of fruit ripening-associated DzCAMTAs. BMC Genomics 2021; 22:743. [PMID: 34649525 PMCID: PMC8518175 DOI: 10.1186/s12864-021-08022-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022] Open
Abstract
Background Fruit ripening is an intricate developmental process driven by a highly coordinated action of complex hormonal networks. Ethylene is considered as the main phytohormone that regulates the ripening of climacteric fruits. Concomitantly, several ethylene-responsive transcription factors (TFs) are pivotal components of the regulatory network underlying fruit ripening. Calmodulin-binding transcription activator (CAMTA) is one such ethylene-induced TF implicated in various stress and plant developmental processes. Results Our comprehensive analysis of the CAMTA gene family in Durio zibethinus (durian, Dz) identified 10 CAMTAs with conserved domains. Phylogenetic analysis of DzCAMTAs, positioned DzCAMTA3 with its tomato ortholog that has already been validated for its role in the fruit ripening process through ethylene-mediated signaling. Furthermore, the transcriptome-wide analysis revealed DzCAMTA3 and DzCAMTA8 as the highest expressing durian CAMTA genes. These two DzCAMTAs possessed a distinct ripening-associated expression pattern during post-harvest ripening in Monthong, a durian cultivar native to Thailand. The expression profiling of DzCAMTA3 and DzCAMTA8 under natural ripening conditions and ethylene-induced/delayed ripening conditions substantiated their roles as ethylene-induced transcriptional activators of ripening. Similarly, auxin-suppressed expression of DzCAMTA3 and DzCAMTA8 confirmed their responsiveness to exogenous auxin treatment in a time-dependent manner. Accordingly, we propose that DzCAMTA3 and DzCAMTA8 synergistically crosstalk with ethylene during durian fruit ripening. In contrast, DzCAMTA3 and DzCAMTA8 antagonistically with auxin could affect the post-harvest ripening process in durian. Furthermore, DzCAMTA3 and DzCAMTA8 interacting genes contain significant CAMTA recognition motifs and regulated several pivotal fruit-ripening-associated pathways. Conclusion Taken together, the present study contributes to an in-depth understanding of the structure and probable function of CAMTA genes in the post-harvest ripening of durian. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08022-1.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Mohammed Shariq Iqbal
- Amity Institute of Biotechnology, Amity University, Lucknow Campus, Lucknow, Uttar Pradesh, India
| | - Lalida Sangpong
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Gholamreza Khaksar
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Supaart Sirikantaramas
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand.,Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand. .,Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Li Z, Xie Q, Yan J, Chen J, Chen Q. Genome-Wide Identification and Characterization of the Abiotic-Stress-Responsive GRF Gene Family in Diploid Woodland Strawberry ( Fragaria vesca). PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10091916. [PMID: 34579449 PMCID: PMC8468544 DOI: 10.3390/plants10091916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 05/07/2023]
Abstract
Growth regulatory factors (GRF) are plant-specific transcription factors that play an important role in plant resistance to stress. This gene family in strawberry has not been investigated previously. In this study, 10 GRF genes were identified in the genome of the diploid woodland strawberry (Fragaria vesca). Chromosome analysis showed that the 10 FvGRF genes were unevenly distributed on five chromosomes. Phylogenetic analysis resolved the FvGRF proteins into five groups. Genes of similar structure were placed in the same group, which was indicative of functional redundance. Whole-genome duplication/segmental duplication and dispersed duplication events effectively promoted expansion of the strawberry GRF gene family. Quantitative reverse transcription-PCR analysis suggested that FvGRF genes played potential roles in the growth and development of vegetative organs. Expression profile analysis revealed that FvGRF3, FvGRF5, and FvGRF7 were up-regulated under low-temperature stress, FvGRF4 and FvGRF9 were up-regulated under high-temperature stress, FvGRF6 and FvGRF8 were up-regulated under drought stress, FvGRF3, FvGRF6, and FvGRF8 were up-regulated under salt stress, FvGRF2, FvGRF7, and FvGRF9 were up-regulated under salicylic acid treatment, and FvGRF3, FvGRF7, FvGRF9, and FvGRF10 were up-regulated under abscisic acid treatment. Promoter analysis indicated that FvGRF genes were involved in plant growth and development and stress response. These results provide a theoretical and empirical foundation for the elucidation of the mechanisms of abiotic stress responses in strawberry.
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Affiliation(s)
- Zhiqi Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (Q.X.); (J.Y.)
| | - Qian Xie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (Q.X.); (J.Y.)
| | - Jiahui Yan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (Q.X.); (J.Y.)
- Horticultural Plant Biology and Metabolomices Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianqing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (Q.X.); (J.Y.)
- Correspondence: (J.C.); (Q.C.)
| | - Qingxi Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.L.); (Q.X.); (J.Y.)
- Correspondence: (J.C.); (Q.C.)
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He J, Halitschke R, Schuman MC, Baldwin IT. Light dominates the diurnal emissions of herbivore-induced volatiles in wild tobacco. BMC PLANT BIOLOGY 2021; 21:401. [PMID: 34461825 PMCID: PMC8404343 DOI: 10.1186/s12870-021-03179-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/09/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Timing is everything when it comes to the fitness outcome of a plant's ecological interactions, and accurate timing is particularly relevant for interactions with herbivores or mutualists that are based on ephemeral emissions of volatile organic compounds. Previous studies of the wild tobacco N. attenuata have found associations between the diurnal timing of volatile emissions, and daytime predation of herbivores by their natural enemies. RESULTS Here, we investigated the role of light in regulating two biosynthetic groups of volatiles, terpenoids and green leaf volatiles (GLVs), which dominate the herbivore-induced bouquet of N. attenuata. Light deprivation strongly suppressed terpenoid emissions while enhancing GLV emissions, albeit with a time lag. Silencing the expression of photoreceptor genes did not alter terpenoid emission rhythms, but silencing expression of the phytochrome gene, NaPhyB1, disordered the emission of the GLV (Z)-3-hexenyl acetate. External abscisic acid (ABA) treatments increased stomatal resistance, but did not truncate the emission of terpenoid volatiles (recovered in the headspace). However, ABA treatment enhanced GLV emissions and leaf internal pools (recovered from tissue), and reduced internal linalool pools. In contrast to the pattern of diurnal terpenoid emissions and nocturnal GLV emissions, transcripts of herbivore-induced plant volatile (HIPV) biosynthetic genes peaked during the day. The promotor regions of these genes were populated with various cis-acting regulatory elements involved in light-, stress-, phytohormone- and circadian regulation. CONCLUSIONS This research provides insights into the complexity of the mechanisms involved in the regulation of HIPV bouquets, a mechanistic complexity which rivals the functional complexity of HIPVs, which includes repelling herbivores, calling for body guards, and attracting pollinators.
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Affiliation(s)
- Jun He
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Xiema Street, Beibei, Chongqing, 400712, People's Republic of China.
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany.
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Meredith C Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
- Current address: Departments of Geography and Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany.
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21
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Singh A. Expression dynamics indicate the role of Jasmonic acid biosynthesis pathway in regulating macronutrient (N, P and K +) deficiency tolerance in rice (Oryza sativa L.). PLANT CELL REPORTS 2021; 40:1495-1512. [PMID: 34089089 DOI: 10.1007/s00299-021-02721-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/24/2021] [Indexed: 05/25/2023]
Abstract
Expression pattern indicates that JA biosynthesis pathway via regulating JA levels might control root system architecture to improve nutrient use efficiency (NUE) and N, P, K+ deficiency tolerance in rice. Deficiencies of macronutrients (N, P and K+) and consequent excessive use of fertilizers have dramatically reduced soil fertility. It calls for development of nutrient use efficient plants. Plants combat nutrient deficiencies by altering their root system architecture (RSA) to enhance the acquisition of nutrients from the soil. Amongst various phytohormones, Jasmonic acid (JA) is known to regulate plant root growth and modulate RSA. Therefore, to understand the role of JA in macronutrient deficiency in rice, expression pattern of JA biosynthesis genes was analyzed under N, P and K+ deficiencies. Several members belonging to different families of JA biosynthesis genes (PLA1, LOX, AOS, AOC, OPR, ACX and JAR1) showed differential expression exclusively in one nutrient deficiency or in multiple nutrient deficiencies. Expression analysis during developmental stages showed that several genes expressed significantly in vegetative tissues, particularly in root. In addition, JA biosynthesis genes were found to have significant expression under the treatment of different phytohormones, including Auxin, cytokinin, gibberellic acid (GA), abscisic acid (ABA), JA and abiotic stresses, such as drought, salinity and cold. Analysis of promoters of these genes revealed various cis-regulatory elements associated with hormone response, plant development and abiotic stresses. These findings suggest that JA biosynthesis pathway by regulating the level of JA might control the RSA thus, it may help rice plant in combating macronutrient deficiency.
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Affiliation(s)
- Amarjeet Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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22
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Chen Q, Song Q, Yang X, Han H, Zhang X, Liao Y, Zhang W, Ye J, Cheng S, Xu F. Characterization of a novel levopimaradiene synthase gene responsible for the biosynthesis of terpene trilactones in Ginkgo biloba. PLANT SIGNALING & BEHAVIOR 2021; 16:1885906. [PMID: 33570442 PMCID: PMC7971208 DOI: 10.1080/15592324.2021.1885906] [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: 12/15/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Terpene trilactones (TTLs) are the main medicinal compounds of Ginkgo biloba. Levopimaradiene synthase (LPS) is the crucial enzyme that catalyzes TTLs biosynthesis in G. biloba. In this study, a novel LPS gene (designated as GbLPS2) was cloned from G. biloba leaves. The open reading frame of GbLPS2 gene was 2520 bp in length, encoding a predicted polypeptide of 840 amino acids. Phylogenetic analysis revealed that the GbLPS2 was highly homologous with reported LPS proteins in other plants. On the basis of the genomic DNA (gDNA) template, a 4308 bp gDNA sequence of GbLPS2 and a 913 bp promoter sequence were amplified. Cis-acting elements in promoter analysis indicated that GbLPS2 could be regulated by methyl jasmonate (MeJA) and abscisic acid (ABA). Tissue-specific expression analysis revealed that GbLPS2 was mainly expressed in roots and ovulate strobilus. MeJA treatment could significantly induce the expression level of GbLPS2 and increase the content of TTLs. This study illustrates the structure and the tissue-specific expression pattern of GbLPS2 and demonstrates that exogenous hormones regulated the expression of GbLPS2 and TTL content in G. biloba. Our results provide a target gene for the enhancement of TTL content in G. biloba via genetic engineering.
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Affiliation(s)
- Qiangwen Chen
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Qiling Song
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Huan Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Xian Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Shuiyuan Cheng
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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Huo Y, Zhang B, Chen L, Zhang J, Zhang X, Zhu C. Isolation and Functional Characterization of the Promoters of Miltiradiene Synthase Genes, TwTPS27a and TwTPS27b, and Interaction Analysis with the Transcription Factor TwTGA1 from Tripterygium wilfordii. PLANTS 2021; 10:plants10020418. [PMID: 33672407 PMCID: PMC7926782 DOI: 10.3390/plants10020418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/19/2022]
Abstract
Miltiradiene synthase (MS) genes, TwTPS27a and TwTPS27b, are the key diterpene synthase genes in the biosynthesis of triptolide, which is an important medicinally active diterpenoid in Tripterygium wilfordii. However, the mechanism underlying the regulation of key genes TwTPS27a/b in triptolide biosynthesis remains unclear. In this study, the promoters of TwTPS27a (1496 bp) and TwTPS27b (1862 bp) were isolated and analyzed. Some hormone-/stress-responsive elements and transcription factor (TF) binding sites were predicted in both promoters, which might be responsible for the regulation mechanism of TwTPS27a/b. The β-glucuronidase (GUS) activity analysis in promoter deletion assays under normal and methyl jasmonate (MeJA) conditions showed that the sequence of −921 to −391 bp is the potential core region of the TwTPS27b promoter. And the TGACG-motif, a MeJA-responsive element found in this core region, might be responsible for MeJA-mediated stress induction of GUS activity. Moreover, the TGACG-motif is also known as the TGA TF-binding site. Yeast one-hybrid and GUS transactivation assays confirmed the interaction between the TwTPS27a/b promoters and the TwTGA1 TF (a MeJA-inducible TGA TF upregulating triptolide biosynthesis in T. wilfordii), indicating that TwTPS27a/b are two target genes regulated by TwTGA1. In conclusion, our results provide important information for elucidating the regulatory mechanism of MS genes, TwTPS27a and TwTPS27b, as two target genes of TwTGA1, in jasmonic acid (JA)-inducible triptolide biosynthesis.
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Affiliation(s)
- Yanbo Huo
- College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Y.H.); (B.Z.); (L.C.); (J.Z.)
| | - Bin Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Y.H.); (B.Z.); (L.C.); (J.Z.)
| | - Ling Chen
- College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Y.H.); (B.Z.); (L.C.); (J.Z.)
| | - Jing Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Y.H.); (B.Z.); (L.C.); (J.Z.)
- Engineering and Research Center of Biological Pesticide of Shaanxi Province, Yangling 712100, China
| | - Xing Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Y.H.); (B.Z.); (L.C.); (J.Z.)
- Engineering and Research Center of Biological Pesticide of Shaanxi Province, Yangling 712100, China
- Correspondence: (X.Z.); (C.Z.)
| | - Chuanshu Zhu
- College of Plant Protection, Northwest A&F University, Yangling 712100, China; (Y.H.); (B.Z.); (L.C.); (J.Z.)
- Engineering and Research Center of Biological Pesticide of Shaanxi Province, Yangling 712100, China
- Correspondence: (X.Z.); (C.Z.)
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Sagar S, Deepika, Biswas DK, Chandrasekar R, Singh A. Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum). Int J Biol Macromol 2020; 169:264-273. [PMID: 33338528 DOI: 10.1016/j.ijbiomac.2020.12.102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 12/19/2022]
Abstract
Phospholipases D (PLDs) are phospholipid hydrolyzing enzymes and crucial components of lipid signaling in plants. PLDs are implicated in stress responses in different plants however, characterization of PLDs in chickpea is missing. Here, we identify 13 PLD genes in the chickpea genome. PLD family could be divided into α, β, δ, ε and ζ isoforms based on sequence and structure. Protein remodeling described that chickpea PLDs are composed of defined arrangements of α-helix, β-sheets and short loops. Phylogenetic analysis suggested evolutionary conservation of chickpea PLD family with dicots. In-planta subcellular localization showed the plasma membrane localization of chickpea PLDs. All PLD promoters had hormone and stress related cis-regulatory elements, which suggested overlapping function of PLDs in hormone and abiotic stress signaling. The qRT-PCR expression analysis revealed that most PLD genes are differentially expressed in multiple abiotic stresses (drought, salt and cold stress). Moreover, several PLD genes had overlapping expression in abiotic stress and ABA and JA treatment. These observations indicate the involvement of PLD gene family in cross-talk of phytohormone and abiotic stress signaling in chickpea. Thus, present study opens new avenues of utilizing PLD related information for understanding hormone-regulated abiotic stress signaling in legume crops.
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Affiliation(s)
- Sushma Sagar
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Deepika
- National Institute of Plant Genome Research, New Delhi 110067, India
| | | | | | - Amarjeet Singh
- National Institute of Plant Genome Research, New Delhi 110067, India.
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Genome-Wide Characterization of OFP Family Genes in Wheat ( Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9708324. [PMID: 33224986 DOI: 10.1155/2020/9708324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022]
Abstract
OVATE family proteins (OFPs) are plant-specific transcription factors that play important roles in plant development. Although common wheat (Triticum aestivum L.) is a major staple food worldwide, OFPs have not been systematically analyzed in this important crop. Here, we performed a genome-wide survey of OFP genes in wheat and identified 100 genes belonging to 34 homoeologous groups. Arabidopsis thaliana, rice (Oryza sativa), and wheat OFP genes were divided into four subgroups based on their phylogenetic relationships. Structural analysis indicated that only four TaOFPs contain introns. We mapped the TaOFP genes onto the wheat chromosomes and determined that TaOFP17 was duplicated in this crop. A survey of cis-acting elements along the promoter regions of TaOFP genes suggested that subfunctionalization of homoeologous genes might have occurred during evolution. The TaOFPs were highly expressed in wheat, with tissue- or organ-specific expression patterns. In addition, these genes were induced by various hormone and stress treatments. For instance, TaOPF29a-A was highly expressed in roots in response to drought stress. Wheat plants overexpressing TaOPF29a-A had longer roots and higher dry weights than nontransgenic plants under drought conditions, suggesting that this gene improves drought tolerance. Our findings provide a starting point for further functional analysis of this important transcription factor family and highlight the potential of using TaOPF29a-A to genetically engineer drought-tolerant crops.
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Rezaee S, Ahmadizadeh M, Heidari P. Genome-wide characterization, expression profiling, and post-transcriptional study of GASA gene family. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Sagar S, Biswas DK, Singh A. Genomic and expression analysis indicate the involvement of phospholipase C family in abiotic stress signaling in chickpea (Cicer arietinum). Gene 2020; 753:144797. [DOI: 10.1016/j.gene.2020.144797] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 12/01/2022]
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Xiong J, Liu L, Ma X, Li F, Tang C, Li Z, Lü B, Zhou T, Lian X, Chang Y, Tang M, Xie S, Lu X. Characterization of PtAOS1 Promoter and Three Novel Interacting Proteins Responding to Drought in Poncirus trifoliata. Int J Mol Sci 2020; 21:ijms21134705. [PMID: 32630273 PMCID: PMC7370134 DOI: 10.3390/ijms21134705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 11/16/2022] Open
Abstract
Jasmonic acid (JA) plays a crucial role in various biological processes including development, signal transduction and stress response. Allene oxide synthase (AOS) catalyzing (13S)-hydroperoxyoctadecatrienoic acid (13-HPOT) to an unstable allene oxide is involved in the first step of JA biosynthesis. Here, we isolated the PtAOS1 gene and its promoter from trifoliate orange (Poncirus trifoliata). PtAOS1 contains a putative chloroplast targeting sequence in N-terminal and shows relative to pistachio (Pistacia vera) AOS. A number of stress-, light- and hormone-related cis-elements were found in the PtAOS1 promoter which may be responsible for the up-regulation of PtAOS1 under drought and JA treatments. Transient expression in tobacco (Nicotiana benthamiana) demonstrated that the P-532 (-532 to +1) fragment conferring drive activity was a core region in the PtAOS1 promoter. Using yeast one-hybrid, three novel proteins, PtDUF886, PtDUF1685 and PtRAP2.4, binding to P-532 were identified. The dual luciferase assay in tobacco illustrated that all three transcription factors could enhance PtAOS1 promoter activity. Genes PtDUF1685 and PtRAP2.4 shared an expression pattern which was induced significantly by drought stress. These findings should be available evidence for trifoliate orange responding to drought through JA modulation.
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Affiliation(s)
- Jiang Xiong
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Lian Liu
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Xiaochuan Ma
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Feifei Li
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
- Institute of Horticulture, Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Chaolan Tang
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Zehang Li
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Biwen Lü
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Tie Zhou
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Xuefei Lian
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Yuanyuan Chang
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Mengjing Tang
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Shenxi Xie
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Xiaopeng Lu
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
- Correspondence: ; Tel./Fax: +86-0731-84618171
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Methyl Jasmonate Affects Photosynthesis Efficiency, Expression of HvTIP Genes and Nitrogen Homeostasis in Barley. Int J Mol Sci 2020; 21:ijms21124335. [PMID: 32570736 PMCID: PMC7352393 DOI: 10.3390/ijms21124335] [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: 05/13/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 12/22/2022] Open
Abstract
Jasmonates modulate many growth and developmental processes and act as stress hormones that play an important role in plant tolerance to biotic and abiotic stresses. Therefore, there is a need to identify the genes that are regulated through the jasmonate signalling pathway. Aquaporins, and among them the Tonoplast Intrinsic Proteins (TIPs), form the channels in cell membranes that are responsible for the precise regulation of the movement of water and other substrates between cell compartments. We identified the cis-regulatory motifs for the methyl jasmonate (MeJA)-induced genes in the promoter regions of all the HvTIP genes, which are active in barley seedlings, and thus we hypothesised that the HvTIP expression could be a response to jasmonate signalling. In the presented study, we determined the effect of methyl jasmonate on the growth parameters and photosynthesis efficiency of barley seedlings that had been exposed to different doses of MeJA (15–1000 µM × 120 h) in a hydroponic solution. All of the applied MeJA concentrations caused a significant reduction of barley seedling growth, which was most evident in the length of the first leaf sheath and dry leaf weight. The observed decrease of the PSII parameters after the exposure to high doses of MeJA (500 µM or higher) was associated with the downregulation of HvPsbR gene encoding one of the extrinsic proteins of the Oxygen Evolving Complex. The reduced expression of HvPsbR might lead to the impairment of the OEC action, manifested by the occurrence of the K-band in an analysis of fluorescence kinetics after MeJA treatment as well as reduced photosynthesis efficiency. Furthermore, methyl jasmonate treatment caused a decrease in the nitrogen content in barley leaves, which was associated with an increased expression the four tonoplast aquaporin genes (HvTIP1;2, HvTIP2;2, HvTIP4;1 and HvTIP4;2) predicted to transport the nitrogen compounds from the vacuole to the cytosol. The upregulation of the nitrogen-transporting HvTIPs might suggest their involvement in the vacuolar unloading of ammonia and urea, which both could be remobilised when the nitrogen content in the leaves decreases. Our research provides tips on physiological role of the individual TIP subfamily members of aquaporins under methyl jasmonate action.
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Jasmonate and Ethylene-Regulated Ethylene Response Factor 22 Promotes Lanolin-Induced Anthocyanin Biosynthesis in 'Zaosu' Pear ( Pyrus bretschneideri Rehd.) Fruit. Biomolecules 2020; 10:biom10020278. [PMID: 32054132 PMCID: PMC7072184 DOI: 10.3390/biom10020278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 12/02/2022] Open
Abstract
Anthocyanin contributes to the coloration of pear fruit and enhances plant defenses. Members of the ethylene response factor (ERF) family play vital roles in hormone and stress signaling and are involved in anthocyanin biosynthesis. Here, PbERF22 was identified from the lanolin-induced red fruit of ‘Zaosu’ pear (Pyrus bretschneideri Rehd.) using a comparative transcriptome analysis. Its expression level was up- and down-regulated by methyl jasmonate and 1-methylcyclopropene plus lanolin treatments, respectively, which indicated that PbERF22 responded to the jasmonate- and ethylene-signaling pathways. In addition, transiently overexpressed PbERF22 induced anthocyanin biosynthesis in ‘Zaosu’ fruit, and a quantitative PCR analysis further confirmed that PbERF22 facilitated the expression of anthocyanin biosynthetic structural and regulatory genes. Moreover, a dual luciferase assay showed that PbERF22 enhanced the activation effects of PbMYB10 and PbMYB10b on the PbUFGT promoter. Therefore, PbERF22 responses to jasmonate and ethylene signals and regulates anthocyanin biosynthesis. This provides a new perspective on the correlation between jasmonate–ethylene crosstalk and anthocyanin biosynthesis.
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Gan Z, Shan N, Fei L, Wan C, Chen J. Isolation of the 9-cis-epoxycarotenoid dioxygenase (NCED) gene from kiwifruit and its effects on postharvest softening and ripening. SCIENTIA HORTICULTURAE 2020. [DOI: 10.1016/j.scienta.2019.109020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Upadhyay S, Jeena GS, Kumar S, Shukla RK. Asparagus racemosus bZIP transcription factor-regulated squalene epoxidase (ArSQE) promotes germination and abiotic stress tolerance in transgenic tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110291. [PMID: 31779892 DOI: 10.1016/j.plantsci.2019.110291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/27/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
A. racemosus is a rich source of pharmacologically active steroidal saponins. Most of the studies are related to its chemistry and pharmacology, but the pathway involved in the biosynthesis of steroidal saponin is not much emphasized. Squalene epoxidase acts as a rate-limiting enzyme in this biosynthesis. In this study, we have selected root specific squalene epoxidase ArSQE from A. racemosus for its characterization. ArSQE was able to complement ergosterol auxotrophy in erg1 yeast mutants. Mutants were sensitive to the antifungal drug terbinafine, whereas ArSQE complementation made them tolerant to the same drug. ArSQE plays a significant role in early germination in transgenic tobacco. The transgenic tobacco seedlings overexpressing ArSQE were tolerant to terbinafine and abiotic stress. Expression analysis of transcripts in ArSQE transgenic lines suggests that it mostly affects ABA, GA, stress, and sterol related functions in transgenic tobacco. Further, root specific MeJA responsive A. racemosus bZIP transcription factors (TFs), ArTGA1 and ArTGA2, were identified that bind to MeJA responsive cis-element present in the promoter region of ArSQE. Characterization of ArSQE of A. racemosus provides new information about its regulation through MeJA responsive bZIP TF along with its role in the development and abiotic stress response in transgenic tobacco.
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Affiliation(s)
- Swati Upadhyay
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP) P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Gajendra Singh Jeena
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP) P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Sunil Kumar
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP) P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Rakesh Kumar Shukla
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP) P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India.
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Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-like (SBP) Transcription Factors in Wheat (Triticum aestivum L.). AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9090527] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) play fundamental roles in the developmental processes of all living organisms. Squamosa Promoter Binding Protein-like (SBP/SBP-Box) is a major family of plant-specific TFs, which plays important roles in multiple processes involving plant growth and development. While some work has been done, there is a lot more that is yet to be discovered in the hexaploid wheat SBP (TaSBP) family. With the completion of whole genome sequencing, genome-wide analysis of SBPs in common hexaploid wheat is now possible. In this study, we used protein–protein Basic Local Alignment Search Tool (BLASTp) to hunt the newly released reference genome sequence of hexaploid wheat (Chinese spring). Seventy-four TaSBP proteins (belonging to 56 genes) were identified and clustered into five groups. Gene structure and motif analysis indicated that most TaSBPs have relatively conserved exon–intron arrangements and motif composition. Analysis of transcriptional data showed that many TaSBP genes responded to some biological and abiotic stresses with different expression patterns. Moreover, three TaSBP genes were generally expressed in the majority of tissues throughout the wheat growth and also responded to many environmental biotic and abiotic stresses. Collectively, the detailed analyses presented here will help in understanding the roles of the TaSBP and also provide a reference for the further study of its biological function in wheat.
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Zhang C, Wang Y, Wang W, Cao Z, Fu Q, Bao M, He Y. Functional Analysis of the Marigold (Tagetes erecta) Lycopene ε-cyclase (TeLCYe) Promoter in Transgenic Tobacco. Mol Biotechnol 2019; 61:703-713. [PMID: 31286381 DOI: 10.1007/s12033-019-00197-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lycopene ε-cyclases (LCYEs) are key enzymes in carotenoid biosynthesis converting red lycopene to downstream lutein. The flowers of marigold (Tagetes erecta) have been superior sources to supply lutein. However, the transcriptional regulatory mechanisms of LCYe in lutein synthesis are still unclear in marigold. In this work, the expression pattern of the TeLCYe gene in marigold indicated that TeLCYe mainly expressed in floral organs. To gain a better understanding of the expression and regulatory mechanism of TeLCYe gene, the TeLCYe promoter was isolated, sequenced, and analyzed through bioinformatics tools. The results suggested that the sequence of TeLCYe promoter contained various putative cis-acting elements responsive to exogenous and endogenous factors. The full-length TeLCYe promoter and three 5'-deletion fragments were fused to the GUS reporter gene and transferred into tobacco to test the promoter activities. A strong GUS activity was observed in stems of seedlings, leaves of seedlings, middle stems, top leaves, petals, stamens, and stigmas in transgenic tobacco containing full-length TeLCYe promoter LP0-2086. Deletion of - 910 to - 429 bp 5' to ATG significantly increased the GUS activity in chloroplast-rich tissues and floral organs, while deletion occurring from 1170 to 910 bp upstream ATG decreased the TeLCYe promoter strength in stems of seedlings, leaves of seedlings, top leaves and sepals. Functional characterization of the full-length TeLCYe promoter and its' deletion fragments in stable transgenic tobacco indicated that the LP0-2086 contains some specific cis-acting elements, which might result in the high-level expression of in floral organs, and LP2-910 might contain some specific cis-acting elements which improved GUS activities in vegetable tissues.
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Affiliation(s)
- Chunling Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yaqin Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wenjing Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhe Cao
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, S7N5A8, Canada
| | - Qiang Fu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanhong He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Prusińska JM, Boniecka J, Dąbrowska GB, Goc A. Identification and characterization of the Ipomoea nil RelA/SpoT Homologs (InRSHs) and potential directions of their transcriptional regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:161-176. [PMID: 31084869 DOI: 10.1016/j.plantsci.2019.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/13/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Although the stringent response has been known for more than half a century and has been well studied in bacteria, only the research of the past 19 years revealed that the homologous mechanism is conserved in plants. The plant RelA/SpoT Homolog (RSH) genes have been identified and characterized in a limited number of plant species, whereas products of their catalytic activities, (p)ppGpp (alarmones), have been shown to accumulate mainly in chloroplasts. Here, we identified full-length sequences of the Ipomoea nil RSH genes (InRSH1, InRSH2 and InCRSH), determined their copy number in the I. nil genome as well as the structural conservancy between InRSHs and their Arabidopsis and rice orthologs. We showed that InRSHs are differentially expressed in I. nil organ tissues and that only InRSH2 is upregulated in response to salt, osmotic and drought stress. Our results of the E. coli relA/spoT mutant complementation test suggest that InRSH1 is likely a (p)ppGpp hydrolase, InCRSH - synthetase and InRSH2 shows both activities. Finally, we referred our results to the recently published I. nil genomic and proteomic data and uncovered the complexity of the I. nil RSH family as well as potential ways of the InRSH transcriptional regulation.
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Affiliation(s)
- Justyna M Prusińska
- Nicolaus Copernicus University in Toruń, Department of Genetics, Lwowska 1, 87-100, Toruń, Poland.
| | - Justyna Boniecka
- Nicolaus Copernicus University in Toruń, Department of Genetics, Lwowska 1, 87-100, Toruń, Poland
| | - Grażyna B Dąbrowska
- Nicolaus Copernicus University in Toruń, Department of Genetics, Lwowska 1, 87-100, Toruń, Poland
| | - Anna Goc
- Nicolaus Copernicus University in Toruń, Department of Genetics, Lwowska 1, 87-100, Toruń, Poland
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Yuan X, Wang H, Cai J, Bi Y, Li D, Song F. Rice NAC transcription factor ONAC066 functions as a positive regulator of drought and oxidative stress response. BMC PLANT BIOLOGY 2019; 19:278. [PMID: 31238869 PMCID: PMC6593515 DOI: 10.1186/s12870-019-1883-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/12/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND NAC (NAM, ATAF and CUC) transcriptional factors constitute a large family with more than 150 members in rice and several members of this family have been demonstrated to play crucial roles in rice abiotic stress response. In the present study, we report the function of a novel stress-responsive NAC gene, ONAC066, in rice drought and oxidative stress tolerance. RESULTS ONAC066 was localized in nuclei of cells when transiently expressed in Nicotiana benthamiana and is a transcription activator with the binding ability to NAC recognition sequence (NACRS) and AtJUB1 binding site (JBS). Expression of ONAC066 was significantly induced by PEG, NaCl, H2O2 and abscisic acid (ABA). Overexpression of ONAC066 in transgenic rice improved drought and oxidative stress tolerance and increased ABA sensitivity, accompanied with decreased rate of water loss, increased contents of proline and soluble sugars, decreased accumulation of reactive oxygen species (ROS) and upregulated expression of stress-related genes under drought stress condition. By contrast, RNAi-mediated suppression of ONAC066 attenuated drought and oxidative stress tolerance and decreased ABA sensitivity, accompanied with increased rate of water loss, decreased contents of proline and soluble sugars, elevated accumulation of ROS and downregulated expression of stress-related genes under drought stress condition. Furthermore, yeast one hybrid and chromatin immunoprecipitation-PCR analyses revealed that ONAC066 bound directly to a JBS-like cis-elements in OsDREB2A promoter and activated the transcription of OsDREB2A. CONCLUSION ONAC066 is a nucleus-localized transcription activator that can respond to multiple abiotic stress factors. Functional analyses using overexpression and RNAi-mediated suppression transgenic lines demonstrate that ONAC066 is a positive regulator of drought and oxidative stress tolerance in rice.
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Affiliation(s)
- Xi Yuan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Hui Wang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Jiating Cai
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yan Bi
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
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Gong XX, Yan BY, Tan YR, Gao X, Wang D, Zhang H, Wang P, Li SJ, Wang Y, Zhou LY, Liu JP. Identification of cis-regulatory regions responsible for developmental and hormonal regulation of HbHMGS1 in transgenic Arabidopsis thaliana. Biotechnol Lett 2019; 41:1077-1091. [PMID: 31236789 DOI: 10.1007/s10529-019-02703-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/21/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVES 3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase (HMGS) is an important enzyme in mevalonate (MVA) pathway of isoprenoid biosynthesis, which regulates the rubber biosynthetic pathway in rubber tree (Hevea brasiliensis) in coordination with HMG-CoA reductase (HMGR). However, little information is available about the regulation of HMGS gene expression. To understand the mechanism controlling the HbHMGS1 gene expression, we characterized the HbHMGS1 promoter sequence in transgenic plants with the β-glucuronidase (GUS) reporter gene. RESULTS GUS activity analysis of the transgenic plants showed that the HbHMGS1 promoter is active in all organs of the transgenic Arabidopsis plants during various developmental stages (from 6 to 45-day-old). Deletion of different portions of the upstream HbHMGS1 promoter identified sequences responsible for either positive or negative regulation of the GUS expression. Particularly, the - 454 bp HbHMGS1 promoter resulted in a 2.19-fold increase in promoter activity compared with the CaMV 35S promoter, suggesting that the - 454 bp HbHMGS1 promoter is a super-strong near-constitutive promoter. In addition, a number of promoter regions important for the responsiveness to ethylene, methyl jasmonate (MeJA) and gibberellic acid (GA) were identified. CONCLUSION The - 454 bp HbHMGS1 promoter has great application potential in plant transformation studies as an alternative to the CaMV 35S promoter. The HbHMGS1 promoter may play important roles in regulating ethylene-, MeJA- and GA-mediated gene expression. The functional complexity of cis-elements revealed by this study remains to be elucidated.
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Affiliation(s)
- Xiao-Xiao Gong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Bing-Yu Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Yu-Rong Tan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Xuan Gao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Dan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Heng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Peng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Shuang-Jiang Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Yi Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Lu-Yao Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China.
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Wang Q, Xu G, Zhai J, Yuan H, Huang X. Identification of the targets of HbEIN3/EILs in genomic wide in Hevea brasiliensis. Biosci Biotechnol Biochem 2019; 83:1270-1283. [PMID: 30915888 DOI: 10.1080/09168451.2019.1597619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
EIN3/EILs are key regulators in ET signaling pathway. In this work, 4 members of EIN3/EILs of Hevea brasiliensis (HbEIN3/EILs) showed interaction with two F box proteins, HbEBF1 and HbEBF2. HbEIN3 located in nucleus and exhibited strong transcriptional activity. HbEIN3 was induced by ET treatment in C-serum, but not in B-serum of latex. HbEIN3/EILs bound to G-box cis-element. To globally search the potential targets of HbEIN3/EILs, genomic sequences of H. brasiliensis was re-annotated and an HCES (Hevea Cis-Elements Scanning) program was developed ( www.h-brasiliensis.com ). HCES scanning results showed that ET- and JA- responsive cis-elements distribute overlapping in gene promoters. 3146 genes containing G-box in promoters are potential targets of HbEIN3, including 41 genes involved in biosynthesis and drainage of latex, of which 7 rate-limiting genes of latex production were regulated by both ET and JA, suggesting that ET and JA signaling pathways coordinated the latex biosynthesis and drainage in H. brasiliensis. Abbreviations: ABRE: ABA responsive elements; bHLH: basic helix-loop-helix; COG: Orthologous Groups; DRE: dehydration response element; ERE: ethylene responsive element; ET: Ethylene; GO: Gene Ontology; HCES: Hevea Cis-Elements Scanning; JA: jasmonates; JRE: Jasmonate-responsive element; KEGG: Kyoto Encyclopedia of Genes and Genomes; NR: non-redundant database; PLACE: Plant Cis-acting Regulatory DNA Elements; qRT-PCR: quantitative real-time RT-PCR.
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Affiliation(s)
- Qichao Wang
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
| | - Gang Xu
- b School of Life Sciences , Tsinghua University , Beijing , China
| | - Jinling Zhai
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
| | - Hongmei Yuan
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
| | - Xi Huang
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
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Li M, Wang R, Liang Z, Wu X, Wang J. Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization. BMC PLANT BIOLOGY 2019; 19:110. [PMID: 30898097 PMCID: PMC6429743 DOI: 10.1186/s12870-019-1716-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/12/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good group for studying the problems associated with polyploidization. On the other hand, the EIN3/EIL gene family is an important gene family in plants, all members of which are key genes in the ethylene signaling pathway. Until now, the EIN3/EIL gene family in B. napus and its diploid progenitors have been largely unknown, so it is necessary to comprehensively identify and analyze this gene family. RESULTS In this study, 13, 7 and 7 EIN3/EIL genes were identified in B. napus (2n = 4x = 38, AnCn), B. rapa (2n = 2x = 20, Ar) and B. oleracea (2n = 2x = 18, Co). All of the identified EIN3/EIL proteins were divided into 3 clades and further divided into 8 sub-clades. Ka/Ks analysis showed that all identified EIN3/EIL genes underwent purifying selection after the duplication events. Moreover, gene structure analysis showed that some EIN3/EIL genes in B. napus acquired introns during polyploidization, and homolog expression bias analysis showed that B. napus was biased towards its diploid progenitor B. rapa. The promoters of the EIN3/EIL genes in B. napus contained more cis-acting elements, which were mainly involved in endosperm gene expression and light responsiveness, than its diploid progenitors. Thus, B. napus might have potential advantages in some biological aspects. CONCLUSIONS The results indicated allotetraploid B. napus might have potential advantages in some biological aspects. Moreover, our results can increase the understanding of the evolution of the EIN3/EIL gene family in B. napus, and provided more reference for future research about polyploidization.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ziwei Liang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062 China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
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Jin B, Sheng Z, Muhammad I, Chen J, Yang H. Cloning and functional analysis of the promoter of a stress-inducible gene (Zmap) in maize. PLoS One 2019; 14:e0211941. [PMID: 30735543 PMCID: PMC6368321 DOI: 10.1371/journal.pone.0211941] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/29/2018] [Indexed: 11/23/2022] Open
Abstract
The anionic peroxidases play an important role in a variety of plant physiological processes. We characterized and isolated the Zmap promoter (PZmap) at the 5' flanking region in order to better understand the regulatory mechanisms of Zmap gene expression. A series of PZmap deletion derivatives, termed a1 -a6, at positions -1694, -1394, -1138, -784, -527 and -221 from the translation start site were blended to the β-glucuronidase reporter gene. Agrobacterium-mediated transformation method was used to study each deletion construct in tobaccos. Sequence analysis showed that several cis-acting elements (MYB binding site, Box-II, a TGACG-element, a CGTCA-element and a low temperature responsive element) were located within the promoter. Deletion analysis suggested the sequence between -1,694 and -1394bp may contain cis-elements associated with GUS up regulation. The MYB binding site (-757) might act as a negative drought-responsive element. There might be repressor elements located in the region (-1,694 to -1394bp) to repress Zmap expression under 4°C. The characterized promoter would be an ideal candidate for genetic engineering for improving the resistance of maize to different stressors.
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Affiliation(s)
- Bo Jin
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
| | - Zunlai Sheng
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, P. R. China
| | - Ishfaq Muhammad
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
| | - Jianqing Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, P. R. China
| | - Hongliang Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, P. R. China
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Neller KCM, Diaz CA, Platts AE, Hudak KA. De novo Assembly of the Pokeweed Genome Provides Insight Into Pokeweed Antiviral Protein (PAP) Gene Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:1002. [PMID: 31447869 PMCID: PMC6691146 DOI: 10.3389/fpls.2019.01002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/17/2019] [Indexed: 05/21/2023]
Abstract
Ribosome-inactivating proteins (RIPs) are RNA glycosidases thought to function in defense against pathogens. These enzymes remove purine bases from RNAs, including rRNA; the latter activity decreases protein synthesis in vitro, which is hypothesized to limit pathogen proliferation by causing host cell death. Pokeweed antiviral protein (PAP) is a RIP synthesized by the American pokeweed plant (Phytolacca americana). PAP inhibits virus infection when expressed in crop plants, yet little is known about the function of PAP in pokeweed due to a lack of genomic tools for this non-model species. In this work, we de novo assembled the pokeweed genome and annotated protein-coding genes. Sequencing comprised paired-end reads from a short-insert library of 83X coverage, and our draft assembly (N50 = 42.5 Kb) accounted for 74% of the measured pokeweed genome size of 1.3 Gb. We obtained 29,773 genes, 73% of which contained known protein domains, and identified several PAP isoforms. Within the gene models of each PAP isoform, a long 5' UTR intron was discovered, which was validated by RT-PCR and sequencing. Presence of the intron stimulated reporter gene expression in tobacco. To gain further understanding of PAP regulation, we complemented this genomic resource with expression profiles of pokeweed plants subjected to stress treatments [jasmonic acid (JA), salicylic acid, polyethylene glycol, and wounding]. Cluster analysis of the top differentially expressed genes indicated that some PAP isoforms shared expression patterns with genes involved in terpenoid biosynthesis, JA-mediated signaling, and metabolism of amino acids and carbohydrates. The newly sequenced promoters of all PAP isoforms contained cis-regulatory elements associated with diverse biotic and abiotic stresses. These elements mediated response to JA in tobacco, based on reporter constructs containing promoter truncations of PAP-I, the most abundant isoform. Taken together, this first genomic resource for the Phytolaccaceae plant family provides new insight into the regulation and function of PAP in pokeweed.
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Affiliation(s)
| | | | - Adrian E. Platts
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - Katalin A. Hudak
- Department of Biology, York University, Toronto, ON, Canada
- *Correspondence: Katalin A. Hudak,
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Wang Y, Zhang N, Li T, Yang J, Zhu X, Fang C, Li S, Si H. Genome-wide identification and expression analysis of StTCP transcription factors of potato (Solanum tuberosum L.). Comput Biol Chem 2018; 78:53-63. [PMID: 30497020 DOI: 10.1016/j.compbiolchem.2018.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022]
Abstract
The plant-specific TCP transcription factors, which play critical roles in diverse aspects of biological processes, have been identified and analyzed in various plant species. However, no systematical study of TCP family genes in potato (Solanum tuberosum L.) has been undertaken. In this study, a total of 31 non-redundant TCP transcription factors of potato were identified and divided into two subfamilies including three distinct subclades. The various orthologous TCP genes in Arabidopsis, rice, potato and tomato were identified using synteny and phylogenetic analysis. Protein motif analysis demonstrated that StTCPs in the same subclade shared similar conserved motif structures. Gene structure analysis showed that almost all StTCPs displayed highly conserved exon-intron organization. The analysis of StTCP gene promoter regions revealed that multiple cis-acting elements were involved in plant growth, development, hormone responses as well as stress responses. The result of StTCP gene expression profiles showed they had tissue-specific expression patterns which implied their differentiated functions. According to the results of quantitative RT-PCR (qRT-PCR), 7 StTCP genes were dramatically up-regulated during the release of tuber dormancy and some specific StTCP genes were strongly responding to different abiotic stresses and multiple hormones, which suggested they had important roles in potato growth and development processes. The results of our findings could provide comprehensive insights in StTCP family genes of potato for further functional investigations.
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Affiliation(s)
- Yapeng Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jiangwei Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xi Zhu
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Chenxi Fang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Shigui Li
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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Xu Z, Sun M, Jiang X, Sun H, Dang X, Cong H, Qiao F. Glycinebetaine Biosynthesis in Response to Osmotic Stress Depends on Jasmonate Signaling in Watermelon Suspension Cells. FRONTIERS IN PLANT SCIENCE 2018; 9:1469. [PMID: 30369936 PMCID: PMC6194323 DOI: 10.3389/fpls.2018.01469] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/18/2018] [Indexed: 05/02/2023]
Abstract
Glycinebetaine is an important non-toxic osmoprotectant, which is accumulated in higher plants under various stresses. The biosynthesis of glycinebetaine achieved via is a two-step oxidation from choline and betaine aldehyde, catalyzed by choline monooxygenase (CMO) and betaine aldehyde dehydrogenase (BADH), respectively. Up-regulated gene expression of BADH and CMO induced by stress is clearly observed, but the signal transduction is poorly understood. Here, glycinebetaine accumulation in response to osmotic stress and growth recovery induced by exogenous glycinebetaine were observed in a watermelon cell line. When tracing back to the genome sequence of watermelon, it shows that there exists only one member of ClCMO or ClBADH corresponding to glycinebetaine biosynthesis. Both genes harbor a CGTCA-motif in their promoter region which is involved in methyl jasmonate (MeJA)-responsiveness. Amongst MeJA, Ethephon, abscisic acid (ABA), and salicylic acid (SA), MeJA was most effective in gene inducing the expression of ClCMO and ClBADH, and the accumulation of glycinebetaine could also reach an amount comparable to that after osmotic stress by mannitol. Moreover, when ibuprofen (IBU), a JA biosynthesis inhibitor, was pre-perfused into the cells before osmotic stress, glycinebetaine accumulation was suppressed significantly. Interestingly, newly grown cells can keep a high content of glycinebetaine when they are sub-cultured from osmotic stressed cells. This study suggests that osmotic stress induced glycinebetaine biosynthesis occurs via JA signal transduction and not only plays a key role in osmotic stress resistance but also contributes to osmotic stress hardening.
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Affiliation(s)
- Zijian Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Mengli Sun
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xuefei Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Huapeng Sun
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Xuanmin Dang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Hanqing Cong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
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Zhao J, Zhai Z, Li Y, Geng S, Song G, Guan J, Jia M, Wang F, Sun G, Feng N, Kong X, Chen L, Mao L, Li A. Genome-Wide Identification and Expression Profiling of the TCP Family Genes in Spike and Grain Development of Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1282. [PMID: 30298074 PMCID: PMC6160802 DOI: 10.3389/fpls.2018.01282] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
The TCP family genes are plant-specific transcription factors and play important roles in plant development. TCPs have been evolutionarily and functionally studied in several plants. Although common wheat (Triticum aestivum L.) is a major staple crop worldwide, no systematic analysis of TCPs in this important crop has been conducted. Here, we performed a genome-wide survey in wheat and found 66 TCP genes that belonged to 22 homoeologous groups. We then mapped these genes on wheat chromosomes and found that several TCP genes were duplicated in wheat including the ortholog of the maize TEOSINTE BRANCHED 1. Expression study using both RT-PCR and in situ hybridization assay showed that most wheat TCP genes were expressed throughout development of young spike and immature seed. Cis-acting element survey along promoter regions suggests that subfunctionalization may have occurred for homoeologous genes. Moreover, protein-protein interaction experiments of three TCP proteins showed that they can form either homodimers or heterodimers. Finally, we characterized two TaTCP9 mutants from tetraploid wheat. Each of these two mutant lines contained a premature stop codon in the A subgenome homoeolog that was dominantly expressed over the B subgenome homoeolog. We observed that mutation caused increased spike and grain lengths. Together, our analysis of the wheat TCP gene family provides a start point for further functional study of these important transcription factors in wheat.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Long Mao
- *Correspondence: Long Mao, Aili Li,
| | - Aili Li
- *Correspondence: Long Mao, Aili Li,
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Castelblanque L, Balaguer B, Marti C, Orozco M, Vera P. LOL2 and LOL5 loci control latex production by laticifer cells in Euphorbia lathyris. THE NEW PHYTOLOGIST 2018; 219:1467-1479. [PMID: 29878406 DOI: 10.1111/nph.15253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Laticifers are specialized plant cells capable of indefinite elongation that ramify extensively and are responsible for latex biosynthesis and accumulation. However, the mechanisms underlying laticifer cell differentiation, growth and production of latex remain largely unknown. In a search for mutants showing enhanced accumulation of latex we identified two LOT OF LATEX (LOL) loci in Euphorbia lathyris. lol2 and lol5 mutants show enhanced production of latex contained within laticifer cells. The recessive lol2 mutant carries increased biosynthesis of the plant hormone jasmonoyl-isoleucine (JA-Ile) and therefore establishes a genetic link between jasmonic acid (JA) signaling and latex production in laticifers. Instead, heightened production of latex in lol5 plants obeys to enhanced proliferation of laticifer cells. Phylogenetic analysis of laticifer-expressed genes in E. lathyris and in two other latex-bearing species, Euphorbia corallioides and Euphorbia palustris, allowed the identification of canonical JA responsive elements present in the gene promoter regions of laticifer marker genes. Moreover, we identified that the hormone JA functions not as a morphogen for laticifer differentiation but as a trigger for the fill out of laticifers with latex and the associated triterpenoids. The identification of LOL loci represents a further step towards the understanding of mechanisms controlling latex production in laticifer cells.
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Affiliation(s)
- Lourdes Castelblanque
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C., Ciudad Politécnica de la Innovación, Edificio 8E, Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain
| | - Begoña Balaguer
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C., Ciudad Politécnica de la Innovación, Edificio 8E, Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain
| | - Cristina Marti
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C., Ciudad Politécnica de la Innovación, Edificio 8E, Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain
| | - Marianela Orozco
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C., Ciudad Politécnica de la Innovación, Edificio 8E, Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain
| | - Pablo Vera
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C., Ciudad Politécnica de la Innovación, Edificio 8E, Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain
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Punjabi M, Bharadvaja N, Sachdev A, Krishnan V. Molecular characterization, modeling, and docking analysis of late phytic acid biosynthesis pathway gene, inositol polyphosphate 6-/ 3-/ 5-kinase, a potential candidate for developing low phytate crops. 3 Biotech 2018; 8:344. [PMID: 30073129 PMCID: PMC6064606 DOI: 10.1007/s13205-018-1343-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
The coding sequence of inositol polyphosphate 6-/3-/5-kinase (GmIPK2) gene was identified and cloned from popular Indian soybean cultivar Pusa-16. The clone was predicted to encode 279 amino acids long, 30.97 kDa protein. Multiple sequence alignment revealed an inositol phosphate-binding motif, PxxxDxKxG throughout the IPK2 sequences along with other motifs unique to inositol phosphate kinase superfamily. Eight α-helices and eight β-strands in antiparallel β-sheets arrangement were predicted in the secondary structure of GmIPK2. The temporal analysis of GmIPK2 revealed maximum expression in the seed tissues during later stages of development while spatially the transcript levels were lowest in leaf and stem tissues. Endosperm-specific cis-regulatory motifs (GCN4 and Skn_1) which support high levels of expression, as observed in the developing seeds, were detected in its promoter region. The protein structure of GmIPK2 was modeled based on the crystal structure of inositol polyphosphate multikinase from Arabidopsis thaliana (PDB:4FRF) and subsequently docked with inositol phosphate ligands (PDB: 5GUG-I3P and PDB: 4A69-I0P). Molecular dynamics (MD) simulation established the structural stability of both, modeled enzyme and ligand-bound complexes. Docking in combination with trajectory analysis for 50 ns MD run confirmed the participation of Lys105, Lys126 and Arg153 residues in the formation of a network of hydrogen bonds to stabilize the ligand-receptor interaction. Results of the present study thus provide valuable information on structural and functional aspects of GmIPK2 which shall assist in strategizing our long-term goal of achieving phytic acid reduction in soybean by genetic modification of its biosynthetic pathway to develop a nutritionally enhanced crop in the future.
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Affiliation(s)
- Mansi Punjabi
- Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), New Delhi, 110042 India
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Navneeta Bharadvaja
- Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), New Delhi, 110042 India
| | - Archana Sachdev
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Veda Krishnan
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
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Ali M, Luo DX, Khan A, Haq SU, Gai WX, Zhang HX, Cheng GX, Muhammad I, Gong ZH. Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications. Int J Mol Sci 2018; 19:E2216. [PMID: 30060631 PMCID: PMC6121964 DOI: 10.3390/ijms19082216] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 11/26/2022] Open
Abstract
Chitin-binding proteins are pathogenesis-related gene family, which play a key role in the defense response of plants. However, thus far, little is known about the chitin-binding family genes in pepper (Capsicum annuum L.). In current study, 16 putative chitin genes (CaChi) were retrieved from the latest pepper genome database, and were classified into four distinct classes (I, III, IV and VI) based on their sequence structure and domain architectures. Furthermore, the structure of gene, genome location, gene duplication and phylogenetic relationship were examined to clarify a comprehensive background of the CaChi genes in pepper. The tissue-specific expression analysis of the CaChi showed the highest transcript levels in seed followed by stem, flower, leaf and root, whereas the lowest transcript levels were noted in red-fruit. Phytophthora capsici post inoculation, most of the CaChi (CaChiI3, CaChiIII1, CaChiIII2, CaChiIII4, CaChiIII6, CaChiIII7, CaChiIV1, CaChiVI1 and CaChiVI2) were induced by both strains (PC and HX-9). Under abiotic and exogenous hormonal treatments, the CaChiIII2, CaChiIII7, CaChiVI1 and CaChiVI2 were upregulated by abiotic stress, while CaChiI1, CaChiIII7, CaChiIV1 and CaChiIV2 responded to hormonal treatments. Furthermore, CaChiIV1-silenced plants display weakened defense by reducing (60%) root activity and increase susceptibility to NaCl stress. Gene ontology (GO) enrichment analysis revealed that CaChi genes primarily contribute in response to biotic, abiotic stresses and metabolic/catabolic process within the biological process category. These results exposed that CaChi genes are involved in defense response and signal transduction, suggesting their vital roles in growth regulation as well as response to stresses in pepper plant. In conclusion, these finding provide basic insights for functional validation of the CaChi genes in different biotic and abiotic stresses.
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Affiliation(s)
- Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - De-Xu Luo
- Xuhuai Region Huaiyin Institute of Agricultural Sciences, Huaian 223001, China.
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Saeed Ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Guo-Xin Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses. Sci Rep 2018; 8:5500. [PMID: 29615685 PMCID: PMC5883049 DOI: 10.1038/s41598-018-23761-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/19/2018] [Indexed: 11/22/2022] Open
Abstract
The dirigent (DIR and DIR-like) proteins involved in lignification, play a pivotal role against biotic and abiotic stresses in plants. However, no information is available about DIR gene family in pepper (Capsicum annuum L.). In this study, 24 putative dirigent genes (CaDIRs) were identified, their gene structure, genome location, gene duplication and phylogenetic relationship were elucidated. Tissue-specific expression analysis displayed the highest transcription levels in flower, stem and leaf. Some CaDIRs were up-regulated by virulent (CaDIR2, 3, 6, 7, 11, 14, 16, 22 and 23) and avirulent (CaDIR3, 5, 7, 16, 20, 22, 23 and 24) Phytophthora capsici strains, as well as by Methyl jasmonate, salicylic acid, NaCl and mannitol stresses. Acid-soluble lignin content increased (103.21%) after P. capsici inoculation (48-hour). Silencing of CaDIR7 weakened plant defense by reducing (~50%) root activity and made plants more susceptible (35.7%) to P. capsici and NaCl (300 mM). Leaf discs of the CaDIR7:silenced plants exposed to NaCl and mannitol (300 mM each), exhibited a significant decrease (56.25% and 48% respectively) in the chlorophyll content. These results suggested that CaDIR7 is involved in pepper defense response against pathogen and abiotic stresses and the study will provide basic insights for future research regarding CaDIRs.
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49
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Zhu D, Chu W, Wang Y, Yan H, Chen Z, Xiang Y. Genome-wide identification, classification and expression analysis of the serine carboxypeptidase-like protein family in poplar. PHYSIOLOGIA PLANTARUM 2018; 162:333-352. [PMID: 28902414 DOI: 10.1111/ppl.12642] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/03/2017] [Accepted: 08/31/2017] [Indexed: 05/22/2023]
Abstract
Previous studies have shown that the serine carboxypeptidase-like (SCPL) proteins in several plants play a key part in plant growth, development and stress responses. However, little is known about the functions of the SCPL genes in poplar. We identified 57 SCPL genes and divided into 3 subfamilies, which were unevenly distributed on 19 poplar chromosomes. Gene structure indicated that SCPL genes contain more introns, and motifs of each subfamily were relatively conserved. There were a total of 14 pairs of paralogs, with 6 pairs of these paralogs generated by segmental duplication and 1 generated by tandem duplication. In microsynteny analysis, large-scale duplication events played a key part in the expansion of Carboxypeptidase III genes. Expression of these genes was higher in mature leaf. Quantitative real-time PCR showed that majority of the SCPL genes were induced by methyl jasmonate (MeJA) treatment. PtSCPL27 and PtSCPL40 were located on the cytomembrane by conducting subcellular localization analysis. Our paper provides a theoretical basis for further functional research of PtSCPL genes and will benefit the molecular breeding for resistance to disease in poplar.
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Affiliation(s)
- Dongyue Zhu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Wenyuan Chu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yujiao Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Zhu Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
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50
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Yusuf CYL, Abdullah JO, Shaharuddin NA, Abu Seman I, Abdullah MP. Characterization of promoter of EgPAL1, a novel PAL gene from the oil palm Elaeis guineensis Jacq. PLANT CELL REPORTS 2018; 37:265-278. [PMID: 29090330 DOI: 10.1007/s00299-017-2228-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
The oil palm EgPAL1 gene promoter and its regulatory region were functional as a promoter in the heterologous system of Arabidopsis according to the cis-acting elements present in that region. The promoter was developmentally regulated, vascular tissue specific and responsive to water stress agents. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the key enzyme of the phenylpropanoid pathway which plays important roles in plant development and adaptation. To date, there is no report on the study of PAL from oil palm (Elaeis guineensis), an economically important oil crop. In this study, the 5' regulatory sequence of a highly divergent oil palm PAL gene (EgPAL1) was isolated and fused with GUS in Arabidopsis to create two transgenic plants carrying the minimal promoter with (2302 bp) and without its regulatory elements (139 bp). The regulatory sequence contained cis-acting elements known to be important for plant development and stress response including the AC-II element for lignin biosynthesis and several stress responsive elements. The promoter and its regulatory region were fully functional in Arabidopsis. Its activities were characterised by two common fundamental features of PAL which are responsive to plant internal developmental programme and external factors. The promoter was developmentally regulated in certain organs; highly active in young organs but less active or inactive in mature organs. The presence of the AC elements and global activity of the EgPAL1 promoter in all organs resembled the property of lignin-related genes. The existence of the MBS element and enhancement of the promoter activity by PEG reflected the behaviour of drought-responsive genes. Our findings provide a platform for evaluating oil palm gene promoters in the heterologous system of Arabidopsis and give insights into the activities of EgPAL1 promoter in oil palm.
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Affiliation(s)
- Chong Yu Lok Yusuf
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, Kampus Jasin, 77300, Merlimau, Melaka, Malaysia
| | - Janna Ong Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Idris Abu Seman
- Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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