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Li X, Gong X, Lin H, Rao S, Shen L, Chen C, Wu Z, Li H, Liu Q, Zhong Y. Genome-wide analysis of the bZIP gene family in Cinnamomum camphora ('Gantong 1') reveals the putative function in anthocyanin biosynthesis. Heliyon 2024; 10:e34311. [PMID: 39082037 PMCID: PMC11284375 DOI: 10.1016/j.heliyon.2024.e34311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Basic leucine zipper (bZIP) transcription factors (TFs) regulate plant development, growth, and secondary metabolism. The formation of red bark of new ornamental cultivar 'Gantong 1' is regulated mainly by anthocyanin anabolism. However, it is unclear whether and which bZIP TFs are involved in this process. We identified 89 genes encoding CcbZIP TFs in Cinnamomum camphora genome that could be divided into 14 subfamilies with similar gene structures and conserved motifs. CcbZIP38 and CcbZIP57 were highly conserved compared to HY5 in Arabidopsis thaliana and they were highly expressed in the bark and leaves of 'Gantong 1' at different stages. The target gene enrichment analysis showed that indicating indirect involvement of CcbZIP38 and CcbZIP57 in the regulation of anthocyanin synthesis. Our study contributes to understanding the molecular mechanism of anthocyanin synthesis regulation by CcbZIP TFs and provides a theoretical basis for genetic improvement of ornamental traits in C. camphora.
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Affiliation(s)
- Xiuqi Li
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Xue Gong
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Hanbin Lin
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Shupei Rao
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Le Shen
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Caihui Chen
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Zhaoxiang Wu
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Huihu Li
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Qiaoli Liu
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Yongda Zhong
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
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Wang G, Chen B, Zhang X, Du G, Han G, Liu J, Peng Y. The basic leucine zipper domain (bZIP) transcription factor BbYap1 promotes evasion of host humoral immunity and regulates lipid homeostasis contributing to fungal virulence in Beauveria bassiana. mSphere 2024; 9:e0035124. [PMID: 38926907 PMCID: PMC11288043 DOI: 10.1128/msphere.00351-24] [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: 04/26/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Basic leucine zipper domain transcription factors (TFs), of which yeast activator protein (Yap) is a significant class, are crucial for the development of sclerotia, the stress response, vegetative growth, and spore adhesion. Nevertheless, nothing is known about how Yap TFs contribute to the pathogenicity of entomopathogenic fungus. In this work, Beauveria bassiana was used to identify and knock out the yeast gene BbYap1, which is similar to Yap. The BbYap1 gene deletion has an impact on lipid homeostasis of B. bassiana; oleic acid, for example, dropped by 95.69%. The BbYap1 mutant exhibited much less virulence and vegetative development in comparison to the wild strain, while demonstrating a greater sensitivity to chemical stress. It is noteworthy that the physiological abnormalities brought on by BbYap1 deletion were largely repaired by the addition of exogenous oleic acid, as seen by the notable increase in insect survival in the blood cavity injection group. Following infection with the BbYap1 mutant, the host exhibits a considerable down-regulation of the expression of β-1,3-glucan recognition protein, gallerimycin, gloverin, and moricin-like protein genes. Likewise, the introduction of exogenous oleic acid markedly increased the host's expression of the aforementioned genes. In summary, BbYap1 regulates cellular enzyme lipid homeostasis and fungal virulence by eluding host humoral defense, which contributes to fungal chemical stress and vegetative development. IMPORTANCE Entomopathogenic fungi (EPF) offer an effective and eco-friendly alternative to curb insect populations in biocontrol strategy. When EPF enter the hemolymph of their host, they encounter a variety of stress reactions, such as immunological and oxidative stress. Basic leucine zipper domain transcription factors, of which yeast activator protein (Yap) is a significant class, have diverse biological functions related to metabolism, development, reproduction, conidiation, stress responses, and pathogenicity. This study demonstrates that BbYap1 of Beauveria bassiana regulates cellular enzyme lipid homeostasis and fungal virulence by eluding host humoral defense, which contributes to fungal chemical stress and vegetative development. These findings offer fresh perspectives for comprehending molecular roles of YAP in EPF.
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Affiliation(s)
- Guang Wang
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Bin Chen
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Xu Zhang
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Guangzu Du
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Guangyu Han
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology, School of Life Science, Yunnan Normal University, Kunming, China
| | - Yuejin Peng
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, Yunnan Agricultural University, College of Plant Protection, Kunming, China
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Aerts N, Hickman R, Van Dijken AJH, Kaufmann M, Snoek BL, Pieterse CMJ, Van Wees SCM. Architecture and dynamics of the abscisic acid gene regulatory network. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38949092 DOI: 10.1111/tpj.16899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
The plant hormone abscisic acid (ABA) regulates essential processes in plant development and responsiveness to abiotic and biotic stresses. ABA perception triggers a post-translational signaling cascade that elicits the ABA gene regulatory network (GRN), encompassing hundreds of transcription factors (TFs) and thousands of transcribed genes. To further our knowledge of this GRN, we performed an RNA-seq time series experiment consisting of 14 time points in the 16 h following a one-time ABA treatment of 5-week-old Arabidopsis rosettes. During this time course, ABA rapidly changed transcription levels of 7151 genes, which were partitioned into 44 coexpressed modules that carry out diverse biological functions. We integrated our time-series data with publicly available TF-binding site data, motif data, and RNA-seq data of plants inhibited in translation, and predicted (i) which TFs regulate the different coexpression clusters, (ii) which TFs contribute the most to target gene amplitude, (iii) timing of engagement of different TFs in the ABA GRN, and (iv) hierarchical position of TFs and their targets in the multi-tiered ABA GRN. The ABA GRN was found to be highly interconnected and regulated at different amplitudes and timing by a wide variety of TFs, of which the bZIP family was most prominent, and upregulation of genes encompassed more TFs than downregulation. We validated our network models in silico with additional public TF-binding site data and transcription data of selected TF mutants. Finally, using a drought assay we found that the Trihelix TF GT3a is likely an ABA-induced positive regulator of drought tolerance.
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Affiliation(s)
- Niels Aerts
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Richard Hickman
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Anja J H Van Dijken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Michael Kaufmann
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
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Zhou L, Cao H, Zeng X, Wu Q, Li Q, Martin JJJ, Fu D, Liu X, Li X, Li R, Ye J. Oil Palm AP2 Subfamily Gene EgAP2.25 Improves Salt Stress Tolerance in Transgenic Tobacco Plants. Int J Mol Sci 2024; 25:5621. [PMID: 38891808 PMCID: PMC11171577 DOI: 10.3390/ijms25115621] [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: 04/11/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
AP2/ERF transcription factor genes play an important role in regulating the responses of plants to various abiotic stresses, such as cold, drought, high salinity, and high temperature. However, less is known about the function of oil palm AP2/ERF genes. We previously obtained 172 AP2/ERF genes of oil palm and found that the expression of EgAP2.25 was significantly up-regulated under salinity, cold, or drought stress conditions. In the present study, the sequence characterization and expression analysis for EgAP2.25 were conducted, showing that it was transiently over-expressed in Nicotiana tabacum L. The results indicated that transgenic tobacco plants over-expressing EgAP2.25 could have a stronger tolerance to salinity stress than wild-type tobacco plants. Compared with wild-type plants, the over-expression lines showed a significantly higher germination rate, better plant growth, and less chlorophyll damage. In addition, the improved salinity tolerance of EgAP2.25 transgenic plants was mainly attributed to higher antioxidant enzyme activities, increased proline and soluble sugar content, reduced H2O2 production, and lower MDA accumulation. Furthermore, several stress-related marker genes, including NtSOD, NtPOD, NtCAT, NtERD10B, NtDREB2B, NtERD10C, and NtP5CS, were significantly up-regulated in EgAP2.25 transgenic tobacco plants subjected to salinity stress. Overall, over-expression of the EgAP2.25 gene significantly enhanced salinity stress tolerance in transgenic tobacco plants. This study lays a foundation for further exploration of the regulatory mechanism of the EgAP2.25 gene in conferring salinity tolerance in oil palm.
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Affiliation(s)
- Lixia Zhou
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Hongxing Cao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xianhai Zeng
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qiufei Wu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Qihong Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jerome Jeyakumar John Martin
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Dengqiang Fu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xiaoyu Liu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xinyu Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Rui Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Jianqiu Ye
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (L.Z.); (H.C.); (X.Z.); (Q.W.); (Q.L.); (J.J.J.M.); (D.F.); (X.L.); (X.L.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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Parajuli A, Borphukan B, Sanguinet KA, Zhang Z. In silico analysis identified bZIP transcription factors genes responsive to abiotic stress in Alfalfa (Medicago sativa L.). BMC Genomics 2024; 25:497. [PMID: 38773372 PMCID: PMC11106943 DOI: 10.1186/s12864-024-10277-3] [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: 03/23/2023] [Accepted: 04/02/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa. RESULT In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in A. thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. RT-qPCR analysis on selected genes further verified these differential expression patterns. CONCLUSIONS Taken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.
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Affiliation(s)
- Atit Parajuli
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA
| | - Bhabesh Borphukan
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA.
| | - Zhiwu Zhang
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA.
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Yang X, Chen Y, Liu W, Huang T, Yang Y, Mao Y, Meng Y. Combined transcriptomics and metabolomics to analyse the response of Cuminum cyminum L. under Pb stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171497. [PMID: 38453091 DOI: 10.1016/j.scitotenv.2024.171497] [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: 01/21/2024] [Revised: 02/25/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
Lead (Pb) can disrupt plant gene expression, modify metabolite contents, and influence the growth of plants. Cuminum cyminum L. is highly adaptable to adversity, but molecular mechanism by which it responds to Pb stress is unknown. For this study, transcriptomic and metabolomic sequencing was performed on root tissues of C. cyminum under Pb stress. Our results showed that high Pb stress increased the activity of peroxidase (POD), the contents of malondialdehyde (MDA) and proline by 80.03 %, 174.46 % and 71.24 %, respectively. Meanwhile, Pb stress decreased the activities of superoxide dismutase (SOD) and catalase (CAT) as well as contents of soluble sugars and GSH, which thus affected the growth of C. cyminum. In addition, Pb stress influenced the accumulation and transport of Pb in C. cyminum. Metabolomic results showed that Pb stress affected eight metabolic pathways involving 108 differentially expressed metabolites, primarily amino acids, organic acids, and carbohydrates. The differentially expressed genes identified through transcriptome analysis were mainly involved the oxidation reductase activity, transmembrane transport, phytohormone signaling, and MAPK signaling pathway. The results of this study will help to understand the molecular mechanisms of C. cyminum response to Pb stress, and provide a basis for screening seeds with strong resistance to heavy metals.
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Affiliation(s)
- Xinlong Yang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; Key Laboratory of Oasis Ecology of Education Ministry, Urumqi 830017, China
| | - Yinguang Chen
- School of Environment Science and Engineering, Tongji University, Shanghai 200092, China
| | - Weiguo Liu
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; Key Laboratory of Oasis Ecology of Education Ministry, Urumqi 830017, China.
| | - Tingwen Huang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; Key Laboratory of Oasis Ecology of Education Ministry, Urumqi 830017, China
| | - Yang Yang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; Key Laboratory of Oasis Ecology of Education Ministry, Urumqi 830017, China
| | - Yuqing Mao
- Wuwei Academy of Agricultural Sciences, Wuwei 733000, China
| | - Yao Meng
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; Key Laboratory of Oasis Ecology of Education Ministry, Urumqi 830017, China
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Fan J, Chen N, Rao W, Ding W, Wang Y, Duan Y, Wu J, Xing S. Genome-wide analysis of bZIP transcription factors and their expression patterns in response to methyl jasmonate and low-temperature stresses in Platycodon grandiflorus. PeerJ 2024; 12:e17371. [PMID: 38708338 PMCID: PMC11067905 DOI: 10.7717/peerj.17371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Background Platycodon grandiflorus belongs to the genus Platycodon and has many pharmacological effects, such as expectorant, antitussive, and anti-tumor properties. Among transcription factor families peculiar to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important, which exists widely in plants and participates in many biological processes, such as plant growth, development, and stress responses. However, genomic analysis of the bZIP gene family and related stress response genes has not yet been reported in P. grandiflorus. Methods P. grandiflorus bZIP (PgbZIP) genes were first identified here, and the phylogenetic relationships and conserved motifs in the PgbZIPs were also performed. Meanwhile, gene structures, conserved domains, and the possible protein subcellular localizations of these PgbZIPs were characterized. Most importantly, the cis-regulatory elements and expression patterns of selected genes exposed to two different stresses were analyzed to provide further information on PgbZIPs potential biological roles in P. grandiflorus upon exposure to environmental stresses. Conclusions Forty-six PgbZIPs were identified in P. grandiflorus and divided into nine groups, as displayed in the phylogenetic tree. The results of the chromosomal location and the collinearity analysis showed that forty-six PgbZIP genes were distributed on eight chromosomes, with one tandem duplication event and eleven segmental duplication events identified. Most PgbZIPs in the same phylogenetic group have similar conserved motifs, domains, and gene structures. There are cis-regulatory elements related to the methyl jasmonate (MeJA) response, low-temperature response, abscisic acid response, auxin response, and gibberellin response. Ten PgbZIP genes were selected to study their expression patterns upon exposure to low-temperature and MeJA treatments, and all ten genes responded to these stresses. The real-time quantitative polymerase chain reaction (RT-qPCR) results suggest that the expression levels of most PgbZIPs decreased significantly within 6 h and then gradually increased to normal or above normal levels over the 90 h following MeJA treatment. The expression levels of all PgbZIPs were significantly reduced after 3 h of the low-temperature treatment. These results reveal the characteristics of the PgbZIP family genes and provide valuable information for improving P. grandiflorus's ability to cope with environmental stresses during growth and development.
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Affiliation(s)
- Jizhou Fan
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Na Chen
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Joint Research Center for Chinese Herbal Medicine of Anhui, Bozhou, Anhui, China
- College of Pharmacy, Bozhou Vocational and Technical College, Bozhou, Anhui, China
| | - Weiyi Rao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
| | - Wanyue Ding
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yuqing Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yingying Duan
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Joint Research Center for Chinese Herbal Medicine of Anhui, Bozhou, Anhui, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
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Huang X, Zhou Y, Shi X, Wen J, Sun Y, Chen S, Hu T, Li R, Wang J, Jia X. PfbZIP85 Transcription Factor Mediates ω-3 Fatty Acid-Enriched Oil Biosynthesis by Down-Regulating PfLPAT1B Gene Expression in Plant Tissues. Int J Mol Sci 2024; 25:4375. [PMID: 38673960 PMCID: PMC11050522 DOI: 10.3390/ijms25084375] [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: 03/12/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The basic leucine zipper (bZIP) transcription factor (TF) family is one of the biggest TF families identified so far in the plant kingdom, functioning in diverse biological processes including plant growth and development, signal transduction, and stress responses. For Perilla frutescens, a novel oilseed crop abundant in polyunsaturated fatty acids (PUFAs) (especially α-linolenic acid, ALA), the identification and biological functions of bZIP members remain limited. In this study, 101 PfbZIPs were identified in the perilla genome and classified into eleven distinct groups (Groups A, B, C, D, E, F, G, H, I, S, and UC) based on their phylogenetic relationships and gene structures. These PfbZIP genes were distributed unevenly across 18 chromosomes, with 83 pairs of them being segmental duplication genes. Moreover, 78 and 148 pairs of orthologous bZIP genes were detected between perilla and Arabidopsis or sesame, respectively. PfbZIP members belonging to the same subgroup exhibited highly conserved gene structures and functional domains, although significant differences were detected between groups. RNA-seq and RT-qPCR analysis revealed differential expressions of 101 PfbZIP genes during perilla seed development, with several PfbZIPs exhibiting significant correlations with the key oil-related genes. Y1H and GUS activity assays evidenced that PfbZIP85 downregulated the expression of the PfLPAT1B gene by physical interaction with the promoter. PfLPAT1B encodes a lysophosphatidate acyltransferase (LPAT), one of the key enzymes for triacylglycerol (TAG) assembly. Heterogeneous expression of PfbZIP85 significantly reduced the levels of TAG and UFAs (mainly C18:1 and C18:2) but enhanced C18:3 accumulation in both seeds and non-seed tissues in the transgenic tobacco lines. Furthermore, these transgenic tobacco plants showed no significantly adverse phenotype for other agronomic traits such as plant growth, thousand seed weight, and seed germination rate. Collectively, these findings offer valuable perspectives for understanding the functions of PfbZIPs in perilla, particularly in lipid metabolism, showing PfbZIP85 as a suitable target in plant genetic improvement for high-value vegetable oil production.
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Affiliation(s)
- Xusheng Huang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Yali Zhou
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Xianfei Shi
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Jing Wen
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Yan Sun
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Shuwei Chen
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Ting Hu
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Runzhi Li
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Jiping Wang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Xiaoyun Jia
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, China
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9
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Yang X, Wang M, Zhou Q, Xu X, Li Y, Hou X, Xiao D, Liu T. BcABF1 Plays a Role in the Feedback Regulation of Abscisic Acid Signaling via the Direct Activation of BcPYL4 Expression in Pakchoi. Int J Mol Sci 2024; 25:3877. [PMID: 38612692 PMCID: PMC11011251 DOI: 10.3390/ijms25073877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Abscisic acid-responsive element-binding factor 1 (ABF1), a key transcription factor in the ABA signal transduction process, regulates the expression of downstream ABA-responsive genes and is involved in modulating plant responses to abiotic stress and developmental processes. However, there is currently limited research on the feedback regulation of ABF1 in ABA signaling. This study delves into the function of BcABF1 in Pakchoi. We observed a marked increase in BcABF1 expression in leaves upon ABA induction. The overexpression of BcABF1 not only spurred Arabidopsis growth but also augmented the levels of endogenous IAA. Furthermore, BcABF1 overexpression in Arabidopsis significantly decreased leaf water loss and enhanced the expression of genes associated with drought tolerance in the ABA pathway. Intriguingly, we found that BcABF1 can directly activate BcPYL4 expression, a critical receptor in the ABA pathway. Similar to BcABF1, the overexpression of BcPYL4 in Arabidopsis also reduces leaf water loss and promotes the expression of drought and other ABA-responsive genes. Finally, our findings suggested a novel feedback regulation mechanism within the ABA signaling pathway, wherein BcABF1 positively amplifies the ABA signal by directly binding to and activating the BcPYL4 promoter.
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Affiliation(s)
- Xiaoxue Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Meiyun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Qian Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Xinfeng Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Ying Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Xilin Hou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Dong Xiao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Tongkun Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
- Sanya Research Institute, Nanjing Agricultural University, Nanjing 210095, China
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10
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Jha DK, Chanwala J, Barla P, Dey N. "Genome-wide identification of bZIP gene family in Pearl millet and transcriptional profiling under abiotic stress, phytohormonal treatments; and functional characterization of PgbZIP9". FRONTIERS IN PLANT SCIENCE 2024; 15:1352040. [PMID: 38469329 PMCID: PMC10925649 DOI: 10.3389/fpls.2024.1352040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Abiotic stresses are major constraints in crop production, and are accountable for more than half of the total crop loss. Plants overcome these environmental stresses using coordinated activities of transcription factors and phytohormones. Pearl millet an important C4 cereal plant having high nutritional value and climate resilient features is grown in marginal lands of Africa and South-East Asia including India. Among several transcription factors, the basic leucine zipper (bZIP) is an important TF family associated with diverse biological functions in plants. In this study, we have identified 98 bZIP family members (PgbZIP) in pearl millet. Phylogenetic analysis divided these PgbZIP genes into twelve groups (A-I, S, U and X). Motif analysis has shown that all the PgbZIP proteins possess conserved bZIP domains and the exon-intron organization revealed conserved structural features among the identified genes. Cis-element analysis, RNA-seq data analysis, and real-time expression analysis of PgbZIP genes suggested the potential role of selected PgbZIP genes in growth/development and abiotic stress responses in pearl millet. Expression profiling of selected PgbZIPs under various phytohormones (ABA, SA and MeJA) treatment showed differential expression patterns of PgbZIP genes. Further, PgbZIP9, a homolog of AtABI5 was found to localize in the nucleus and modulate gene expression in pearl millet under stresses. Our present findings provide a better understanding of bZIP genes in pearl millet and lay a good foundation for the further functional characterization of multi-stress tolerant PgbZIP genes, which could become efficient tools for crop improvement.
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Affiliation(s)
- Deepak Kumar Jha
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jeky Chanwala
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Preeti Barla
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
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11
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Ahmed M, Tóth Z, Decsi K. The Impact of Salinity on Crop Yields and the Confrontational Behavior of Transcriptional Regulators, Nanoparticles, and Antioxidant Defensive Mechanisms under Stressful Conditions: A Review. Int J Mol Sci 2024; 25:2654. [PMID: 38473901 DOI: 10.3390/ijms25052654] [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: 02/05/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
One of the most significant environmental challenges to crop growth and yield worldwide is soil salinization. Salinity lowers soil solution water potential, causes ionic disequilibrium and specific ion effects, and increases reactive oxygen species (ROS) buildup, causing several physiological and biochemical issues in plants. Plants have developed biological and molecular methods to combat salt stress. Salt-signaling mechanisms regulated by phytohormones may provide additional defense in salty conditions. That discovery helped identify the molecular pathways that underlie zinc-oxide nanoparticle (ZnO-NP)-based salt tolerance in certain plants. It emphasized the need to study processes like transcriptional regulation that govern plants' many physiological responses to such harsh conditions. ZnO-NPs have shown the capability to reduce salinity stress by working with transcription factors (TFs) like AP2/EREBP, WRKYs, NACs, and bZIPs that are released or triggered to stimulate plant cell osmotic pressure-regulating hormones and chemicals. In addition, ZnO-NPs have been shown to reduce the expression of stress markers such as malondialdehyde (MDA) and hydrogen peroxide (H2O2) while also affecting transcriptional factors. Those systems helped maintain protein integrity, selective permeability, photosynthesis, and other physiological processes in salt-stressed plants. This review examined how salt stress affects crop yield and suggested that ZnO-NPs could reduce plant salinity stress instead of osmolytes and plant hormones.
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Affiliation(s)
- Mostafa Ahmed
- Festetics Doctoral School, Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
- Department of Agricultural Biochemistry, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Zoltán Tóth
- Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
| | - Kincső Decsi
- Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
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12
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Lai H, Wang M, Yan L, Feng C, Tian Y, Tian X, Peng D, Lan S, Zhang Y, Ai Y. Genome-Wide Identification of bZIP Transcription Factors in Cymbidium ensifolium and Analysis of Their Expression under Low-Temperature Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:219. [PMID: 38256772 PMCID: PMC10818551 DOI: 10.3390/plants13020219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
The basic leucine zipper (bZIP) transcription factors constitute the most widely distributed and conserved eukaryotic family. They play crucial roles in plant growth, development, and responses to both biotic and abiotic stresses, exerting strong regulatory control over the expression of downstream genes. In this study, a genome-wide characterization of the CebZIP transcription factor family was conducted using bioinformatic analysis. Various aspects, including physicochemical properties, phylogenetics, conserved structural domains, gene structures, chromosomal distribution, gene covariance relationships, promoter cis-acting elements, and gene expression patterns, were thoroughly analyzed. A total of 70 CebZIP genes were identified from the C. ensifolium genome, and they were randomly distributed across 18 chromosomes. The phylogenetic tree clustered them into 11 subfamilies, each exhibiting complex gene structures and conserved motifs arranged in a specific order. Nineteen pairs of duplicated genes were identified among the 70 CebZIP genes, with sixteen pairs affected by purifying selection. Cis-acting elements analysis revealed a plethora of regulatory elements associated with stress response, plant hormones, and plant growth and development. Transcriptome and qRT-PCR results demonstrated that the expression of CebZIP genes was universally up-regulated under low temperature conditions. However, the expression patterns varied among different members. This study provides theoretical references for identifying key bZIP genes in C. ensifolium that confer resistance to low-temperature stress, and lays the groundwork for further research into their broader biological functions.
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Affiliation(s)
- Huiping Lai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Mengyao Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Lu Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Caiyun Feng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Yang Tian
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Xinyue Tian
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China;
| | - Donghui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Yanping Zhang
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China;
| | - Ye Ai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
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13
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Zhang H, He Q, Xing L, Wang R, Wang Y, Liu Y, Zhou Q, Li X, Jia Z, Liu Z, Miao Y, Lin T, Li W, Du H. The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones. PLANT COMMUNICATIONS 2024; 5:100677. [PMID: 37634079 PMCID: PMC10811376 DOI: 10.1016/j.xplc.2023.100677] [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: 04/23/2023] [Revised: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023]
Abstract
Rheum officinale, a member of the Polygonaceae family, is an important medicinal plant that is widely used in traditional Chinese medicine. Here, we report a 7.68-Gb chromosome-scale assembly of R. officinale with a contig N50 of 3.47 Mb, which was clustered into 44 chromosomes across four homologous groups. Comparative genomics analysis revealed that transposable elements have made a significant contribution to its genome evolution, gene copy number variation, and gene regulation and expression, particularly of genes involved in metabolite biosynthesis, stress resistance, and root development. We placed the recent autotetraploidization of R. officinale at ∼0.58 mya and analyzed the genomic features of its homologous chromosomes. Although no dominant monoploid genomes were observed at the overall expression level, numerous allele-differentially-expressed genes were identified, mainly with different transposable element insertions in their regulatory regions, suggesting that they functionally diverged after polyploidization. Combining genomics, transcriptomics, and metabolomics, we explored the contributions of gene family amplification and tetraploidization to the abundant anthraquinone production of R. officinale, as well as gene expression patterns and differences in anthraquinone content among tissues. Our report offers unprecedented genomic resources for fundamental research on the autopolyploid herb R. officinale and guidance for polyploid breeding of herbs.
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Affiliation(s)
- Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ruyu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qinghong Zhou
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Xuanzhao Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Zheng Jia
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yuqing Miao
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Tao Lin
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China.
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14
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Wang S, Zhao Y, Chen Y, Gao M, Wang Y. The Association between BZIP Transcription Factors and Flower Development in Litsea cubeba. Int J Mol Sci 2023; 24:16646. [PMID: 38068969 PMCID: PMC10705912 DOI: 10.3390/ijms242316646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The basic leucine zipper (bZIP) family is one of the largest families of transcription factors among eukaryotic organisms. Members of the bZIP family play various roles in regulating the intricate process of flower development in plants. Litsea cubeba (Lour.) (family: Lauraceae) is an aromatic, dioecious plant used in China for a wide range of applications. However, no study to date has undertaken a comprehensive analysis of the bZIP gene family in L. cubeba. In this work, we identified 68 members of the bZIP gene family in L. cubeba and classified them into 12 subfamilies based on previous studies on Arabidopsis thaliana. Transcriptome data analysis revealed that multiple LcbZIP genes exhibit significantly high expression levels in the flowers of L. cubeba, while some also demonstrate distinct temporal specificity during L. cubeba flower development. In particular, some LcbZIP genes displayed specific and high expression levels during the stamen and pistil degradation process. Using differential gene expression analysis, weighted gene co-expression network analysis, and Gene Ontology enrichment analysis, we identified six candidate LcbZIP genes that potentially regulate stamen or pistil degradation during flower development. In summary, our findings provide a framework for future functional analysis of the LcbZIP gene family in L. cubeba and offer novel insights for investigating the mechanism underlying pistil and stamen degeneration in this plant.
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Affiliation(s)
- Siqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
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15
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Huang X, Zhang W, Liao Y, Ye J, Xu F. Contemporary understanding of transcription factor regulation of terpenoid biosynthesis in plants. PLANTA 2023; 259:2. [PMID: 37971670 DOI: 10.1007/s00425-023-04268-z] [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: 06/20/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
KEY MESSAGE This review summarized how TFs function independently or in response to environmental factors to regulate terpenoid biosynthesis via fine-tuning the expression of rate-limiting enzymes. Terpenoids are derived from various species and sources. They are essential for interacting with the environment and defense mechanisms, such as antimicrobial, antifungal, antiviral, and antiparasitic properties. Almost all terpenoids have high medicinal value and economic performance. Recently, the control of enzyme genes on terpenoid biosynthesis has received a great deal of attention, but transcriptional factors regulatory network on terpenoid biosynthesis and accumulation has yet to get a thorough review. Transcription factors function as activators or suppressors independently or in response to environmental stimuli, fine-tuning terpenoid accumulation through regulating rate-limiting enzyme expression. This study investigates the advancements in transcription factors related to terpenoid biosynthesis and systematically summarizes previous works on the specific mechanisms of transcription factors that regulate terpenoid biosynthesis via hormone signal-transcription regulatory networks in plants. This will help us to better comprehend the regulatory network of terpenoid biosynthesis and build the groundwork for terpenoid development and effective utilization.
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Affiliation(s)
- Xinru Huang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
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Zhang H, Ding X, Wang H, Chen H, Dong W, Zhu J, Wang J, Peng S, Dai H, Mei W. Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1243323. [PMID: 37719219 PMCID: PMC10499555 DOI: 10.3389/fpls.2023.1243323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 09/19/2023]
Abstract
Introduction Agarwood, the dark-brown resin produced by Aquilaria trees, has been widely used as incense, spice, perfume or traditional medicine and 2-(2-phenethyl) chromones (PECs) are the key markers responsible for agarwood formation. But the biosynthesis and regulatory mechanism of PECs were still not illuminated. The transcription factor of basic leucine zipper (bZIP) presented the pivotal regulatory roles in various secondary metabolites biosynthesis in plants, which might also contribute to regulate PECs biosynthesis. However, molecular evolution and function of bZIP are rarely reported in Malvales plants, especially in Aquilaria trees. Methods and results Here, 1,150 bZIPs were comprehensively identified from twelve Malvales and model species genomes and the evolutionary process were subsequently analyzed. Duplication types and collinearity indicated that bZIP is an ancient or conserved TF family and recent whole genome duplication drove its evolution. Interesting is that fewer bZIPs in A. sinensis than that species also experienced two genome duplication events in Malvales. 62 AsbZIPs were divided into 13 subfamilies and gene structures, conservative domains, motifs, cis-elements, and nearby genes of AsbZIPs were further characterized. Seven AsbZIPs in subfamily D were significantly regulated by ethylene and agarwood inducer. As the typical representation of subfamily D, AsbZIP14 and AsbZIP41 were localized in nuclear and potentially regulated PECs biosynthesis by activating or suppressing type III polyketide synthases (PKSs) genes expression via interaction with the AsPKS promoters. Discussion Our results provide a basis for molecular evolution of bZIP gene family in Malvales and facilitate the understanding the potential functions of AsbZIP in regulating 2-(2-phenethyl) chromone biosynthesis and agarwood formation.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xupo Ding
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hao Wang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Huiqin Chen
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenhua Dong
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiahong Zhu
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jian Wang
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, College of Forestry, Hainan University, Haikou, China
| | - Shiqing Peng
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Haofu Dai
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenli Mei
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Huang LT, Liu CY, Li L, Han XS, Chen HW, Jiao CH, Sha AH. Genome-Wide Identification of bZIP Transcription Factors in Faba Bean Based on Transcriptome Analysis and Investigation of Their Function in Drought Response. PLANTS (BASEL, SWITZERLAND) 2023; 12:3041. [PMID: 37687286 PMCID: PMC10490193 DOI: 10.3390/plants12173041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Faba bean is an important cool-season edible legume crop that is constantly threatened by abiotic stresses such as drought. The basic leucine zipper (bZIP) gene family is one of the most abundant and diverse families of transcription factors in plants. It regulates plant growth and development and plays an important role in the response to biotic and abiotic stresses. In this study, we identified 18 members of the faba bean bZIP transcription factor family at the genome-wide level based on previous faba bean drought stress transcriptome sequencing data. A phylogenetic tree was constructed to group the 18 VfbZIP proteins into eight clades. Analysis of cis-acting elements in the promoter region suggested that these 18 VfbZIPs may be involved in regulating abiotic stress responses such as drought. Transcriptome data showed high expression of seven genes (VfbZIP1, VfbZIP2, VfbZIP5, VfbZIP7, VfbZIP15, VfbZIP17, and VfbZIP18) in the drought-tolerant cultivar under drought stress, in which VfbZIP1, VfbZIP2, and VfbZIP5 were consistently expressed as detected by quantitative real-time polymerase chain reaction (qRT-PCR) compared to the transcriptome data. Ectopic overexpression of the three VfbZIPs in tobacco, based on the potato Virus X (PVX) vector, revealed that VfbZIP5 enhanced the drought tolerance. Overexpressed VfbZIP5 in plants showed lower levels of proline (PRO), malondialdehyde (MDA), and peroxidase (POD) compared to those overexpressing an empty vector under 10 days of drought stress. Protein-protein interaction (PPI) analysis showed that VfbZIP5 interacted with seven proteins in faba bean, including VfbZIP7 and VfbZIP10. The results depict the importance of VfbZIPs in response to drought stress, and they would be useful for the improvement of drought tolerance.
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Affiliation(s)
- Lin-Tao Huang
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, China
| | - Chang-Yan Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Li Li
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Xue-Song Han
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Hong-Wei Chen
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Chun-Hai Jiao
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China; (C.-Y.L.); (L.L.); (X.-S.H.); (H.-W.C.)
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan 430063, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430063, China
| | - Ai-Hua Sha
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434025, China
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18
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Zhang Y, Xu J, Li R, Ge Y, Li Y, Li R. Plants' Response to Abiotic Stress: Mechanisms and Strategies. Int J Mol Sci 2023; 24:10915. [PMID: 37446089 DOI: 10.3390/ijms241310915] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Abiotic stress is the adverse effect of any abiotic factor on a plant in a given environment, impacting plants' growth and development. These stress factors, such as drought, salinity, and extreme temperatures, are often interrelated or in conjunction with each other. Plants have evolved mechanisms to sense these environmental challenges and make adjustments to their growth in order to survive and reproduce. In this review, we summarized recent studies on plant stress sensing and its regulatory mechanism, emphasizing signal transduction and regulation at multiple levels. Then we presented several strategies to improve plant growth under stress based on current progress. Finally, we discussed the implications of research on plant response to abiotic stresses for high-yielding crops and agricultural sustainability. Studying stress signaling and regulation is critical to understand abiotic stress responses in plants to generate stress-resistant crops and improve agricultural sustainability.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Jing Xu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Ruofan Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yanrui Ge
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yufei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Ruili Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
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19
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Liu S, Peng X, Wang X, Zhuang W. Transcriptome Analysis Reveals Differentially Expressed Genes Involved in Cadmium and Arsenic Accumulation in Tea Plant ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:1182. [PMID: 36904042 PMCID: PMC10007383 DOI: 10.3390/plants12051182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Tea (Camellia sinensis) is the second most consumed drink in the world. Rapid industrialization has caused various impacts on nature and increased pollution by heavy metals. However, the molecular mechanisms of cadmium (Cd) and arsenic (As) tolerance and accumulation in tea plants are poorly understood. The present study focused on the effects of heavy metals Cd and As on tea plants. Transcriptomic regulation of tea roots after Cd and As exposure was analyzed to explore the candidate genes involved in Cd and As tolerance and accumulation. In total, 2087, 1029, 1707, and 366 differentially expressed genes (DEGs) were obtained in Cd1 (with Cd treatment for 10 days) vs. CK (without Cd treatment), Cd2 (with Cd treatment for 15 days) vs. CK, As1 (with As treatment for 10 days) vs. CK (without Cd treatment), and As2 (with As treatment for 15 days) vs. CK, respectively. Analysis of DEGs showed that a total of 45 DEGs with the same expression patterns were identified in four pairwise comparison groups. One ERF transcription factor (CSS0000647) and six structural genes (CSS0033791, CSS0050491, CSS0001107, CSS0019367, CSS0006162, and CSS0035212) were only increased at 15 d of Cd and As treatments. Using weighted gene co-expression network analysis (WGCNA) revealed that the transcription factor (CSS0000647) was positively correlated with five structural genes (CSS0001107, CSS0019367, CSS0006162, CSS0033791, and CSS0035212). Moreover, one gene (CSS0004428) was significantly upregulated in both Cd and As treatments, suggesting that these genes might play important roles in enhancing the tolerance to Cd and As stresses. These results provide candidate genes to enhance multi-metal tolerance through the genetic engineering technology.
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Affiliation(s)
- Shiqi Liu
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Xuqian Peng
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Xiaojing Wang
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
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20
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Kajla M, Roy A, Singh IK, Singh A. Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1126567. [PMID: 36938003 PMCID: PMC10017880 DOI: 10.3389/fpls.2023.1126567] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.
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Affiliation(s)
- Mohini Kajla
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Jagdish Chandra Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
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21
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Rai GK, Kumar P, Choudhary SM, Singh H, Adab K, Kosser R, Magotra I, Kumar RR, Singh M, Sharma R, Corrado G, Rouphael Y. Antioxidant Potential of Glutathione and Crosstalk with Phytohormones in Enhancing Abiotic Stress Tolerance in Crop Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:1133. [PMID: 36903992 PMCID: PMC10005112 DOI: 10.3390/plants12051133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/19/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Glutathione (GSH) is an abundant tripeptide that can enhance plant tolerance to biotic and abiotic stress. Its main role is to counter free radicals and detoxify reactive oxygen species (ROS) generated in cells under unfavorable conditions. Moreover, along with other second messengers (such as ROS, calcium, nitric oxide, cyclic nucleotides, etc.), GSH also acts as a cellular signal involved in stress signal pathways in plants, directly or along with the glutaredoxin and thioredoxin systems. While associated biochemical activities and roles in cellular stress response have been widely presented, the relationship between phytohormones and GSH has received comparatively less attention. This review, after presenting glutathione as part of plants' feedback to main abiotic stress factors, focuses on the interaction between GSH and phytohormones, and their roles in the modulation of the acclimatation and tolerance to abiotic stress in crops plants.
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Affiliation(s)
- Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Pradeep Kumar
- Division of Integrated Farming System, ICAR—Central Arid Zone Research Institute, Jodhpur 342003, India
| | - Sadiya M. Choudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Hira Singh
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana 141004, India
| | - Komal Adab
- Department of Biotechnology, BGSB University, Rajouri 185131, India
| | - Rafia Kosser
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Isha Magotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, ICAR—Indian Agricultural Research Institute, New Delhi 110001, India
| | - Monika Singh
- GLBajaj Institute of Technology and Management, Greater Noida 201306, India
| | - Rajni Sharma
- Department of Agronomy, Punjab Agricultural University, Ludhiana 141004, India
| | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
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22
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Wang J, Wang Y, Wu X, Wang B, Lu Z, Zhong L, Li G, Wu X. Insight into the bZIP gene family in Lagenaria siceraria: Genome and transcriptome analysis to understand gene diversification in Cucurbitaceae and the roles of LsbZIP gene expression and function under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1128007. [PMID: 36874919 PMCID: PMC9981963 DOI: 10.3389/fpls.2022.1128007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The basic leucine zipper (bZIP) as a well-known transcription factor family, figures prominently in diverse biological and developmental processes and response to abiotic/biotic stresses. However, no knowledge of the bZIP family is available for the important edible Cucurbitaceae crop bottle gourd. Herein, we identified 65 putative LsbZIP genes and characterized their gene structure, phylogenetic and orthologous relationships, gene expression profiles in different tissues and cultivars, and responsive genes under cold stress. The phylogenetic tree of 16 released Cucurbitaceae plant genomes revealed the evolutionary convergence and divergence of bZIP family. Based on the specific domains, LsbZIP family were classified into 12 clades (A-K, S) with similar motifs and exon-intron distribution. 65 LsbZIP genes have undergone 19 segmental and two tandem duplication events with purifying selection. The expression profiling of LsbZIP genes showed tissue-specific but no cultivar-specific pattern. The cold stress-responsive candidate LsbZIP genes were analyzed and validated by RNA-Seq and RT-PCR, providing new insights of transcriptional regulation of bZIP family genes in bottle gourd and their potential functions in cold-tolerant variety breeding.
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Affiliation(s)
- Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liping Zhong
- College of Horticulture Science, Zhejiang Agriculture and Forestry (A&F) University, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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23
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Phytohormones regulate the non-redundant response of ω-3 fatty acid desaturases to low temperatures in Chorispora bungeana. Sci Rep 2023; 13:2799. [PMID: 36797352 PMCID: PMC9935925 DOI: 10.1038/s41598-023-29910-4] [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: 11/11/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
To explore the contributions of ω-3 fatty acid desaturases (FADs) to cold stress response in a special cryophyte, Chorispora bungeana, two plastidial ω-3 desaturase genes (CbFAD7, CbFAD8) were cloned and verified in an Arabidopsis fad7fad8 mutant, before being compared with the microsomal ω-3 desaturase gene (CbFAD3). Though these genes were expressed in all tested tissues of C. bungeana, CbFAD7 and CbFAD8 have the highest expression in leaves, while CbFAD3 was mostly expressed in suspension-cultured cells. Low temperatures resulted in significant increases in trienoic fatty acids (TAs), corresponding to the cooperation of CbFAD3 and CbFAD8 in cultured cells, and the coordination of CbFAD7 and CbFAD8 in leaves. Furthermore, the cold induction of CbFAD8 in the two systems were increased with decreasing temperature and independently contributed to TAs accumulation at subfreezing temperature. A series of experiments revealed that jasmonie acid and brassinosteroids participated in the cold-responsive expression of ω-3 CbFAD genes in both C. bungeana cells and leaves, while the phytohormone regulation in leaves was complex with the participation of abscisic acid and gibberellin. These results point to the hormone-regulated non-redundant contributions of ω-3 CbFADs to maintain appropriate level of TAs under low temperatures, which help C. bungeana survive in cold environments.
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Ban Y, Tan J, Xiong Y, Mo X, Jiang Y, Xu Z. Transcriptome analysis reveals the molecular mechanisms of Phragmites australis tolerance to CuO-nanoparticles and/or flood stress induced by arbuscular mycorrhizal fungi. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130118. [PMID: 36303351 DOI: 10.1016/j.jhazmat.2022.130118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/24/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
The molecular mechanism of arbuscular mycorrhizal fungi (AMF) in vertical flow constructed wetlands (VFCWs) for the purification of copper oxide nanoparticles (CuO-NPs) contaminated wastewater remains unclear. In this study, transcriptome analysis was used to explore the effect of AMF inoculation on the gene expression profile of Phragmites australis roots under different concentrations of CuO-NPs and/or flood stress. 551, 429 and 2281 differentially expressed genes (DEGs) were specially regulated by AMF under combined stresses of CuO-NPs and flood, single CuO-NPs stress and single flood stress, respectively. Based on the results of DEG function annotation and enrichment analyses, AMF inoculation under CuO-NPs and/or flood stress up-regulated the expression of a number of genes involved in antioxidant defense systems, cell wall biosynthesis and transporter protein, which may contribute to plant tolerance. The expression of 30 transcription factors (TFs) was up-regulated by AMF inoculation under combined stresses of CuO-NPs and flood, and 44 and 44 TFs were up-regulated under single CuO-NPs or flood condition, respectively, which may contribute to the alleviating effect of symbiosis on CuO-NPs and/or flood stress. These results provided a theoretical basis for enhancing the ecological restoration function of wetland plants for metallic nanoparticles (MNPs) by mycorrhizal technology in the future.
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Affiliation(s)
- Yihui Ban
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, Hubei, China
| | - Jiayuan Tan
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, Hubei, China
| | - Yang Xiong
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, Hubei, China
| | - Xiantong Mo
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, Hubei, China
| | - Yinghe Jiang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, Hubei, China
| | - Zhouying Xu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, Hubei, China.
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Chirivì D, Betti C. Molecular Links between Flowering and Abiotic Stress Response: A Focus on Poaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:331. [PMID: 36679044 PMCID: PMC9866591 DOI: 10.3390/plants12020331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Extreme temperatures, drought, salinity and soil pollution are the most common types of abiotic stresses crops can encounter in fields; these variations represent a general warning to plant productivity and survival, being more harmful when in combination. Plant response to such conditions involves the activation of several molecular mechanisms, starting from perception to signaling, transcriptional reprogramming and protein modifications. This can influence the plant's life cycle and development to different extents. Flowering developmental transition is very sensitive to environmental stresses, being critical to reproduction and to agricultural profitability for crops. The Poacee family contains some of the most widespread domesticated plants, such as wheat, barley and rice, which are commonly referred to as cereals and represent a primary food source. In cultivated Poaceae, stress-induced modifications of flowering time and development cause important yield losses by directly affecting seed production. At the molecular level, this reflects important changes in gene expression and protein activity. Here, we present a comprehensive overview on the latest research investigating the molecular pathways linking flowering control to osmotic and temperature extreme conditions in agronomically relevant monocotyledons. This aims to provide hints for biotechnological strategies that can ensure agricultural stability in ever-changing climatic conditions.
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Yue L, Pei X, Kong F, Zhao L, Lin X. Divergence of functions and expression patterns of soybean bZIP transcription factors. FRONTIERS IN PLANT SCIENCE 2023; 14:1150363. [PMID: 37123868 PMCID: PMC10146240 DOI: 10.3389/fpls.2023.1150363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Soybean (Glycine max) is a major protein and oil crop. Soybean basic region/leucine zipper (bZIP) transcription factors are involved in many regulatory pathways, including yield, stress responses, environmental signaling, and carbon-nitrogen balance. Here, we discuss the members of the soybean bZIP family and their classification: 161 members have been identified and clustered into 13 groups. Our review of the transcriptional regulation and functions of soybean bZIP members provides important information for future study of bZIP transcription factors and genetic resources for soybean breeding.
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Affiliation(s)
- Lin Yue
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xinxin Pei
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, China
- *Correspondence: Xiaoya Lin, ; Lin Zhao,
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- *Correspondence: Xiaoya Lin, ; Lin Zhao,
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Guan R, Xu S, Lu Z, Su L, Zhang L, Sun W, Zhang Y, Jiang C, Liu Z, Duan L, Ji A. Genomic characterization of bZIP transcription factors related to andrographolide biosynthesis in Andrographis paniculata. Int J Biol Macromol 2022; 223:1619-1631. [PMID: 36356875 DOI: 10.1016/j.ijbiomac.2022.10.283] [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: 07/28/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
Abstract
The basic leucine zipper (bZIP) transcription factor family plays an important role in various biological processes in plants. Andrographis paniculata (Burm.f) Nees, belonging to the family Acanthaceae, has been widely used as an important traditional herb with a wide range of pharmacological activities, such as antivenom, antiretroviral, anticancer and so on. However, there was no comprehensive analysis of bZIP gene family in the Andrographis paniculata been reported. In this study, we identified 62 bZIPs in Andrographis paniculata and grouped them into 12 subfamilies through the phylogenetic tree analysis. The bZIPs in the same groups have similar motif composition, exon-intron structure and domain distribution. In addition, the RNA-seq data gave a reference for selecting candidate bZIPs to make further function verification. Lastly, qRT-PCR analyses revealed seven ApbZIPs (ApbZIP4, ApbZIP19, ApbZIP30, ApbZIP42, ApbZIP50, ApbZIP52, ApbZIP62) were the most highly expressed in leaf and significantly up-regulated with MeJA and ABA treatment which may be involved in biosynthesis regulation of andrographolide. These data pave the way for further revealing the function of the bZIPs in Andrographis paniculata.
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Affiliation(s)
- Rui Guan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shun Xu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhimei Lu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lirong Su
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Libing Zhang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, 100070 Beijing, China
| | - Yu Zhang
- Shanxi University of Chinese Medicine, 030619 Jinzhong, China
| | - Chunhong Jiang
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi Qingfeng Pharmaceutical Co. Ltd., Ganzhou 100022, China
| | - Zhongqiu Liu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Lixin Duan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Aijia Ji
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
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Transcriptome Analysis and Screening of Genes Associated with Flower Size in Tomato ( Solanum lycopersicum). Int J Mol Sci 2022; 23:ijms232415624. [PMID: 36555271 PMCID: PMC9778759 DOI: 10.3390/ijms232415624] [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: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Flower development is not only an important way for tomato reproduction but also an important guarantee for tomato fruit production. Although more and more attention has been paid to the study of flower development, there are few studies on the molecular mechanism and gene expression level of tomato flower development. In this study, RNA-seq analysis was performed on two stages of tomato flower development using the Illumina sequencing platform. A total of 8536 DEGs were obtained by sequencing, including 3873 upregulated DEGs and 4663 down-regulated DEGs. These differentially expressed genes are related to plant hormone signaling, starch and sucrose metabolism. The pathways such as pentose, glucuronate interconversion, and Phenylpropanoid biosynthesis are closely related and mainly involved in plant cellular and metabolic processes. According to the enrichment analysis results of DEGs, active energy metabolism can be inferred during flower development, indicating that flower development requires a large amount of energy and material supply. In addition, some plant hormones, such as GA, may also have effects on flower development. Combined with previous studies, the expression levels of Solyc02g087860 and three of bZIPs were significantly increased in the full flowering stage compared with the flower bud stage, indicating that these genes may be closely related to flower development. These genes were previously reported in Arabidopsis but not in tomatoes. Our next work will conduct a detailed functional analysis of the identified bZIP family genes to characterize their association with tomato flower size. This study will provide new genetic resources for flower formation and provide a basis for tomato yield breeding.
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Brhane H, Haileselassie T, Tesfaye K, Ortiz R, Hammenhag C, Abreha KB, Vetukuri RR, Geleta M. Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources. FRONTIERS IN PLANT SCIENCE 2022; 13:1068383. [PMID: 36570897 PMCID: PMC9780683 DOI: 10.3389/fpls.2022.1068383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet's genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.
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Affiliation(s)
- Haftom Brhane
- Biology Department, Aksum University, Aksum, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kibrom B. Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Wai AH, Rahman MM, Waseem M, Cho LH, Naing AH, Jeon JS, Lee DJ, Kim CK, Chung MY. Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of PLATZ Gene Family Members in Solanum Lycopersicum L. under Multiple Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223112. [PMID: 36432841 PMCID: PMC9697139 DOI: 10.3390/plants11223112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 05/29/2023]
Abstract
PLATZ (plant AT-rich sequence and zinc-binding) family proteins with two conserved zinc-dependent DNA-binding motifs are transcription factors specific to the plant kingdom. The functions of PLATZ proteins in growth, development, and adaptation to multiple abiotic stresses have been investigated in various plant species, but their role in tomato has not been explored yet. In the present work, 20 non-redundant Solanum lycopersicum PLATZ (SlPLATZ) genes with three segmentally duplicated gene pairs and four tandemly duplicated gene pairs were identified on eight tomato chromosomes. The comparative modeling and gene ontology (GO) annotations of tomato PLATZ proteins indicated their probable roles in defense response, transcriptional regulation, and protein metabolic processes as well as their binding affinity for various ligands, including nucleic acids, peptides, and zinc. SlPLATZ10 and SlPLATZ17 were only expressed in 1 cm fruits and flowers, respectively, indicating their preferential involvement in the development of these organs. The expression of SlPLATZ1, SlPLATZ12, and SlPLATZ19 was up- or down-regulated following exposure to various abiotic stresses, whereas that of SlPLATZ11 was induced under temperature stresses (i.e., cold and heat stress), revealing their probable function in the abiotic stress tolerance of tomato. Weighted gene co-expression network analysis corroborated the aforementioned findings by spotlighting the co-expression of several stress-associated genes with SlPLATZ genes. Confocal fluorescence microscopy revealed the localization of SlPLATZ−GFP fusion proteins in the nucleus, hinting at their functions as transcription factors. These findings provide a foundation for a better understanding of the structure and function of PLATZ genes and should assist in the selection of potential candidate genes involved in the development and abiotic stress adaptation in tomato.
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Affiliation(s)
- Antt Htet Wai
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
- Department of Biology, Yangon University of Education, Kamayut Township 11041, Yangon Region, Myanmar
| | - Md Mustafizur Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Muhammad Waseem
- Department of Botany, University of Narowal, Narowal 51600, Pakistan
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si 50463, Gyeongsangnam-do, Republic of Korea
| | - Aung Htay Naing
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Do-jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
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Hussain S, Cheng Y, Li Y, Wang W, Tian H, Zhang N, Wang Y, Yuan Y, Hussain H, Lin R, Wang C, Wang T, Wang S. AtbZIP62 Acts as a Transcription Repressor to Positively Regulate ABA Responses in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2022; 11:3037. [PMID: 36432766 PMCID: PMC9699195 DOI: 10.3390/plants11223037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The basic region/leucine zipper (bZIP) transcription factor AtbZIP62 is involved in the regulation of plant responses to abiotic stresses, including drought and salinity stresses, NO3 transport, and basal defense in Arabidopsis. It is unclear if it plays a role in regulating plant responses to abscisic acid (ABA), a phytohormone that can regulate plant abiotic stress responses via regulating downstream ABA-responsive genes. Using RT-PCR analysis, we found that the expression level of AtbZIP62 was increased in response to exogenously applied ABA. Protoplast transfection assays show that AtbZIP62 is predominantly localized in the nucleus and functions as a transcription repressor. To examine the roles of AtbZIP62 in regulating ABA responses, we generated transgenic Arabidopsis plants overexpressing AtbZIP62 and created gene-edited atbzip62 mutants using CRISPR/Cas9. We found that in both ABA-regulated seed germination and cotyledon greening assays, the 35S:AtbZIP62 transgenic plants were hypersensitive, whereas atbzip62 mutants were hyposensitive to ABA. To examine the functional mechanisms of AtbZIP62 in regulating ABA responses, we generated Arabidopsis transgenic plants overexpressing 35S:AtbZIP62-GR, and performed transcriptome analysis to identify differentially expressed genes (DEGs) in the presence and absence of DEX, and found that DEGs are highly enriched in processes including response to abiotic stresses and response to ABA. Quantitative RT-PCR results further show that AtbZIP62 may regulate the expression of several ABA-responsive genes, including USP, ABF2, and SnRK2.7. In summary, our results show that AtbZIP62 is an ABA-responsive gene, and AtbZIP62 acts as a transcription repressor to positively regulate ABA responses in Arabidopsis.
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Affiliation(s)
- Saddam Hussain
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Yuxin Cheng
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Yingying Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Wei Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China
| | - Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Na Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Yating Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Yuan Yuan
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Hadia Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Rao Lin
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Chen Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China
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Transcriptome analysis of response strategy in Hemerocallis fulva under drought stress. Genes Genomics 2022; 45:593-610. [PMID: 36348249 DOI: 10.1007/s13258-022-01335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Hemerocallis fulva is an important ground cover plant widely used in urban greening. The analysis of the molecular mechanism underlying the drought response of H. fulva can lay a foundation for improving its adaptability and expanding its planting area. OBJECTIVE To reveal the drought response mechanisms of H. fulva, identify candidate unigenes associated with drought response, and lay a foundation for further unigenes functional study and drought resistance improvement of H. fulva via genetic engineering. METHODS RNA was isolated from H. fulva under different experimental conditions. De novo transcriptomic analysis of the samples was performed to screen drought response unigenes. The transcriptional changes of candidate drought response unigenes were verified by quantitative real-time PCR. RESULTS The differentially expressed unigenes and their functions were analyzed after H. fulva treated by PEG-simulated drought stress and rewatering. The candidate unigenes, associated with H. fulva drought response, were identified after transcriptome analysis. Then, the transcription level of drought response unigenes of H. fulva under different conditions was further verified. Abscisic acid, protein phosphorylation, sterol biosynthesis and ion transport were involved in drought response with quick restore in H. fulva. The response unigenes, involved in hormone (ABA, JA, CK and GA) signaling pathways, defense response, high light response, karrikin response and leaf shaping, can maintain at changed expression levels even after stress withdraw. CONCLUSION Hemerocallis fulva has unique drought response mechanism. Negative regulation mechanism may play more important roles in drought response of H. fulva. The analysis of candidate unigenes, associated with drought response, lays a foundation for further drought resistance improvement of H. fulva.
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Zhang Y, Gao H, Fang J, Wang H, Chen J, Li J, Dong L. Up-regulation of bZIP88 transcription factor is involved in resistance to three different herbicides in both Echinochloa crus-galli and E. glabrescens. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6916-6930. [PMID: 35867472 DOI: 10.1093/jxb/erac319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The resistance of weeds to herbicides poses a major threat to agricultural production, and non-target-site resistance (NTSR) is often a serious problem as its mechanisms can in some cases confer resistance to herbicides with different modes of action. In this study, we hypothesized that bZIP transcription factors (TFs), which regulate abiotic stress responses in many plants, play a regulatory role in NTSR. Whole-plant assays indicated that the wild grasses Echinochloa crus-galli and E. glabrescens are resistant to the herbicides penoxsulam, cyhalofop-butyl, and quintrione. Transcriptome sequencing then identified 101 and 49 bZIP TFs with differential expression following penoxsulam treatment in E. crus-galli and E. glabrescens, respectively. Twelve of these genes had >60% homology with rice genes. The expression of bZIP88 was considerably up-regulated 6 h after treatment with the three different herbicides, and it was similar between resistant and susceptible populations; however, the relative expression levels before herbicide treatment and 24 h after were the same. We used rice (Oryza sativa ssp. japonica cv Nipponbare) as a model system for functional validation and found that CRISPR-Cas9-knockout of the rice bZIP88 ortholog increased the sensitivity to herbicide, whereas overexpression reduced it. The OsbZIP88 protein was localized to the nucleus. Using ChIP coupled with high-throughput sequencing, OsbZIP88 was found to form a network regulatory center with other TFs such as bZIP20/52/59 to regulate OsKS1, OsCOE1, and OsIM1, which are related to auxin, abscisic acid, brassinosteroids, and gibberellic acid. Based on these results, we have established a database of bZIP TFs corresponding to herbicide stress, and resolved the mechanisms of the positive regulation of herbicide resistance by bZIP88, thereby providing new insights for NTSR.
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Affiliation(s)
- Yuhua Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, China
| | - Haitao Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, China
| | - Jiapeng Fang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, China
| | - Hao Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, China
| | - Jinyi Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, China
| | - Jun Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, China
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, China
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Weng W, Lu X, Zhou M, Gao A, Yao X, Tang Y, Wu W, Ma C, Bai Q, Xiong R, Ruan J. FtbZIP12 Positively Regulates Responses to Osmotic Stress in Tartary Buckwheat. Int J Mol Sci 2022; 23:ijms232113072. [PMID: 36361858 PMCID: PMC9658761 DOI: 10.3390/ijms232113072] [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: 10/06/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
ABFs play a key role in regulating plant osmotic stress. However, in Tartary buckwheat, data on the role of ABF genes in osmotic stress remain limited and its associated mechanism in osmoregulation remain nebulous. Herein, a novel ABF family in Tartary buckwheat, FtbZIP12, was cloned and characterized. FtbZIP12 is a transcriptional activator located in the nucleus; its expression is induced by NaCl, mannitol, and abscisic acid (ABA). Atopic expression of FtbZIP12 in Arabidopsis promoted seed germination, reduced damage to primary roots, and improved the tolerance of seedlings to osmotic stress. The quantitative realtime polymerase chain reaction (RT-qPCR) results showed that the expressions of the typical genes related to stress, the SOS pathway, and the proline synthesis pathway in Arabidopsis were significantly (p < 0.05) upregulated under osmotic stress. FtbZIP12 improved the osmotic pressure resistance by reducing the damage caused by reactive oxygen species to plants and maintained plant homeostasis by upregulating the expression of genes related to stress, osmotic regulation, and ion homeostasis. This study identified a key candidate gene for understanding the mechanism underlying osmotic-stress-regulated function in Tartary buckwheat, thereby providing a theoretical basis for improving its yield and quality.
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Affiliation(s)
- Wenfeng Weng
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Xiang Lu
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Meiliang Zhou
- Institute of Crop Science, Chinese Academy of Agriculture Science, Beijing 100081, China
| | - Anjing Gao
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Xin Yao
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Yong Tang
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Weijiao Wu
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Chao Ma
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Qing Bai
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Ruiqi Xiong
- College of Agronomy, Guizhou University, Guiyang 550025, China
| | - Jingjun Ruan
- College of Agronomy, Guizhou University, Guiyang 550025, China
- Correspondence:
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Ahmad M. Genomics and transcriptomics to protect rice ( Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger. FRONTIERS IN PLANT SCIENCE 2022; 13:1002596. [PMID: 36340401 PMCID: PMC9630331 DOI: 10.3389/fpls.2022.1002596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.
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Affiliation(s)
- Mushtaq Ahmad
- Visiting Scientist Plant Sciences, University of Nebraska, Lincoln, NE, United States
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Transcriptome Analysis of Low-Temperature-Treated Tetraploid Yellow Actinidia chinensis Planch. Tissue Culture Plantlets. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101573. [PMID: 36295009 PMCID: PMC9604649 DOI: 10.3390/life12101573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
Simple Summary Yellow kiwifruit (Actinidia chinensis Planch.) is popular in the market. However, it is highly susceptible to severe weather, including as low temperatures and frost, which may affect its production in the coming year. The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. To better understand cold-adaptive mechanisms, we grew plants under low-temperature conditions, which was followed by transcriptome analysis to discern the genes that play an active role in growth under low temperatures. The findings and dataset obtained in this study advance our knowledge of the cold-adaptive genes in regulatory networks and helps us to understand the cold-tolerance mechanisms in the tetraploid yellow kiwifruit. Abstract The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. In this study, to provide insight into the causes of differences in low-temperature tolerance and to better understand cold-adaptive mechanisms, we treated yellow tetraploid kiwifruit ‘SWFU03’ tissue culture plantlets at low temperatures, used these plantlets for transcriptome analysis, and validated the expression levels of ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. A number of 1630 differentially expressed genes (DEGs) were identified, of which 619 pathway genes were up-regulated, and 1011 were down-regulated in the cold treatment group. The DEGs enriched in the cold tolerance-related pathways mainly included the plant hormone signal transduction and the starch and sucrose metabolism pathway. RT-qPCR analysis confirmed the expression levels of eight up-regulated genes in these pathways in the cold-resistant mutants. In this study, cold tolerance-related pathways (the plant hormone signal transduction and starch and sucrose metabolism pathway) and genes, e.g., CEY00_Acc03316 (abscisic acid receptor PYL), CEY00_Acc13130 (bZIP transcription factor), CEY00_Acc33627 (TIFY protein), CEY00_Acc26744 (alpha-trehalose-phosphate synthase), CEY00_Acc28966 (beta-amylase), CEY00_Acc16756 (trehalose phosphatase), and CEY00_Acc08918 (beta-amylase 4) were found.
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Lu C, Tian Y, Hou X, Hou X, Jia Z, Li M, Hao M, Jiang Y, Wang Q, Pu Q, Yin Z, Li Y, Liu B, Kang X, Zhang G, Ding X, Liu Y. Multiple forms of vitamin B 6 regulate salt tolerance by balancing ROS and abscisic acid levels in maize root. STRESS BIOLOGY 2022; 2:39. [PMID: 37676445 PMCID: PMC10441934 DOI: 10.1007/s44154-022-00061-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/22/2022] [Indexed: 09/08/2023]
Abstract
Salt stress causes osmotic stress, ion toxicity and oxidative stress, inducing the accumulation of abscisic acid (ABA) and excessive reactive oxygen species (ROS) production, which further damage cell structure and inhibit the development of roots in plants. Previous study showed that vitamin B6 (VB6) plays a role in plant responses to salt stress, however, the regulatory relationship between ROS, VB6 and ABA under salt stress remains unclear yet in plants. In our study, we found that salt stress-induced ABA accumulation requires ROS production, in addition, salt stress also promoted VB6 (including pyridoxamine (PM), pyridoxal (PL), pyridoxine (PN), and pyridoxal 5'-phosphate (PLP)) accumulation, which involved in ROS scavenging and ABA biosynthesis. Furthermore, VB6-deficient maize mutant small kernel2 (smk2) heterozygous is more susceptible to salt stress, and which failed to scavenge excessive ROS effectively or induce ABA accumulation in maize root under salt stress, interestingly, which can be restored by exogenous PN and PLP, respectively. According to these results, we proposed that PN and PLP play an essential role in balancing ROS and ABA levels under salt stress, respectively, it laid a foundation for VB6 to be better applied in crop salt resistance than ABA.
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Affiliation(s)
- Chongchong Lu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xuanxuan Hou
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xin Hou
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Zichang Jia
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Min Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Mingxia Hao
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yanke Jiang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Qingbin Wang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
- Shandong Pengbo Biotechnology Co., LTD, Taian, 271018, China
| | - Qiong Pu
- Shandong Agriculture and Engineering University, Jinan, 250000, Shandong, China
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Baoyou Liu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
- Yantai Academy of Agricultural Sciences, Yantai, 265500, Shandong, China
| | - Xiaojing Kang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Guangyi Zhang
- Shandong Xinyuan Seed Industry Co., LTD, Taian, 271000, China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China.
| | - Yinggao Liu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection; Shandong Agricultural University, Taian, 271018, Shandong, China.
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Xu Z, Wang F, Ma Y, Dang H, Hu X. Transcription Factor SlAREB1 Is Involved in the Antioxidant Regulation under Saline–Alkaline Stress in Tomato. Antioxidants (Basel) 2022; 11:antiox11091673. [PMID: 36139748 PMCID: PMC9495317 DOI: 10.3390/antiox11091673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/05/2022] Open
Abstract
Basic leucine zipper (bZIP) transcription factors of the ABA-responsive element binding factor/ABA-responsive element binding proteins (ABF/AREB) subfamily have been implicated in abscisic acid (ABA) and abiotic stress responses in plants. However, the specific function of ABF/AREB transcription factors under saline–alkaline stress is unclear. Here, we identified four ABF/AREB transcription factors in tomato and found that SlAREB1 strongly responded to both ABA and saline–alkaline stress. To further explore the function of SlAREB1 under saline–alkaline stress, SlAREB1-overexpressing lines were constructed. Compared with wild-type plants, SlAREB1-overexpressing transgenic tomato plants showed reduced malondialdehyde content, increased the relative water content, and alleviated the degradation of chlorophyll under saline–alkaline stress. Importantly, SlAREB1 directly physically interacted with SlMn-SOD, which improved the activity of antioxidant enzymes and increased the scavenging of excess reactive oxygen species. Overall, the overexpression of SlAREB1 increased the antioxidant capacity of the transgenic tomato under saline–alkaline stress.
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Affiliation(s)
- Zijian Xu
- College of Horticulture, Northwest AF University, Xianyang 712100, China
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Xianyang 712100, China
- Shaanxi Protected Agriculture Research Centre, Xianyang 712100, China
| | - Fan Wang
- College of Horticulture, Northwest AF University, Xianyang 712100, China
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Xianyang 712100, China
- Shaanxi Protected Agriculture Research Centre, Xianyang 712100, China
| | - Yongbo Ma
- College of Horticulture, Northwest AF University, Xianyang 712100, China
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Xianyang 712100, China
- Shaanxi Protected Agriculture Research Centre, Xianyang 712100, China
| | - Haoran Dang
- College of Horticulture, Northwest AF University, Xianyang 712100, China
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Xianyang 712100, China
- Shaanxi Protected Agriculture Research Centre, Xianyang 712100, China
| | - Xiaohui Hu
- College of Horticulture, Northwest AF University, Xianyang 712100, China
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Xianyang 712100, China
- Shaanxi Protected Agriculture Research Centre, Xianyang 712100, China
- Correspondence:
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Ahmar S, Gruszka D. In-Silico Study of Brassinosteroid Signaling Genes in Rice Provides Insight Into Mechanisms Which Regulate Their Expression. Front Genet 2022; 13:953458. [PMID: 35873468 PMCID: PMC9299959 DOI: 10.3389/fgene.2022.953458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022] Open
Abstract
Brassinosteroids (BRs) regulate a diverse spectrum of processes during plant growth and development and modulate plant physiology in response to environmental fluctuations and stress factors. Thus, the BR signaling regulators have the potential to be targeted for gene editing to optimize the architecture of plants and make them more resilient to environmental stress. Our understanding of the BR signaling mechanism in monocot crop species is limited compared to our knowledge of this process accumulated in the model dicot species - Arabidopsis thaliana. A deeper understanding of the BR signaling and response during plant growth and adaptation to continually changing environmental conditions will provide insight into mechanisms that govern the coordinated expression of the BR signaling genes in rice (Oryza sativa) which is a model for cereal crops. Therefore, in this study a comprehensive and detailed in silico analysis of promoter sequences of rice BR signaling genes was performed. Moreover, expression profiles of these genes during various developmental stages and reactions to several stress conditions were analyzed. Additionally, a model of interactions between the encoded proteins was also established. The obtained results revealed that promoters of the 39 BR signaling genes are involved in various regulatory mechanisms and interdependent processes that influence growth, development, and stress response in rice. Different transcription factor-binding sites and cis-regulatory elements in the gene promoters were identified which are involved in regulation of the genes’ expression during plant development and reactions to stress conditions. The in-silico analysis of BR signaling genes in O. sativa provides information about mechanisms which regulate the coordinated expression of these genes during rice development and in response to other phytohormones and environmental factors. Since rice is both an important crop and the model species for other cereals, this information may be important for understanding the regulatory mechanisms that modulate the BR signaling in monocot species. It can also provide new ways for the plant genetic engineering technology by providing novel potential targets, either cis-elements or transcriptional factors, to create elite genotypes with desirable traits.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
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Gao W, Li M, Yang S, Gao C, Su Y, Zeng X, Jiao Z, Xu W, Zhang M, Xia K. miR2105 and the kinase OsSAPK10 co-regulate OsbZIP86 to mediate drought-induced ABA biosynthesis in rice. PLANT PHYSIOLOGY 2022; 189:889-905. [PMID: 35188194 PMCID: PMC9157147 DOI: 10.1093/plphys/kiac071] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/15/2022] [Indexed: 05/27/2023]
Abstract
Mediating induced abscisic acid (ABA) biosynthesis is important for enhancing plant stress tolerance. Here, we found that rice (Oryza sativa L.) osa-miR2105 (miR2105) and the Stress/ABA-activated protein kinase (OsSAPK10) coordinately regulate the rice basic region-leucine zipper transcription factor (bZIP TF; OsbZIP86) at the posttranscriptional and posttranslational levels to control drought-induced ABA biosynthesis via modulation of rice 9-cis-epoxycarotenoid dioxygenase (OsNCED3) expression. OsbZIP86 expression is regulated by miR2105-directed cleavage of the OsbZIP86 mRNA. OsbZIP86 encodes a nuclear TF that binds to the promoter of the ABA biosynthetic gene OsNCED3. OsSAPK10 can phosphorylate and activate OsbZIP86 to enhance the expression of OsNCED3. Under normal growth conditions, altered expression of miR2105 and OsbZIP86 displayed no substantial effect on rice growth. However, under drought conditions, miR2105 knockdown or OsbZIP86 overexpression transgenic rice plants showed higher ABA content, enhanced tolerance to drought, lower rates of water loss, and more stomatal closure of seedlings, compared with wild-type rice Zhonghua 11; in contrast, miR2105 overexpression, OsbZIP86 downregulation, and OsbZIP86 knockout plants displayed opposite phenotypes. Collectively, our results show that the "miR2105-(OsSAPK10)-OsbZIP86-OsNCED3" module regulates the drought-induced ABA biosynthesis without penalty on rice growth under normal conditions, suggesting candidates for improving drought tolerance in rice.
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Affiliation(s)
- Weiwei Gao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Mingkang Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chunzhi Gao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yan Su
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuan Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhengli Jiao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weijuan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L. Int J Mol Sci 2022; 23:ijms23115961. [PMID: 35682645 PMCID: PMC9180593 DOI: 10.3390/ijms23115961] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 01/08/2023] Open
Abstract
Basic leucine zipper (bZIP), a conserved transcription factor widely found in eukaryotes, has important regulatory roles in plant growth. To understand the information related to the bZIP gene family in walnut, 88 JrbZIP genes were identified at the genome-wide level and classified into 13 subfamilies (A, B, C, D, E, F, G, H, I, J, K, M, and S) using a bioinformatic approach. The number of exons in JrbZIPs ranged from 1 to 12, the number of amino acids in JrbZIP proteins ranged from 145 to 783, and the isoelectric point ranged from 4.85 to 10.05. The majority of JrbZIP genes were localized in the nucleus. The promoter prediction results indicated that the walnut bZIP gene contains a large number of light-responsive and jasmonate-responsive action elements. The 88 JrbZIP genes were involved in DNA binding and nucleus and RNA biosynthetic processes of three ontological categories, molecular functions, cellular components and biological processes. The codon preference analysis showed that the bZIP gene family has a stronger bias for AGA, AGG, UUG, GCU, GUU, and UCU than other codons. Moreover, the transcriptomic data showed that JrbZIP genes might play an important role in floral bud differentiation. The results of a protein interaction network map and kegg enrichment analysis indicated that bZIP genes were mainly involved in phytohormone signaling, anthocyanin synthesis and flowering regulation. qRT-PCR demonstrated the role of the bZIP gene family in floral bud differentiation. Co-expression network maps were constructed for 29 walnut bZIP genes and 6 flowering genes, and JrCO (a homolog of AtCO) was significantly correlated (p < 0.05) with 13 JrbZIP genes in the level of floral bud differentiation expression, including JrbZIP31 (homolog of AtFD), and JrLFY was significantly and positively correlated with JrbZIP10,11,51,59,67 (p < 0.05), and the above results suggest that bZIP family genes may act together with flowering genes to regulate flower bud differentiation in walnut. This study was the first genome-wide report of the walnut bZIP gene family, which could improve our understanding of walnut bZIP proteins and provide a solid foundation for future cloning and functional analyses of this gene family.
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Lu Z, Qiu W, Jin K, Yu M, Han X, He X, Wu L, Wu C, Zhuo R. Identification and Analysis of bZIP Family Genes in Sedum plumbizincicola and Their Potential Roles in Response to Cadmium Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:859386. [PMID: 35574076 PMCID: PMC9094143 DOI: 10.3389/fpls.2022.859386] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/29/2022] [Indexed: 05/23/2023]
Abstract
Sedum plumbizincicola (Crassulaceae), a cadmium (Cd)/zinc (Zn)/lead (Pb) hyperaccumulator native to Southeast China, is potentially useful for the phytoremediation of heavy metal-contaminated soil. Basic leucine zipper (bZIP) transcription factors play vital roles in plant growth, development, and abiotic stress responses. However, there has been minimal research on the effects of Cd stress on the bZIP gene family in S. plumbizincicola. In this study, 92 SpbZIP genes were identified in the S. plumbizincicola genome and then classified into 12 subgroups according to their similarity to bZIP genes in Arabidopsis. Gene structure and conserved motif analyses showed that SpbZIP genes within the same subgroup shared similar intron-exon structures and motif compositions. In total, eight pairs of segmentally duplicated SpbZIP genes were identified, but there were no tandemly duplicated SpbZIP genes. Additionally, the duplicated SpbZIP genes were mainly under purifying selection pressure. Hormone-responsive, abiotic and biotic stress-responsive, and plant development-related cis-acting elements were detected in the SpbZIP promoter sequences. Expression profiles derived from RNA-seq and quantitative real-time PCR analyses indicated that the expression levels of most SpbZIP genes were upregulated under Cd stress conditions. Furthermore, a gene co-expression network analysis revealed that most edge genes regulated by hub genes were related to metal transport, responses to stimuli, and transcriptional regulation. Because its expression was significantly upregulated by Cd stress, the hub gene SpbZIP60 was selected for a functional characterization to elucidate its role in the root response to Cd stress. In a transient gene expression analysis involving Nicotiana benthamiana leaves, SpbZIP60 was localized in the nucleus. The overexpression of SpbZIP60 enhanced the Cd tolerance of transgenic Arabidopsis plants by inhibiting ROS accumulation, protecting the photosynthetic apparatus, and decreasing the Cd content. These findings may provide insights into the potential roles of the bZIP family genes during the S. plumbizincicola response to Cd stress.
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Affiliation(s)
- Zhuchou Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Faculty of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wenmin Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Kangming Jin
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Miao Yu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xiaoyang He
- Agricultural Technology Extension Centre of Dongtai, Yancheng, China
| | - Longhua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Chao Wu
- Institute of Horticulture, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Renyin Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Comparative Transcriptome Analysis of Two Sweet Sorghum Genotypes with Different Salt Tolerance Abilities to Reveal the Mechanism of Salt Tolerance. Int J Mol Sci 2022; 23:ijms23042272. [PMID: 35216389 PMCID: PMC8877675 DOI: 10.3390/ijms23042272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 12/13/2022] Open
Abstract
Sweet sorghum is a C4 crop that can be grown for silage forage, fiber, syrup and fuel production. It is generally considered a salt-tolerant plant. However, the salt tolerance ability varies among genotypes, and the mechanism is not well known. To further uncover the salt tolerance mechanism, we performed comparative transcriptome analysis with RNA samples in two sweet sorghum genotypes showing different salt tolerance abilities (salt-tolerant line RIO and salt-sensitive line SN005) upon salt treatment. These response processes mainly focused on secondary metabolism, hormone signaling and stress response. The expression pattern cluster analysis showed that RIO-specific response genes were significantly enriched in the categories related to secondary metabolic pathways. GO enrichment analysis indicated that RIO responded earlier than SN005 in the 2 h after treatment. In addition, we identified more transcription factors (TFs) in RIO than SN005 that were specifically expressed differently in the first 2 h of salt treatment, and the pattern of TF change was obviously different. These results indicate that an early response in secondary metabolism might be essential for salt tolerance in sweet sorghum. In conclusion, we found that an early response, especially in secondary metabolism and hormone signaling, might be essential for salt tolerance in sweet sorghum.
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Muhammad Aslam M, Waseem M, Jakada BH, Okal EJ, Lei Z, Saqib HSA, Yuan W, Xu W, Zhang Q. Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants. Int J Mol Sci 2022; 23:ijms23031084. [PMID: 35163008 PMCID: PMC8835272 DOI: 10.3390/ijms23031084] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.
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Affiliation(s)
- Mehtab Muhammad Aslam
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Muhammad Waseem
- Department of Botany, University of Narowal, Narowal 51600, Pakistan;
- College of Horticulture, Hainan University, Haikou 570100, China
| | - Bello Hassan Jakada
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, College of Life Science, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou 350002, China;
| | - Eyalira Jacob Okal
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
| | - Zuliang Lei
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
| | - Hafiz Sohaib Ahmad Saqib
- Guangdong Provincial Key Laboratory of Marine Biology, College of Science, Shantou University, Shantou 515063, China;
| | - Wei Yuan
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Correspondence: (W.Y.); (Q.Z.)
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qian Zhang
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (Z.L.); (W.X.)
- Correspondence: (W.Y.); (Q.Z.)
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Insight into gene regulatory networks involved in sesame (Sesamum indicum L.) drought response. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Abuslima E, Kanbar A, Raorane ML, Eiche E, Junker BH, Hause B, Riemann M, Nick P. Gain time to adapt: How sorghum acquires tolerance to salinity. FRONTIERS IN PLANT SCIENCE 2022; 13:1008172. [PMID: 36325549 PMCID: PMC9619063 DOI: 10.3389/fpls.2022.1008172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/05/2022] [Indexed: 05/14/2023]
Abstract
Salinity is a global environmental threat to agricultural production and food security around the world. To delineate salt-induced damage from adaption events we analysed a pair of sorghum genotypes which are contrasting in their response to salt stress with respect to physiological, cellular, metabolomic, and transcriptional responses. We find that the salt-tolerant genotype Della can delay the transfer of sodium from the root to the shoot, more swiftly deploy accumulation of proline and antioxidants in the leaves and transfer more sucrose to the root as compared to its susceptible counterpart Razinieh. Instead Razinieh shows metabolic indicators for a higher extent photorespiration under salt stress. Following sodium accumulation by a fluorescent dye in the different regions of the root, we find that Della can sequester sodium in the vacuoles of the distal elongation zone. The timing of the adaptive responses in Della leaves indicates a rapid systemic signal from the roots that is travelling faster than sodium itself. We arrive at a model where resistance and susceptibility are mainly a matter of temporal patterns in signalling.
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Affiliation(s)
- Eman Abuslima
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Egypt
- *Correspondence: Eman Abuslima,
| | - Adnan Kanbar
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Manish L. Raorane
- Institute of Pharmacy, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
| | - Elisabeth Eiche
- Institute of Applied Geosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Laboratory for Environmental and Raw Materials Analysis (LERA), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Björn H. Junker
- Institute of Pharmacy, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
| | - Bettina Hause
- Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry (IPB), Halle, Germany
| | - Michael Riemann
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Li M, Hwarari D, Li Y, Ahmad B, Min T, Zhang W, Wang J, Yang L. The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:1035627. [PMID: 36420021 PMCID: PMC9676487 DOI: 10.3389/fpls.2022.1035627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 05/08/2023]
Abstract
The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.
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Affiliation(s)
- Mingyue Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yang Li
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Baseer Ahmad
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tian Min
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Wenting Zhang
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jinyan Wang
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Jinyan Wang, ; Liming Yang,
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jinyan Wang, ; Liming Yang,
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Jiménez VM, Carvajal-Campos P. Ingeniería genética contra estrés abiótico en cultivos neotropicales: osmolitos, factores de transcripción y CRISPR/Cas9. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2021. [DOI: 10.15446/rev.colomb.biote.v23n2.88487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El neotrópico es sitio de origen de gran variedad de plantas que actualmente son cultivadas con éxito en diferentes regiones del mundo. Sin embargo, condiciones climáticas adversas, que se pueden ver acrecentadas por efectos del cambio climático antropogénico, pueden afectar su rendimiento y productividad debido a las situaciones de estrés abiótico que se pueden generar. Como alternativa para contrarrestar estos efectos, se ha experimentado con modificaciones genéticas, particularmente en genes relacionados con la producción de osmolitos y factores de transcripción que han llevado a que estas plantas, a nivel experimental, tengan mayor tolerancia a estrés oxidativo, altas y bajas temperaturas y fotoinhibición, sequía y salinidad, mediante la acumulación de osmoprotectores, la regulación en la expresión de genes y cambios en el fenotipo. En este trabajo se presentan y describen las estrategias metodológicas planteadas con estos fines y se complementan con ejemplos de trabajos realizados en cultivos de origen neotropical de importancia económica, como maíz, algodón, papa y tomate. Además, y debido a la novedad y potencial que ofrece la edición génica por medio del sistema CRISPR/Cas9, también se mencionan trabajos realizados en plantas con origen neotropical, enfocados en comprender e implementar mecanismos de tolerancia a sequía. Las metodologías aquí descritas podrían constituirse en opciones prácticas para mejorar la seguridad alimentaria con miras a contrarrestar las consecuencias negativas del cambio climático antropogénico.
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Pi B, Pan J, Xiao M, Hu X, Zhang L, Chen M, Liu B, Ruan Y, Huang Y. Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance. BMC PLANT BIOLOGY 2021; 21:555. [PMID: 34814855 PMCID: PMC8609832 DOI: 10.1186/s12870-021-03340-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/10/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND CCCH zinc finger family is one of the largest transcription factor families related to multiple biotic and abiotic stresses. Brassica napus L., an allotetraploid oilseed crop formed by natural hybridization between two diploid progenitors, Brassica rapa and Brassica oleracea. A systematic identification of rapeseed CCCH family genes is missing and their functional characterization is still in infancy. RESULTS In this study, 155 CCCH genes, 81 from its parent B. rapa and 74 from B. oleracea, were identified and divided into 15 subfamilies in B. napus. Organization and syntenic analysis explained the distribution and collinearity relationship of CCCH genes, the selection pressure and evolution of duplication gene pairs in B. napus genome. 44 diploid duplication gene pairs and 4 triple duplication gene groups were found in B. napus of CCCH family and the segmental duplication is attributed to most CCCH gene duplication events in B. napus. Nine types of CCCH motifs exist in B. napus CCCH family members, and motif C-X7/8-C-X5-C-X3-H is the most common and a new conserved CCH motif (C-X5-C-X3-H) has been identified. In addition, abundant stress-related cis-elements exist in promoters of 27 subfamily IX (RR-TZF) genes and their expression profiles indicated that RR-TZF genes could be involved in responses to hormone and abiotic stress. CONCLUSIONS The results provided a foundation to understand the basic characterization and genes evolution of CCCH gene family in B. napus, and provided potential targets for genetic engineering in Brassicaceae crops in pursuit of stress-tolerant traits.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Jiao Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Mu Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Xinchang Hu
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Lei Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Min Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Boyu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China.
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50
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Wai AH, Cho LH, Peng X, Waseem M, Lee DJ, Lee JM, Kim CK, Chung MY. Genome-wide identification and expression profiling of Alba gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.). BMC PLANT BIOLOGY 2021; 21:530. [PMID: 34772358 PMCID: PMC8588595 DOI: 10.1186/s12870-021-03310-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/02/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Alba (Acetylation lowers binding affinity) proteins are an ancient family of nucleic acid-binding proteins that function in gene regulation, RNA metabolism, mRNA translatability, developmental processes, and stress adaptation. However, comprehensive bioinformatics analysis on the Alba gene family of Solanum lycopersicum has not been reported previously. RESULTS In the present study, we undertook the first comprehensive genome-wide characterization of the Alba gene family in tomato (Solanum lycopersicum L.). We identified eight tomato Alba genes, which were classified into two groups: genes containing a single Alba domain and genes with a generic Alba domain and RGG/RG repeat motifs. Cis-regulatory elements and target sites for miRNAs, which function in plant development and stress responses, were prevalent in SlAlba genes. To explore the structure-function relationships of tomato Alba proteins, we predicted their 3D structures, highlighting their likely interactions with several putative ligands. Confocal microscopy revealed that SlAlba-GFP fusion proteins were localized to the nucleus and cytoplasm, consistent with putative roles in various signalling cascades. Expression profiling revealed the differential expression patterns of most SlAlba genes across diverse organs. SlAlba1 and SlAlba2 were predominantly expressed in flowers, whereas SlAlba5 expression peaked in 1 cm-diameter fruits. The SlAlba genes were differentially expressed (up- or downregulated) in response to different abiotic stresses. All but one of these genes were induced by abscisic acid treatment, pointing to their possible regulatory roles in stress tolerance via an abscisic acid-dependent pathway. Furthermore, co-expression of SlAlba genes with multiple genes related to several metabolic pathways spotlighted their crucial roles in various biological processes and signalling. CONCLUSIONS Our characterization of SlAlba genes should facilitate the discovery of additional genes associated with organ and fruit development as well as abiotic stress adaptation in tomato.
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Affiliation(s)
- Antt Htet Wai
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950 Republic of Korea
- Department of Biology, Yangon University of Education, Kamayut Township, Yangon Region 11041 Myanmar
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do 50463 Republic of Korea
| | - Xin Peng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Muhammad Waseem
- College of horticulture, South China Agricultural University, Guangzhou, China
| | - Do-jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950 Republic of Korea
| | - Je-Min Lee
- Department of Horticulture, Kyungpook National University, Daegu, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu, Republic of Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950 Republic of Korea
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