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Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gordân R, Llinás M. DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2024:gkae585. [PMID: 38966997 DOI: 10.1093/nar/gkae585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/30/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized two additional ApiAP2 TFs, PfAP2-G and PfAP2-EXP, which bind unique DNA motifs (GTAC and TGCATGCA). We also interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We found that DNA sequence context minimally impacts binding site selection for paralogous CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization correlate with differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we determined that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.
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Affiliation(s)
- Victoria A Bonnell
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Yuning Zhang
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Program in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan S Brown
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - John Horton
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Gabrielle A Josling
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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Guo Y, Jiang Y, Wu M, Tu A, Yin J, Yang J. TaWRKY50-TaSARK7 module-mediated cysteine-rich protein phosphorylation suppresses the programmed cell death response to Chinese wheat mosaic virus infection. Virology 2024; 595:110071. [PMID: 38593594 DOI: 10.1016/j.virol.2024.110071] [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: 02/01/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
WRKY transcription factors are widely involved in plant responses to biotic and abiotic stresses. However, there is currently a limited understanding of the regulation of viral infection by WRKY transcription factors in wheat (Triticum aestivum). The WRKY transcription factor TaWRKY50 in group IIb wheat exhibited a significant response to Chinese wheat mosaic virus infection. TaWRKY50 is localized in the nucleus and is an activating transcription factor. Interestingly, we found that silencing TaWRKY50 induces cell death following inoculation with CWMV. The protein kinase TaSAPK7 is specific to plants, whereas NbSRK is a closely related kinase with high homology to TaSAPK7. The transcriptional activities of both TaSAPK7 and NbSRK can be enhanced by TaWRKY50 binding to their promoters. CRP is an RNA silencing suppressor. Furthermore, TaWRKY50 may regulate CWMV infection by regulating the expression of TaSAPK7 and NbSRK to increase CRP phosphorylation and reduce the amount of programmed cell death (PCD).
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Affiliation(s)
- Yunfei Guo
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yaoyao Jiang
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Mila Wu
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Aizhu Tu
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jingliang Yin
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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3
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Chen X, Bai Y, Lin Y, Liu H, Han F, Chang H, Li M, Liu Q. Genome-Wide Identification and Characterization of the PHT1 Gene Family and Its Response to Mycorrhizal Symbiosis in Salvia miltiorrhiza under Phosphate Stress. Genes (Basel) 2024; 15:589. [PMID: 38790218 PMCID: PMC11120713 DOI: 10.3390/genes15050589] [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: 03/26/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
Phosphorus (P) is a vital nutrient element that is essential for plant growth and development, and arbuscular mycorrhizal fungi (AMF) can significantly enhance P absorption. The phosphate transporter protein 1 (PHT1) family mediates the uptake of P in plants. However, the PHT1 gene has not yet been characterized in Salvia miltiorrhiza. In this study, to gain insight into the functional divergence of PHT1 genes, nine SmPHT1 genes were identified in the S. miltiorrhiza genome database via bioinformatics tools. Phylogenetic analysis revealed that the PHT1 proteins of S. miltiorrhiza, Arabidopsis thaliana, and Oryza sativa could be divided into three groups. PHT1 in the same clade has a similar gene structure and motif, suggesting that the features of each clade are relatively conserved. Further tissue expression analysis revealed that SmPHT1 was expressed mainly in the roots and stems. In addition, phenotypic changes, P content, and PHT1 gene expression were analyzed in S. miltiorrhiza plants inoculated with AMF under different P conditions (0 mM, 0.1 mM, and 10 mM). P stress and AMF significantly affected the growth and P accumulation of S. miltiorrhiza. SmPHT1;6 was strongly expressed in the roots colonized by AMF, implying that SmPHT1;6 was a specific AMF-inducible PHT1. Taken together, these results provide new insights into the functional divergence and genetic redundancy of the PHT1 genes in response to P stress and AMF symbiosis in S. miltiorrhiza.
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Affiliation(s)
- Xue Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.C.); (Y.B.); (Y.L.); (F.H.); (M.L.)
| | - Yanhong Bai
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.C.); (Y.B.); (Y.L.); (F.H.); (M.L.)
| | - Yanan Lin
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.C.); (Y.B.); (Y.L.); (F.H.); (M.L.)
| | - Hongyan Liu
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Fengxia Han
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.C.); (Y.B.); (Y.L.); (F.H.); (M.L.)
| | - Hui Chang
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Menglin Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.C.); (Y.B.); (Y.L.); (F.H.); (M.L.)
| | - Qian Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.C.); (Y.B.); (Y.L.); (F.H.); (M.L.)
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Rajendran S, Kang YM, Yang IB, Eo HB, Baek KL, Jang S, Eybishitz A, Kim HC, Je BI, Park SJ, Kim CM. Functional characterization of plant specific Indeterminate Domain (IDD) transcription factors in tomato (Solanum lycopersicum L.). Sci Rep 2024; 14:8015. [PMID: 38580719 PMCID: PMC10997639 DOI: 10.1038/s41598-024-58903-0] [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: 11/14/2023] [Accepted: 04/04/2024] [Indexed: 04/07/2024] Open
Abstract
Plant-specific transcription factors (TFs) are responsible for regulating the genes involved in the development of plant-specific organs and response systems for adaptation to terrestrial environments. This includes the development of efficient water transport systems, efficient reproductive organs, and the ability to withstand the effects of terrestrial factors, such as UV radiation, temperature fluctuations, and soil-related stress factors, and evolutionary advantages over land predators. In rice and Arabidopsis, INDETERMINATE DOMAIN (IDD) TFs are plant-specific TFs with crucial functions, such as development, reproduction, and stress response. However, in tomatoes, IDD TFs remain uncharacterized. Here, we examined the presence, distribution, structure, characteristics, and expression patterns of SlIDDs. Database searches, multiple alignments, and motif alignments suggested that 24 TFs were related to Arabidopsis IDDs. 18 IDDs had two characteristic C2H2 domains and two C2HC domains in their coding regions. Expression analyses suggest that some IDDs exhibit multi-stress responsive properties and can respond to specific stress conditions, while others can respond to multiple stress conditions in shoots and roots, either in a tissue-specific or universal manner. Moreover, co-expression database analyses suggested potential interaction partners within IDD family and other proteins. This study functionally characterized SlIDDs, which can be studied using molecular and bioinformatics methods for crop improvement.
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Affiliation(s)
- Sujeevan Rajendran
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Yu Mi Kang
- Department of Horticultural and Life Science, Pusan National University, Milyang, 50463, Korea
| | - In Been Yang
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Hye Bhin Eo
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Kyung Lyung Baek
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Assaf Eybishitz
- World Vegetable Center, P.O. Box 42, Tainan, 74199, Shanhua, Taiwan
| | - Ho Cheol Kim
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Byeong Il Je
- Department of Horticultural and Life Science, Pusan National University, Milyang, 50463, Korea
| | - Soon Ju Park
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Chul Min Kim
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea.
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Wang T, Long C, Chang M, Wu Y, Su S, Wei J, Jiang S, Wang X, He J, Xing D, He Y, Ran Y, Li W. Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening. Sci Rep 2024; 14:2226. [PMID: 38278802 PMCID: PMC10817905 DOI: 10.1038/s41598-023-51080-6] [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: 09/20/2023] [Accepted: 12/30/2023] [Indexed: 01/28/2024] Open
Abstract
In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.
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Affiliation(s)
- Tao Wang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Cha Long
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China
| | - Meixia Chang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yuan Wu
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Shixian Su
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jingjiang Wei
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China
| | - Suyan Jiang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xiujun Wang
- College of Brewing and Food Engineering, Guizhou University, Guiyang, 550025, China
| | - Jianwen He
- Pepper Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Dan Xing
- Pepper Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Yangbo He
- Agriculture Development and Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Yaoqi Ran
- Agriculture Development and Research Institute of Guizhou Province, Guiyang, 550006, China
| | - Wei Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
- Vegetable Research Institute, Guizhou University, Guiyang, 550025, China.
- Engineering Research Center for Protected Vegetable Crops in Higher Learning Institutions of Guizhou Province, Guiyang, 550025, China.
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Blanc-Mathieu R, Dumas R, Turchi L, Lucas J, Parcy F. Plant-TFClass: a structural classification for plant transcription factors. TRENDS IN PLANT SCIENCE 2024; 29:40-51. [PMID: 37482504 DOI: 10.1016/j.tplants.2023.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.
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Affiliation(s)
- Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France.
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Song H, Zhao K, Jiang G, Sun S, Li J, Tu M, Wang L, Xie H, Chen D. Genome-Wide Identification and Expression Analysis of the SBP-Box Gene Family in Loquat Fruit Development. Genes (Basel) 2023; 15:23. [PMID: 38254913 PMCID: PMC10815216 DOI: 10.3390/genes15010023] [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: 11/14/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
The loquat (Eriobotrya japonica L.) is a special evergreen tree, and its fruit is of high medical and health value as well as having stable market demand around the world. In recent years, research on the accumulation of nutrients in loquat fruit, such as carotenoids, flavonoids, and terpenoids, has become a hotspot. The SBP-box gene family encodes transcription factors involved in plant growth and development. However, there has been no report on the SBP-box gene family in the loquat genome and their functions in carotenoid biosynthesis and fruit ripening. In this study, we identified 28 EjSBP genes in the loquat genome, which were unevenly distributed on 12 chromosomes. We also systematically investigated the phylogenetic relationship, collinearity, gene structure, conserved motifs, and cis-elements of EjSBP proteins. Most EjSBP genes showed high expression in the root, stem, leaf, and inflorescence, while only five EjSBP genes were highly expressed in the fruit. Gene expression analysis revealed eight differentially expressed EjSBP genes between yellow- and white-fleshed fruits, suggesting that the EjSBP genes play important roles in loquat fruit development at the breaker stage. Notably, EjSBP01 and EjSBP19 exhibited completely opposite expression patterns between white- and yellow-fleshed fruits during fruit development, and showed a close relationship with SlCnr involved in carotenoid biosynthesis and fruit ripening, indicating that these two genes may participate in the synthesis and accumulation of carotenoids in loquat fruit. In summary, this study provides comprehensive information about the SBP-box gene family in the loquat, and identified two EjSBP genes as candidates involved in carotenoid synthesis and accumulation during loquat fruit development.
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Affiliation(s)
- Haiyan Song
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- College of Life Science, Sichuan University, Chengdu 610065, China
| | - Ke Zhao
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Guoliang Jiang
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Shuxia Sun
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Jing Li
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Meiyan Tu
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Lingli Wang
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Hongjiang Xie
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Dong Chen
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (H.S.); (K.Z.); (G.J.); (S.S.); (J.L.); (M.T.); (L.W.); (H.X.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwestern China of the Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
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Wójcikowska B, Belaidi S, Robert HS. Game of thrones among AUXIN RESPONSE FACTORs-over 30 years of MONOPTEROS research. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6904-6921. [PMID: 37450945 PMCID: PMC10690734 DOI: 10.1093/jxb/erad272] [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: 02/28/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
For many years, research has been carried out with the aim of understanding the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review summarizes over 30 years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, namely embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and, finally, all the genes under its direct control. In addition, information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years.
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Affiliation(s)
- Barbara Wójcikowska
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Samia Belaidi
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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9
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Naseri G, Raasch H, Charpentier E, Erhardt M. A versatile regulatory toolkit of arabinose-inducible artificial transcription factors for Enterobacteriaceae. Commun Biol 2023; 6:1005. [PMID: 37789111 PMCID: PMC10547716 DOI: 10.1038/s42003-023-05363-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
The Gram-negative bacteria Salmonella enterica and Escherichia coli are important model organisms, powerful prokaryotic expression platforms for biotechnological applications, and pathogenic strains constitute major public health threats. To facilitate new approaches for research and biotechnological applications, we here develop a set of arabinose-inducible artificial transcription factors (ATFs) using CRISPR/dCas9 and Arabidopsis-derived DNA-binding proteins to control gene expression in E. coli and Salmonella over a wide inducer concentration range. The transcriptional output of the different ATFs, in particular when expressed in Salmonella rewired for arabinose catabolism, varies over a wide spectrum (up to 35-fold gene activation). As a proof-of-concept, we use the developed ATFs to engineer a Salmonella two-input biosensor strain, SALSOR 0.2 (SALmonella biosenSOR 0.2), which detects and quantifies alkaloid drugs through a measurable fluorescent output. Moreover, we use plant-derived ATFs to regulate β-carotene biosynthesis in E. coli, resulting in ~2.1-fold higher β-carotene production compared to expression of the biosynthesis pathway using a strong constitutive promoter.
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Affiliation(s)
- Gita Naseri
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
| | - Hannah Raasch
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Marc Erhardt
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
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Meher J, Sarkar A, Sarma BK. Binding of stress-responsive OsWRKY proteins through WRKYGQK heptapeptide residue with the promoter region of two rice blast disease resistance genes Pi2 and Pi54 is important for development of blast resistance. 3 Biotech 2023; 13:294. [PMID: 37560615 PMCID: PMC10407006 DOI: 10.1007/s13205-023-03711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Molecular docking was done to investigate the interactions between five differentially expressed rice WRKY proteins when challenged with the rice blast disease caused by Magnaporthe oryzae and drought stresses applied either individually or overlapped, with the promoter region of two blast resistance genes (Pi2 and Pi54). Molecular docking was performed using the HDOCK server. Initially, the homology models for each of the five rice WRKY proteins were prepared using I-TASSER server, and then the secondary structure as well as the DNA-binding pockets were predicted using PSIPRED and BindUP servers, respectively. The molecular docking study revealed a differential binding pattern of the rice WRKYs with the two blast resistance genes. The WRKY proteins (OsWRKY88 and OsWRKY102), whose transcript levels decrease when drought and blast stresses are overlapped, interact with the two resistance genes mostly involving the residues of the zinc finger structure. On the other hand, the WRKY proteins (OsWRKY53-1 and OsWRKY113), whose transcript levels did not reduce significantly when challenged by drought and blast overlapped condition compared to individual treatment of blast, interact mostly involving the residues of the conserved WRKYGQK heptapeptide sequence. Interestingly, the protein OsWRKY74 whose transcript levels are unaffected in both individual and overlapped stresses, interacts with both the blast resistance genes involving few residues of both WRKYGQK heptapeptide and the zinc finger structure. The findings thus indicate that the interaction of OsWRKY proteins involving the conserved WRKYGQK heptapeptide sequence with the blast resistance genes Pi2 and Pi54 is important to mitigate the blast challenge in rice even during overlapping challenges of drought. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03711-y.
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Affiliation(s)
- Jhumishree Meher
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Ankita Sarkar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
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11
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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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12
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Han Z, Zheng Y, Shi Y, Chen F, Wu C, Wang L, Lu S, Li D, Guan X, He L, Zhao J. Transcriptional variation in Babesia gibsoni (Wuhan isolate) between in vivo and in vitro cultures in blood stage. Parasit Vectors 2023; 16:268. [PMID: 37550766 PMCID: PMC10408140 DOI: 10.1186/s13071-023-05869-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/04/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Babesia gibsoni, the causative agent of canine babesiosis, belongs to the phylum Apicomplexa. The development of in vitro culture technology has driven research progress in various kinds of omics studies, including transcriptomic analysis of Plasmodium spp. between in vitro and in vivo environments, which has prompted the observation of diagnostic antigens and vaccine development. Nevertheless, no information on Babesia spp. could be obtained in this respect, which greatly hinders the further understanding of parasite growth and development in the blood stage. METHODS In this study, considerable changes in the morphology and infectivity of continuous in vitro cultured B. gibsoni (Wuhan isolate) were observed compared to in vivo parasites. Based on these changes, B. gibsoni (Wuhan isolate) was collected from both in vivo and in vitro cultures, followed by total RNA extraction and Illumina transcriptome sequencing. The acquired differentially expressed genes (DEGs) were validated using qRT-PCR, and then functionally annotated through several databases. The gene with the greatest upregulation after in vitro culture was cloned from the genome of B. gibsoni (Wuhan isolate) and characterized by western blotting and indirect immunofluorescence assay for detecting the native form and cellular localization. RESULTS Through laboratory cultivation, multiple forms of parasites were observed, and the infectivity of in vitro cultured parasites in dogs was found to be lower. Based on these changes, Illumina transcriptome sequencing was conducted, showing that 377 unigenes were upregulated and 334 unigenes were downregulated. Notably, an AP2 transcription factor family, essential for all developmental stages of parasites, was screened, and the transcriptional changes in these family members were tested. Thus, the novel AP2 transcription factor gene (BgAP2-M) with the highest upregulated expression after in vitro adaptation was selected. This gene comprises an open reading frame (ORF) of 1989 base pairs encoding a full-length protein of 662 amino acids. BgAP2-M contains one AP2 domain and one ACDC conserved domain, which may be involved in the nuclear biology of parasites. The prepared polyclonal antibodies against the BgAP2-M peptides further detected a native size of ~ 73 kDa and were localized to the nuclei of B. gibsoni. CONCLUSION This study presents a thorough transcriptome analysis of B. gibsoni in vivo and in vitro for the first time, contributing to a detailed understanding of the effects of environmental changes on the growth and development of parasites in the blood stage. Moreover, it also provides a deeper investigation for the different members of the ApiAP2 transcription factor family as various life stage regulators in Babesia spp.
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Affiliation(s)
- Zhen Han
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Yaxin Zheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Yu Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Fangwei Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Chenglong Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Lingna Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Shiyu Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Dongfang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Xingai Guan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, 430070, Hubei, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, 430070, Hubei, China.
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13
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Zhang P, He R, Yang J, Cai J, Qu Z, Yang R, Gu J, Wang ZY, Adelson DL, Zhu Y, Cao X, Wang D. The long non-coding RNA DANA2 positively regulates drought tolerance by recruiting ERF84 to promote JMJ29-mediated histone demethylation. MOLECULAR PLANT 2023; 16:1339-1353. [PMID: 37553833 DOI: 10.1016/j.molp.2023.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 06/15/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Tens of thousands of long non-coding RNAs have been uncovered in plants, but few of them have been comprehensively studied for their biological function and molecular mechanism of their mode of action. Here, we show that the Arabidopsis long non-coding RNA DANA2 interacts with an AP2/ERF transcription factor ERF84 in the cell nucleus and then affects the transcription of JMJ29 that encodes a Jumonji C domain-containing histone H3K9 demethylase. Both RNA sequencing (RNA-seq) and genetic analyses demonstrate that DANA2 positively regulates drought stress responses through JMJ29. JMJ29 positively regulates the expression of ERF15 and GOLS2 by modulation of H3K9me2 demethylation. Accordingly, mutation of JMJ29 causes decreased ERF15 and GOLS2 expression, resulting in impaired drought tolerance, in agreement with drought-sensitive phenotypes of dana2 and erf84 mutants. Taken together, these results demonstrate that DANA2 is a positive regulator of drought response and works jointly with the transcriptional activator ERF84 to modulate JMJ29 expression in plant response to drought.
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Affiliation(s)
- Pengxiang Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Rongxin Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China.
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14
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Wang W, Li T, Chen Q, Yao S, Zeng K. Transcriptional regulatory mechanism of a variant transcription factor CsWRKY23 in citrus fruit resistance to Penicillium digitatum. Food Chem 2023; 413:135573. [PMID: 36758387 DOI: 10.1016/j.foodchem.2023.135573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/08/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023]
Abstract
As the most productive fruit in the world, there is a lack of research on disease resistance mechanisms in citrus. WRKY transcription factors are mediators of disease resistance in plants. In this research, CsWRKY23, which could respond to exogenous salicylic acid (SA) was identified. As a variant WRKY, the transient overexpression of CsWRKY23 in citrus peel enhanced the resistance to Penicillium digitatum. The potential targets of CsWRKY23 were identified by using DNA affinity purification sequencing (DAP-seq). In combination with RNA sequencing (RNA-seq) data, 48 direct target genes of CsWRKY23 were identified. In addition, five genes for EMSA and dual-luciferase report system analysis were selected and the results showed that CsWRKY23 activate CsAAE12, CsRbohD, CsSARD1, CsWRKY22 and CsIQM6 expressions. Further analysis revealed that CsWRKY23 contributed to SA synthesis pathway, reactive oxygen species (ROS) accumulation, and cell wall strengthening. This study presented a possible regulatory network for disease resistance involving the CsWRKY23.
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Affiliation(s)
- Wenjun Wang
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Ting Li
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Qi Chen
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Shixiang Yao
- College of Food Science, Southwest University, Chongqing 400715, PR China; Research Center of Food Storage & Logistics, Southwest University, Chongqing 400715, PR China
| | - Kaifang Zeng
- College of Food Science, Southwest University, Chongqing 400715, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China; Research Center of Food Storage & Logistics, Southwest University, Chongqing 400715, PR China.
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15
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Rui W, Ma J, Wei N, Zhu X, Li Z. Genome-Wide Analysis of the PHT Gene Family and Its Response to Mycorrhizal Symbiosis in Tomatoes under Phosphate Starvation Conditions. Int J Mol Sci 2023; 24:10246. [PMID: 37373390 DOI: 10.3390/ijms241210246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/09/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Phosphate is one of the essential mineral nutrients. Phosphate transporter genes (PHTs) play an important role in Pi acquisition and homeostasis in tomato plants. However, basic biological information on PHT genes and their responses of symbiosis with arbuscular mycorrhizal in the genome remains largely unknown. We analyzed the physiological changes and PHT gene expression in tomatoes (Micro-Tom) inoculated with arbuscular mycorrhizal (AM) fungi (Funneliformis mosseae) under different phosphate conditions (P1: 0 µM, P2: 25 µM, and P3: 200 µM Pi). Twenty-three PHT genes were identified in the tomato genomics database. Protein sequence alignment further divided the 23 PHT genes into three groups, with similar classifications of exons and introns. Good colonization of plants was observed under low phosphate conditions (25 µM Pi), and Pi stress and AM fungi significantly affected P and N accumulation and root morphological plasticity. Moreover, gene expression data showed that genes in the SlPHT1 (SlPT3, SlPT4, and SlPT5) gene family were upregulated by Funneliformis mosseae under all conditions, which indicated that these gene levels were significantly increased with AM fungi inoculation. None of the analyzed SlPHT genes in the SlPH2, SlPHT3, SlPHT4, and SlPHO gene families were changed at any Pi concentration. Our results indicate that inoculation with AM fungi mainly altered the expression of the PHT1 gene family. These results will lay a foundation for better understanding the molecular mechanisms of inorganic phosphate transport under AM fungi inoculation.
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Affiliation(s)
- Wenjing Rui
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University (CAU), Yuanmingyuan Xilu 2, Haidian District, Beijing 100193, China
| | - Jing Ma
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University (CAU), Yuanmingyuan Xilu 2, Haidian District, Beijing 100193, China
| | - Ning Wei
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University (CAU), Yuanmingyuan Xilu 2, Haidian District, Beijing 100193, China
| | - Xiaoya Zhu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University (CAU), Yuanmingyuan Xilu 2, Haidian District, Beijing 100193, China
| | - Zhifang Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University (CAU), Yuanmingyuan Xilu 2, Haidian District, Beijing 100193, China
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16
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He H, Li Q, Fang L, Yang W, Xu F, Yan Y, Mao R. Comprehensive analysis of NAC transcription factors in Scutellaria baicalensis and their response to exogenous ABA and GA 3. Int J Biol Macromol 2023:125290. [PMID: 37302633 DOI: 10.1016/j.ijbiomac.2023.125290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
The NAC is a plant-specific family of transcription factor that plays important roles in various biological processes. Scutellaria baicalensis Georgi, belongs to the Lamiaceae family and has been widely used as a traditional herb with a wide range of pharmacological activities, including antitumor, heat-clearing, and detoxifying functions. However, no study on the NAC family in S. baicalensis has been conducted to date. In the present study, we identified 56 SbNAC genes using genomic and transcriptome analyses. These 56 SbNACs were unevenly distributed across nine chromosomes and were phylogenetically divided into six clusters. Cis-element analysis identified plant growth and development-, phytohormone-, light-, and stress-responsive elements were present in SbNAC genes promoter regions. Protein-protein interaction analysis was performed using Arabidopsis homologous proteins. Potential transcription factors, including bHLH, ERF, MYB, WRKY, and bZIP, were identified and constructed a regulatory network with SbNAC genes. The expression of 12 flavonoid biosynthetic genes was significantly upregulated with abscisic acid (ABA) and gibberellin (GA3) treatments. Eight SbNAC genes (SbNAC9/32/33/40/42/43/48/50) also exhibited notable variation with two phytohormone treatments, among which SbNAC9 and SbNAC43 showed the most significant variation and deserved further study. Additionally, SbNAC44 displayed a positive correlation with C4H3, PAL5, OMT3, and OMT6, while SbNAC25 had negatively correlated with OMT2, CHI, F6H2, and FNSII-2. This study constitutes the first analysis of SbNAC genes and lays the basis foundation for further functional studies of SbNAC genes family members, while it may also facilitate the genetic improvement of plants and breeding of elite S. baicalensis varieties.
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Affiliation(s)
- Huan He
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Qiuyue Li
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Liang Fang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Wen Yang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Feican Xu
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Yan Yan
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China; Shaanxi Key Laboratory of Chinese Jujube, Yan'an 716000, Shaanxi, China
| | - Renjun Mao
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China; Shaanxi Key Laboratory of Chinese Jujube, Yan'an 716000, Shaanxi, China.
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17
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Jin Y, Hu J, Su J, Aslan S, Lin Y, Jin L, Isaksson S, Liu C, Wang F, Schnürer A, Sitbon F, Hofvander P, Sun C. Improved bioenergy value of residual rice straw by increased lipid levels from upregulation of fatty acid biosynthesis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:90. [PMID: 37245032 DOI: 10.1186/s13068-023-02342-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/13/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Rice (Oryza sativa) straw is a common waste product that represents a considerable amount of bound energy. This energy can be used for biogas production, but the rate and level of methane produced from rice straw is still low. To investigate the potential for an increased biogas production from rice straw, we have here utilized WRINKLED1 (WRI1), a plant AP2/ERF transcription factor, to increase triacylglycerol (TAG) biosynthesis in rice plants. Two forms of Arabidopsis thaliana WRI1 were evaluated by transient expression and stable transformation of rice plants, and transgenic plants were analyzed both for TAG levels and biogas production from straw. RESULTS Both full-length AtWRI1, and a truncated form lacking the initial 141 amino acids (including the N-terminal AP2 domain), increased fatty acid and TAG levels in vegetative and reproductive tissues of Indica rice. The stimulatory effect of the truncated AtWRI1 was significantly lower than that of the full-length protein, suggesting a role for the deleted AP2 domain in WRI1 activity. Full-length AtWRI1 increased TAG levels also in Japonica rice, indicating a conserved effect of WRI1 in rice lipid biosynthesis. The bio-methane production from rice straw was 20% higher in transformants than in the wild type. Moreover, a higher producing rate and final yield of methane was obtained for rice straw compared with rice husks, suggesting positive links between methane production and a high amount of fatty acids. CONCLUSIONS Our results suggest that heterologous WRI1 expression in transgenic plants can be used to improve the metabolic potential for bioenergy purposes, in particular methane production.
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Affiliation(s)
- Yunkai Jin
- Department of Plant Biology, The Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P. O. Box 7080, 75007, Uppsala, Sweden
| | - Jia Hu
- Department of Plant Biology, The Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P. O. Box 7080, 75007, Uppsala, Sweden
| | - Jun Su
- Department of Plant Biology, The Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P. O. Box 7080, 75007, Uppsala, Sweden
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Selcuk Aslan
- Department of Plant Biology, The Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P. O. Box 7080, 75007, Uppsala, Sweden
| | - Yan Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Lu Jin
- Department of Plant Biology, The Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P. O. Box 7080, 75007, Uppsala, Sweden
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Simon Isaksson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P. O. Box 7015, 750 07, Uppsala, Sweden
| | - Chunlin Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Feng Wang
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P. O. Box 7015, 750 07, Uppsala, Sweden
| | - Folke Sitbon
- Department of Plant Biology, The Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P. O. Box 7080, 75007, Uppsala, Sweden.
| | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 23422, Lomma, Sweden
| | - Chuanxin Sun
- Department of Plant Biology, The Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P. O. Box 7080, 75007, Uppsala, Sweden.
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18
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Bai Y, Zhang T, Zheng X, Li B, Qi X, Xu Y, Li L, Liang C. Overexpression of a WRKY transcription factor McWRKY57-like from Mentha canadensis L. enhances drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2023; 23:216. [PMID: 37098465 PMCID: PMC10126992 DOI: 10.1186/s12870-023-04213-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Drought has become a major environmental problem affecting crop production. Members of the WRKY family play important roles in plant development and stress responses. However, their roles in mint have been barely explored. RESULTS In this study, we isolated a drought-inducible gene McWRKY57-like from mint and investigated its function. The gene encodes a group IIc WRKY transcription factor, McWRKY57-like, which is a nuclear protein with a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has transcription factor activity. Its expression levels were examined in different tissues of mint and under the treatment of mannitol, NaCl, abscisic acid, and methyl jasmonate. We found that McWRKY57-like overexpression in Arabidopsis significantly increased drought tolerance. Further studies showed that under drought stress, McWRKY57-like-overexpressing plants had higher chlorophyll, soluble sugar, soluble protein, and proline contents but lower water loss rate and malondialdehyde content than wild-type plants. Moreover, the activities of antioxidant enzymes catalase, superoxide dismutase, and peroxidase were enhanced in McWRKY57-like transgenic plants. Furthermore, qRT-PCR analysis revealed that the drought-related genes AtRD29A, AtRD29B, AtRD20, AtRAB18, AtCOR15A, AtCOR15B, AtKIN2, and AtDREB1A were upregulated in McWRKY57-like transgenic plants than in wild-type Arabidopsis under simulated drought conditions. CONCLUSION These data demonstrated that McWRKY57-like conferred drought tolerance in transgenic Arabidopsis by regulating plant growth, osmolyte accumulation and antioxidant enzyme activities, and the expression of stress-related genes. The study indicates that McWRKY57-like plays a positive role in drought response in plants.
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Affiliation(s)
- Yang Bai
- 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
| | - Ting Zhang
- 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
| | - Xiaowei Zheng
- 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
| | - Bingxuan Li
- The key laboratory of quality improvement of agriculture products of Zhejiang province, college of advanced agriculture sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xiwu Qi
- 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
| | - Yu Xu
- 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
| | - Li Li
- 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
| | - Chengyuan Liang
- 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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Wang J, Lin Y, Yang J, Zhang Q, Liu M, Hu Y, Dong X. Solution structure of the DNA binding domain of Arabidopsis transcription factor WRKY11. Biochem Biophys Res Commun 2023; 653:133-139. [PMID: 36868077 DOI: 10.1016/j.bbrc.2023.02.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 02/24/2023] [Indexed: 02/27/2023]
Abstract
The Arabidopsis WRKY11 (AtWRKY11) protein is an important transcription factor involved in plant response to biotic and abiotic stresses. Its DNA-binding domain specifically binds to gene promoter regions harboring the W-box consensus motif. Herein we report the high-resolution structure of the AtWRKY11 DNA-binding domain (DBD) determined by solution NMR spectroscopy. The results show that AtWRKY11-DBD adopts an all-β fold comprising five β-strands packed in an antiparallel topology, stabilized by a zinc-finger motif. Structural comparison reveals that the long β1-β2 loop shows the highest structural variation from other available WRKY domain structures. Moreover, this loop was further found to contribute to the binding between AtWRKY11-DBD and W-box DNA. Our current study provides atomic-level structural basis for further understanding the structure-function relationship of plant WRKY proteins.
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Affiliation(s)
- Jiannan Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaling Lin
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ju Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xu Dong
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Cao Y, Fan T, Wang L, Zhang L, Li Y. Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis. BMC PLANT BIOLOGY 2023; 23:145. [PMID: 36927311 PMCID: PMC10022305 DOI: 10.1186/s12870-023-04163-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND MYB transcription factors are widely distributed in the plant kingdom and play key roles in regulatory networks governing plant metabolism and biochemical and physiological processes. RESULTS Here, we first determined the R2R3-MYB genes in five Euphorbiaceae genomes. The three Trp (W) residues from the first MYB domain (R2) were absolutely conserved, whereas the first W residue from the second MYB domain (R3) was preferentially mutated. The R2R3-MYBs were clustered into 48 functional subfamilies, of which 34 had both R2R3-MYBs of Euphorbiaceae species and AtMYBs, and four contained only Euphorbiaceae R2R3-MYBs. The whole-genome duplication (WGD) and/or segmental duplication (SD) played key roles in the expansion of the R2R3-MYB family. Unlike paralogous R2R3-MYB family members, orthologous R2R3-MYB members contained a higher selective pressure and were subject to a constrained evolutionary rate. VfMYB36 was specifically expressed in fruit, and its trend was consistent with the change in oil content, indicating that it might be involved in oil biosynthesis. Overexpression experiments showed that VfMYB36 could significantly provide linolenic acid (C18:3) content, which eventually led to a significant increase in oil content. CONCLUSION Our study first provides insight into understanding the evolution and expression of R2R3-MYBs in Euphorbiaceae species, and also provides a target for the production of biomass diesel and a convenient way for breeding germplasm resources with high linolenic acid content in the future.
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Affiliation(s)
- Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 430074 Wuhan, China
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
- Forestry College, Central South University of Forestry and Technology, 410004 Changsha, Hunan China
| | - Tingting Fan
- Forestry College, Central South University of Forestry and Technology, 410004 Changsha, Hunan China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, 056009 Handan, China
| | - Lin Zhang
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, 430065 Wuhan, China
| | - Yanli Li
- Forestry College, Central South University of Forestry and Technology, 410004 Changsha, Hunan China
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21
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Liu J, Qiao Y, Li C, Hou B. The NAC transcription factors play core roles in flowering and ripening fundamental to fruit yield and quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1095967. [PMID: 36909440 PMCID: PMC9996081 DOI: 10.3389/fpls.2023.1095967] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fruits are derived from flowers and play an important role in human food, nutrition, and health. In general, flowers determine the crop yield, and ripening affects the fruit quality. Although transcription factors (TFs) only account for a small part of plant transcriptomes, they control the global gene expression and regulation. The plant-specific NAC (NAM, ATAF, and CUC) TFs constitute a large family evolving concurrently with the transition of both aquatic-to-terrestrial plants and vegetative-to-reproductive growth. Thus, NACs play an important role in fruit yield and quality by determining shoot apical meristem (SAM) inflorescence and controlling ripening. The present review focuses on the various properties of NACs together with their function and regulation in flower formation and fruit ripening. Hitherto, we have a better understanding of the molecular mechanisms of NACs in ripening through abscisic acid (ABA) and ethylene (ETH), but how NACs regulate the expression of the inflorescence formation-related genes is largely unknown. In the future, we should focus on the analysis of NAC redundancy and identify the pivotal regulators of flowering and ripening. NACs are potentially vital manipulation targets for improving fruit quantity and quality.
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Affiliation(s)
- Jianfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuyuan Qiao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingzhu Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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22
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Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress. Int J Mol Sci 2023; 24:ijms24032088. [PMID: 36768411 PMCID: PMC9916880 DOI: 10.3390/ijms24032088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
The C-Repeat Binding Factor (CBF) gene family has been identified and characterized in multiple plant species, and it plays a crucial role in responding to low temperatures. Presently, only a few studies on tree species demonstrate the mechanisms and potential functions of CBFs associated with cold resistance, while our study is a novel report on the multi-aspect differences of CBFs among three tree species, compared to previous studies. In this study, genome-wide identification and analysis of the CBF gene family in Acer truncatum, Acer pseudosieboldianum, and Acer yangbiense were performed. The results revealed that 16 CBF genes (five ApseCBFs, four AcyanCBFs, and seven AtruCBFs) were unevenly distributed across the chromosomes, and most CBF genes were mapped on chromosome 2 (Chr2) and chromosome 11 (Chr11). The analysis of phylogenetic relationships, gene structure, and conserved motif showed that 16 CBF genes could be clustered into three subgroups; they all contained Motif 1 and Motif 5, and most of them only spanned one exon. The cis-acting elements analysis showed that some CBF genes might be involved in hormone and abiotic stress responsiveness. In addition, CBF genes exhibited tissue expression specificity. High expressions of ApseCBF1, ApseCBF3, AtruCBF1, AtruCBF4, AtruCBF6, AtruCBF7, and ApseCBF3, ApseCBF4, ApseCBF5 were detected on exposure to low temperature for 3 h and 24 h. Low expressions of AtruCBF2, AtruCBF6, AtruCBF7 were detected under cold stress for 24 h, and AtruCBF3 and AtruCBF5 were always down-regulated under cold conditions. Taken together, comprehensive analysis will enhance our understanding of the potential functions of the CBF genes on cold resistance, thereby providing a reference for the introduction of Acer species in our country.
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23
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Vandepoele K, Kaufmann K. Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types. Methods Mol Biol 2023; 2698:1-11. [PMID: 37682465 DOI: 10.1007/978-1-0716-3354-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
A major question in plant biology is to understand how plant growth, development, and environmental responses are controlled and coordinated by the activities of regulatory factors. Gene regulatory network (GRN) analyses require integrated approaches that combine experimental approaches with computational analyses. A wide range of experimental approaches and tools are now available, such as targeted perturbation of gene activities, quantitative and cell-type specific measurements of dynamic gene activities, and systematic analysis of the molecular 'hard-wiring' of the systems. At the computational level, different tools and databases are available to study regulatory sequences, including intuitive visualizations to explore data-driven gene regulatory networks in different plant species. Furthermore, advanced data integration approaches have recently been developed to efficiently leverage complementary regulatory data types and learn context-specific networks.
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Affiliation(s)
- Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universitaet zu Berlin, Berlin, Germany
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Gouesbet G. Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis. Methods Mol Biol 2023; 2642:257-294. [PMID: 36944884 DOI: 10.1007/978-1-0716-3044-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Plant functioning and responses to abiotic stresses largely involve regulations at the transcriptomic level via complex interactions of signal molecules, signaling cascades, and regulators. Nevertheless, all the signaling networks involved in responses to abiotic stresses have not yet been fully established. The in-depth analysis of transcriptomes in stressed plants has become a relevant state-of-the-art methodology to study these regulations and signaling pathways that allow plants to cope with or attempt to survive abiotic stresses. The plant science and molecular biology community has developed databases about genes, proteins, protein-protein interactions, protein-DNA interactions and ontologies, which are valuable sources of knowledge for deciphering such regulatory and signaling networks. The use of these data and the development of bioinformatics tools help to make sense of transcriptomic data in specific contexts, such as that of abiotic stress signaling, using functional biological approaches. The aim of this chapter is to present and assess some of the essential online tools and resources that will allow novices in bioinformatics to decipher transcriptomic data in order to characterize the cellular processes and functions involved in abiotic stress responses and signaling. The analysis of case studies further describes how these tools can be used to conceive signaling networks on the basis of transcriptomic data. In these case studies, particular attention was paid to the characterization of abiotic stress responses and signaling related to chemical and xenobiotic stressors.
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Affiliation(s)
- Gwenola Gouesbet
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, Biodiversité, Evolution)] - UMR 6553, Rennes, France.
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Liu Y, Zhang M, Wang R, Li B, Jiang Y, Sun M, Chang Y, Wu J. Comparison of structural variants detected by PacBio-CLR and ONT sequencing in pear. BMC Genomics 2022; 23:830. [PMID: 36517766 PMCID: PMC9753399 DOI: 10.1186/s12864-022-09074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Structural variations (SVs) have recently become a topic of great interest in the area of genetic diversity and trait regulation. As genomic sequencing technologies have rapidly advanced, longer reads have been used to identify SVs at high resolution and with increased accuracy. It is important to choose a suitable sequencing platform and appropriate sequencing depth for SV detection in the pear genome. RESULTS In this study, two types of long reads from sequencing platforms, continuous long reads from Pacific Biosciences (PB-CLR) and long reads from Oxford Nanopore Technologies (ONT), were used to comprehensively analyze and compare SVs in the pear genome. The mapping rate of long reads was higher when the program Minimap2 rather than the other three mapping tools (NGMLR, LRA and Winnowmap2) was used. Three SV detection programs (Sniffles_v2, CuteSV, and Nanovar) were compared, and Nanovar had the highest sensitivity in detecting SVs at low sequencing depth (10-15×). A sequencing depth of 15× was suitable for SV detection in the pear genome using Nanovar. SVs detected by Sniffles_v2 and CuteSV with ONT reads had the high overlap with presence/absence variations (PAVs) in the pear cultivars 'Bartlett' and 'Dangshansuli', both of them with 38% of insertions and 55% of deletions overlapping with PAVs at sequencing depth of 30×. For the ONT sequencing data, over 37,526 SVs spanning ~ 28 Mb were identified by all three software packages for the 'Bartlett' and 'Dangshansuli' genomes. Those SVs were annotated and combined with transcriptome profiles derived from 'Bartlett' and 'Dangshansuli' fruit flesh at 60 days after cross-pollination. Several genes related to levels of sugars, acid, stone cells, and aromatic compounds were identified among the SVs. Transcription factors were then predicted among those genes, and results included bHLH, ERF, and MYB genes. CONCLUSION SV detection is of great significance in exploring phenotypic differences between pear varieties. Our study provides a framework for assessment of different SV software packages and sequencing platforms that can be applied in other plant genome studies. Based on these analyses, ONT sequencing data was determined to be more suitable than PB-CLR for SV detection in the pear genome. This analysis model will facilitate screening of genes related to agronomic traits in other crops.
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Affiliation(s)
- Yueyuan Liu
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Mingyue Zhang
- grid.440622.60000 0000 9482 4676College of Horticultural Science and engineering, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Runze Wang
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Benping Li
- grid.410753.4Novogene Bioinformatics Institute, Beijing, China
| | - Yafei Jiang
- grid.410753.4Novogene Bioinformatics Institute, Beijing, China
| | - Manyi Sun
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Yaojun Chang
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Jun Wu
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
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Pang F, Niu J, Solanki MK, Nosheen S, Liu Z, Wang Z. PHD-finger family genes in wheat ( Triticum aestivum L.): Evolutionary conservatism, functional diversification, and active expression in abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1016831. [PMID: 36578331 PMCID: PMC9791960 DOI: 10.3389/fpls.2022.1016831] [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: 08/11/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Plant homeodomain (PHD) transcription factors (TFs) are a class of proteins with conserved Cys4-His-Cys3 domains that play important roles in plant growth and development and in response to abiotic stresses. Although characterization of PHDs has been performed in plants, little is known about their function in wheat (Triticum aestivum L.), especially under stress conditions. In the present study, 244 TaPHDs were identified in wheat using comparative genomics. We renamed them TaPHD1-244 based on their chromosomal distribution, and almost all PHD proteins were predicted to be located in the nucleus. According to the unrooted neighbor-joining phylogenetic tree, gene structure, and motif analyses, PHD genes were divided into four clades. A total of 149 TaPHD genes were assigned to arise from duplication events. Furthermore, 230 gene pairs came from wheat itself, and 119, 186, 168, 7, 2, and 6 gene pairs came from six other species (Hordeum vulgareto, Zea mays, Oryza sativa, Arabidopsis thaliana, Brassica rapa, and Gossypium raimondii, respectively). A total of 548 interacting protein branches were identified to be involved in the protein interaction network. Tissue-specific expression pattern analysis showed that TaPHDs were highly expressed in the stigma and ovary during flowering, suggesting that the TaPHD gene plays an active role in the reproductive growth of wheat. In addition, the qRT-PCR results further confirmed that these TaPHD genes are involved in the abiotic stress response of wheat. In conclusion, our study provides a theoretical basis for deciphering the molecular functions of TaPHDs, particularly in response to abiotic stress.
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Affiliation(s)
- Fei Pang
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Junqi Niu
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Shaista Nosheen
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Zhaoliang Liu
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Zhen Wang
- College of Agriculture, Yulin Normal University, Yulin, China
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Stu-miR827-Targeted StWRKY48 Transcription Factor Negatively Regulates Drought Tolerance of Potato by Increasing Leaf Stomatal Density. Int J Mol Sci 2022; 23:ijms232314805. [PMID: 36499135 PMCID: PMC9741430 DOI: 10.3390/ijms232314805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Stomata are specialized portals in plant leaves to modulate water loss from plants to the atmosphere by control of the transpiration, thereby determining the water-use efficiency and drought resistance of plants. Despite that the stomata developmental progression is well-understood at the molecular level, the experimental evidence that miRNA regulates stomata development is still lacking, and the underlying mechanism remains elusive. This study demonstrates the involvement of stu-miR827 in regulating the drought tolerance of potato due to its control over the leaf stomatal density. The expression analysis showed that stu-miR827 was obviously repressed by drought stresses and then rapidly increased after rewatering. Suppressing the expression of stu-miR827 transgenic potato lines showed an increase in stomatal density, correlating with a weaker drought resistance compared with wildtype potato lines. In addition, StWRKY48 was identified as the target gene of stu-miR827, and the expression of StWRKY48 was obviously induced by drought stresses and was greatly upregulated in stu-miR827 knockdown transgenic potato lines, suggesting its involvement in the drought stress response. Importantly, the expression of genes associated with stomata development, such as SDD (stomatal density and distribution) and TMM (too many mouths), was seriously suppressed in transgenic lines. Altogether, these observations demonstrated that suppression of stu-miR827 might lead to overexpression of StWRKY48, which may contribute to negatively regulating the drought adaptation of potato by increasing the stomatal density. The results may facilitate functional studies of miRNAs in the process of drought tolerance in plants.
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Guo J, Liu H, Dai K, Yuan X, Guo P, Shi W, Zhou M. Identification of Brachypodium distachyon B3 genes reveals that BdB3-54 regulates primary root growth. FRONTIERS IN PLANT SCIENCE 2022; 13:1050171. [PMID: 36438129 PMCID: PMC9686306 DOI: 10.3389/fpls.2022.1050171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
B3 is a class of plant-specific transcription factors with important roles in plant development and growth. Here, we identified 69 B3 transcription factors in Brachypodium distachyon that were unevenly distributed across all five chromosomes. The ARF, REM, LAV, and RAV subfamilies were grouped based on sequence characteristics and phylogenetic relationships. The phylogenetically related members in the B3 family shared conserved domains and gene structures. Expression profiles showed that B3 genes were widely expressed in different tissues and varied in response to different abiotic stresses. BdB3-54 protein from the REM subfamily was located in the nucleus by subcellular localization and processed transcriptional activation activity. Overexpression of BdB3-54 in Arabidopsis increased primary root length. Our study provides a basis for further research on the functions of BdB3 genes.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Hanxiao Liu
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Keli Dai
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Meixue Zhou
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
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Thakur S, Vasudev PG. MYB transcription factors and their role in Medicinal plants. Mol Biol Rep 2022; 49:10995-11008. [PMID: 36074230 DOI: 10.1007/s11033-022-07825-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
Transcription factors are multi-domain proteins that regulate gene expression in eukaryotic organisms. They are one of the largest families of proteins, which are structurally and functionally diverse. While there are transcription factors that are plant-specific, such as AP2/ERF, B3, NAC, SBP and WRKY, some transcription factors are present in both plants as well as other eukaryotic organisms. MYB transcription factors are widely distributed among all eukaryotes. In plants, the MYB transcription factors are involved in the regulation of numerous functions such as gene regulation in different metabolic pathways especially secondary metabolic pathways, regulation of different signalling pathways of plant hormones, regulation of genes involved in various developmental and morphological processes etc. Out of the thousands of MYB TFs that have been studied in plants, the majority of them have been studied in the model plants like Arabidopsis thaliana, Oryza sativa etc. The study of MYBs in other plants, especially medicinal plants, has been comparatively limited. But the increasing demand for medicinal plants for the production of biopharmaceuticals and important bioactive compounds has also increased the need to explore more number of these multifaceted transcription factors which play a significant role in the regulation of secondary metabolic pathways. These studies will ultimately contribute to medicinal plants' research and increased production of secondary metabolites, either through transgenic plants or through synthetic biology approaches. This review compiles studies on MYB transcription factors that are involved in the regulation of diverse functions in medicinal plants.
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Affiliation(s)
- Sudipa Thakur
- Plant Biotechnology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, 226015, Lucknow, India.
| | - Prema G Vasudev
- Plant Biotechnology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, 226015, Lucknow, India
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Characterizations of a Class-I BASIC PENTACYSTEINE Gene Reveal Conserved Roles in the Transcriptional Repression of Genes Involved in Seed Development. Curr Issues Mol Biol 2022; 44:4059-4069. [PMID: 36135190 PMCID: PMC9497819 DOI: 10.3390/cimb44090278] [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: 08/15/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The developmental regulation of flower organs involves the spatio-temporal regulation of floral homeotic genes. BASIC PENTACYSTEINE genes are plant-specific transcription factors that is involved in many aspects of plant development through gene transcriptional regulation. Although studies have shown that the BPC genes are involved in the developmental regulation of flower organs, little is known about their role in the formation of double-flower due. Here we characterized a Class I BPC gene (CjBPC1) from an ornamental flower—Camellia japonica. We showed that CjBPC1 is highly expressed in the central whorls of flowers in both single and doubled varieties. Overexpression of CjBPC1 in Arabidopsis thaliana caused severe defects in siliques and seeds. We found that genes involved in ovule and seed development, including SEEDSTICK, LEAFY COTYLEDON2, ABSCISIC ACID INSENSITIVE 3 and FUSCA3, were significantly down-regulated in transgenic lines. We showed that the histone 3 lysine 27 methylation levels of these downstream genes were enhanced in the transgenic plants, indicating conserved roles of CjBPC1 in recruiting the Polycomb Repression Complex for gene suppression.
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Han J, Xie X, Zhang Y, Yu X, He G, Li Y, Yang G. Evolution of the DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN subfamily in green plants. PLANT PHYSIOLOGY 2022; 190:421-440. [PMID: 35695786 PMCID: PMC9434268 DOI: 10.1093/plphys/kiac286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/26/2022] [Indexed: 06/13/2023]
Abstract
Adapting to unfavorable environments is a necessary step in plant terrestrialization and radiation. The dehydration-responsive element-binding (DREB) protein subfamily plays a pivotal role in plant abiotic stress regulation. However, relationships between the origin and expansion of the DREB subfamily and adaptive evolution of land plants are still being elucidated. Here, we constructed the evolutionary history of the DREB subfamily by compiling APETALA2/ethylene-responsive element-binding protein superfamily genes from 169 representative species of green plants. Through extensive phylogenetic analyses and comparative genomic analysis, our results revealed that the DREB subfamily diverged from the ethylene-responsive factor (ERF) subfamily in the common ancestor of Zygnemophyceae and Embryophyta during the colonization of land by plants, followed by expansions to form three different ancient archetypal genes in Zygnemophyceae species, designated as groups archetype-I, archetype-II/III, and archetype-IV. Four large-scale expansions paralleling the evolution of land plants led to the nine-subgroup divergence of group archetype-II/III in angiosperms, and five whole-genome duplications during Brassicaceae and Poaceae radiation shaped the diversity of subgroup IIb-1. We identified a Poaceae-specific gene in subgroup IIb-1, ERF014, remaining in a Poaceae-specific microsynteny block and co-evolving with a small heat shock protein cluster. Expression analyses demonstrated that heat acclimation may have driven the neofunctionalization of ERF014s in Pooideae by engaging in the conserved heat-responsive module in Poaceae. This study provides insights into lineage-specific expansion and neofunctionalization in the DREB subfamily, together with evolutionary information valuable for future functional studies of plant stress biology.
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Affiliation(s)
- Jiapeng Han
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaoxue Xie
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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Ruengsrichaiya B, Nukoolkit C, Kalapanulak S, Saithong T. Plant-DTI: Extending the landscape of TF protein and DNA interaction in plants by a machine learning-based approach. FRONTIERS IN PLANT SCIENCE 2022; 13:970018. [PMID: 36082286 PMCID: PMC9445498 DOI: 10.3389/fpls.2022.970018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
As a sessile organism, plants hold elaborate transcriptional regulatory systems that allow them to adapt to variable surrounding environments. Current understanding of plant regulatory mechanisms is greatly constrained by limited knowledge of transcription factor (TF)-DNA interactions. To mitigate this problem, a Plant-DTI predictor (Plant DBD-TFBS Interaction) was developed here as the first machine-learning model that covered the largest experimental datasets of 30 plant TF families, including 7 plant-specific DNA binding domain (DBD) types, and their transcription factor binding sites (TFBSs). Plant-DTI introduced a novel TFBS feature construction, called TFBS base-preference, which enhanced the specificity of TFBS to DBD types. The proposed model showed better predictive performance with the TFBS base-preference than the simple binary representation. Plant-DTI was validated with 22 independent ChIP-seq datasets. It accurately predicted the measured DBD-TFBS pairs along with their TFBS motifs, and effectively predicted interactions of other TFs containing similar DBD types. Comparing to the existing state-of-art methods, Plant-DTI prediction showed a figure of merit in sensitivity and specificity with respect to the position weight matrix (PWM) and TSPTFBS methods. Finally, the proposed Plant-DTI model helped to fill the knowledge gap in the regulatory mechanisms of the cassava sucrose synthase 1 gene (MeSUS1). Plant-DTI predicted MeERF72 as a regulator of MeSUS1 in consistence with the yeast one-hybrid (Y1H) experiment. Taken together, Plant-DTI would help facilitate the prediction of TF-TFBS and TF-target gene (TG) interactions, thereby accelerating the study of transcriptional regulatory systems in plant species.
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Affiliation(s)
- Bhukrit Ruengsrichaiya
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
| | - Chakarida Nukoolkit
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
- School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang KhunThian), Bangkok, Thailand
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Wang L, Wang S, Tong R, Wang S, Yao J, Jiao J, Wan R, Wang M, Shi J, Zheng X. Overexpression of PgCBF3 and PgCBF7 Transcription Factors from Pomegranate Enhances Freezing Tolerance in Arabidopsis under the Promoter Activity Positively Regulated by PgICE1. Int J Mol Sci 2022; 23:ijms23169439. [PMID: 36012703 PMCID: PMC9408969 DOI: 10.3390/ijms23169439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
Cold stress limits plant growth, development and yields, and the C-repeat binding factors (CBFs) function in the cold resistance in plants. However, how pomegranate CBF transcription factors respond to cold signal remains unclear. Considering the significantly up-regulated expression of PgCBF3 and PgCBF7 in cold-tolerant Punica granatum ‘Yudazi’ in comparison with cold-sensitive ‘Tunisia’ under 4 °C, the present study focused on the two CBF genes. PgCBF3 was localized in the nucleus, while PgCBF7 was localized in the cell membrane, cytoplasm, and nucleus, both owning transcriptional activation activity in yeast. Yeast one-hybrid and dual-luciferase reporter assay further confirmed that PgICE1 could specifically bind to and significantly enhance the activation activity of the promoters of PgCBF3 and PgCBF7. Compared with the wild-type plants, the PgCBF3 and PgCBF7 transgenic Arabidopsis thaliana lines had the higher survival rate after cold treatment; exhibited increased the contents of soluble sugar and proline, while lower electrolyte leakage, malondialdehyde content, and reactive oxygen species production, accompanying with elevated enzyme activity of catalase, peroxidase, and superoxide dismutase; and upregulated the expression of AtCOR15A, AtCOR47, AtRD29A, and AtKIN1. Collectively, PgCBFs were positively regulated by the upstream PgICE1 and mediated the downstream COR genes expression, thereby enhancing freezing tolerance.
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Gao Y, Yang J, Duan W, Ma X, Qu L, Xu Z, Yang Y, Xu J. NtRAV4 negatively regulates drought tolerance in Nicotiana tabacum by enhancing antioxidant capacity and defence system. PLANT CELL REPORTS 2022; 41:1775-1788. [PMID: 35789421 DOI: 10.1007/s00299-022-02896-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE NtRAV4 is a nucleus-localised protein and no self-activation effect. ntrav4 mutants maintain the steady state of the ROS system under drought stress by enhancing antioxidant capacity and defence system. The APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) family plays an important role in plant responses to environmental stresses. In this study, we identified a novel NtRAV4 TF, a member of RAV subfamily among AP2/ERF gene family, which have AP2 and B3 domain in its N- and C-terminus, respectively. Subcellular localisation and self-activation activity analysis revealed that NtRAV4 localised in the nucleus and had no self-activation effect. The overexpression and gene editing vectors of NtRAV4 were constructed by homologous recombination and CRISPR/Cas9 gene editing methods, and transformed into tobacco by agrobacterium-mediated method. ntrav4 led to the appearance of termination codon in advance and lacked the unique B3 domain of RAV subfamily protein. Further analysis displayed that knockout of the NtRAV4 in tobacco increased drought tolerance with high relative water content, accompanied by reduced stomatal aperture, density, and stomatal opening ratio compared to overexpression lines and WT. Moreover, ntrav4 knockout plants also exhibited increased osmotic tolerance with low malondialdehyde (MDA) and ion leakage (EL), less accumulation of O2•- and H2O2, and high enzymatic antioxidant (SOD, POD, CAT) activities, non-enzymatic antioxidant (AsA-GSH cycle) contents and hormone (IAA, ABA, GA3, and ZR) levels under drought stress. Furthermore, ntrav4 mutants in tobacco improved the expression levels of ROS-related proline synthesis and stress-responsive genes under osmotic stress. Our results indicate that NtRAV4 negatively regulates plant tolerance to drought stress by reducing water loss and activating the antioxidant system and stress-related gene expression to maintain the steady state of the ROS system.
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Affiliation(s)
- Yun Gao
- National Tobacco Cultivation and Physiology and Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jie Yang
- China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Wangjun Duan
- China Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, China
| | - Xiaohan Ma
- National Tobacco Cultivation and Physiology and Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lili Qu
- National Tobacco Cultivation and Physiology and Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zicheng Xu
- National Tobacco Cultivation and Physiology and Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongxia Yang
- National Tobacco Cultivation and Physiology and Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jiayang Xu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China.
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Cancé C, Martin-Arevalillo R, Boubekeur K, Dumas R. Auxin response factors are keys to the many auxin doors. THE NEW PHYTOLOGIST 2022; 235:402-419. [PMID: 35434800 DOI: 10.1111/nph.18159] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.
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Affiliation(s)
- Coralie Cancé
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Univ. Lyon, Lyon, France
| | - Kenza Boubekeur
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Renaud Dumas
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
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Sestari I, Campos ML. Into a dilemma of plants: the antagonism between chemical defenses and growth. PLANT MOLECULAR BIOLOGY 2022; 109:469-482. [PMID: 34843032 DOI: 10.1007/s11103-021-01213-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/28/2021] [Indexed: 05/21/2023]
Abstract
Chemical defenses are imperative for plant survival, but their production is often associated with growth restrictions. Here we review the most recent theories to explain this complex dilemma of plants. Plants are a nutritional source for a myriad of pests and pathogens that depend on green tissues to complete their life cycle. Rather than remaining passive victims, plants utilize an arsenal of chemical defenses to fend off biotic attack. While the deployment of such barriers is imperative for survival, the production of these chemical defenses is typically associated with negative impacts on plant growth. Here we discuss the most recent theories which explain this highly dynamic growth versus defense dilemma. Firstly, we discuss the hypothesis that the antagonism between the accumulation of chemical defenses and growth is rooted in the evolutionary history of plants and may be a consequence of terrestrialization. Then, we revise the different paradigms available to explain the growth versus chemical defense antagonism, including recent findings that update these into more comprehensive and plausible theories. Finally, we highlight state-of-the-art strategies that are now allowing the activation of growth and the concomitant production of chemical barriers in plants. Growth versus chemical defense antagonism imposes large ecological and economic costs, including increased crop susceptibility to pests and pathogens. In a world where these plant enemies are the main problem to increase food production, we believe that this review will summarize valuable information for future studies aiming to breed highly defensive plants without the typical accompanying penalties to growth.
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Affiliation(s)
- Ivan Sestari
- Coordenadoria Especial de Ciências Biológicas e Agronômicas, Universidade Federal de Santa Catarina, Curitibanos, SC, Brazil
| | - Marcelo Lattarulo Campos
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
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Panigrahy M, Panigrahi KCS, Poli Y, Ranga A, Majeed N. Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice. BIOLOGY 2022; 11:biology11050798. [PMID: 35625525 PMCID: PMC9138629 DOI: 10.3390/biology11050798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/22/2022]
Abstract
Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade.
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Affiliation(s)
- Madhusmita Panigrahy
- Biofuel & Bioprocessing Research Centre, Institute of Technical Education and Research, Siksha ‘O’ Anusandhan University, Bhubaneswar 751002, India
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
- Correspondence: (M.P.); (K.C.S.P.); Tel.: +91-8762086581 (M.P.); +91-6742494139 (K.C.S.P.)
| | - Kishore Chandra Sekhar Panigrahi
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
- Correspondence: (M.P.); (K.C.S.P.); Tel.: +91-8762086581 (M.P.); +91-6742494139 (K.C.S.P.)
| | - Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad 500030, India;
| | - Aman Ranga
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
| | - Neelofar Majeed
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
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Filyushin MA, Khatefov EB, Kochieva EZ, Shchennikova AV. Comparative Analysis of Transcription Factor Genes liguleless1 and liguleless1-like in Teosinte and Modern Maize Accessions. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542203005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhang L, Chen L, Pang S, Zheng Q, Quan S, Liu Y, Xu T, Liu Y, Qi M. Function Analysis of the ERF and DREB Subfamilies in Tomato Fruit Development and Ripening. FRONTIERS IN PLANT SCIENCE 2022; 13:849048. [PMID: 35310671 PMCID: PMC8931701 DOI: 10.3389/fpls.2022.849048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/02/2022] [Indexed: 05/26/2023]
Abstract
APETALA2/ethylene responsive factors (AP2/ERF) are unique regulators in the plant kingdom and are involved in the whole life activity processes such as development, ripening, and biotic and abiotic stresses. In tomato (Solanum lycopersicum), there are 140 AP2/ERF genes; however, their functionality remains poorly understood. In this work, the 14th and 19th amino acid differences in the AP2 domain were used to distinguish DREB and ERF subfamily members. Even when the AP2 domain of 68 ERF proteins from 20 plant species and motifs in tomato DREB and ERF proteins were compared, the binding ability of DREB and ERF proteins with DRE/CRT and/or GCC boxes remained unknown. During fruit development and ripening, the expressions of 13 DREB and 19 ERF subfamily genes showed some regular changes, and the promoters of most genes had ARF, DRE/CRT, and/or GCC boxes. This suggests that these genes directly or indirectly respond to IAA and/or ethylene (ET) signals during fruit development and ripening. Moreover, some of these may feedback regulate IAA or ET biosynthesis. In addition, 16 EAR motif-containing ERF genes in tomato were expressed in many organs and their total transcripts per million (TPM) values exceeded those of other ERF genes in most organs. To determine whether the EAR motif in EAR motif-containing ERF proteins has repression function, their EAR motifs were retained or deleted in a yeast one-hybrid (YIH) assay. The results indicate that most of EAR motif-containing ERF proteins lost repression activity after deleting the EAR motif. Moreover, some of these were expressed during ripening. Thus, these EAR motif-containing ERF proteins play vital roles in balancing the regulatory functions of other ERF proteins by completing the DRE/CRT and/or GCC box sites of target genes to ensure normal growth and development in tomato.
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Affiliation(s)
- Li Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - LiJing Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - ShengQun Pang
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - Qun Zheng
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - ShaoWen Quan
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - YuFeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - YuDong Liu
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - MingFang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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Shang X, Wang C, Shen L, Sheng F, He X, Wang F, Fan Y, He X, Jiang M. PfAP2-EXP2, an Essential Transcription Factor for the Intraerythrocytic Development of Plasmodium falciparum. Front Cell Dev Biol 2022; 9:782293. [PMID: 35083215 PMCID: PMC8785209 DOI: 10.3389/fcell.2021.782293] [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: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmodium falciparum undergoes a series of asexual replications in human erythrocytes after infection, which are effective targets for combatting malaria. Here, we report roles of an ApiAP2 transcription factor PfAP2-EXP2 (PF3D7_0611200) in the intraerythrocytic developmental cycle of P. falciparum. PfAP2-EXP2 conditional knockdown resulted in an asexual growth defect but without an appreciable effect on parasite morphology. Further ChIP-seq analysis revealed that PfAP2-EXP2 targeted genes related to virulence and interaction between erythrocytes and parasites. Especially, PfAP2-EXP2 regulation of euchromatic genes does not depend on recognizing specific DNA sequences, while a CCCTAAACCC motif is found in its heterochromatic binding sites. Combined with transcriptome profiling, we suggest that PfAP2-EXP2 is participated in the intraerythrocytic development by affecting the expression of genes related to cell remodeling at the schizont stage. In summary, this study explores an ApiAP2 member plays an important role for the P. falciparum blood-stage replication, which suggests a new perspective for malaria elimination.
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Affiliation(s)
- Xiaomin Shang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Changhong Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li Shen
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fei Sheng
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui He
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Fei Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanting Fan
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Mei Jiang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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Dong Q, Duan D, Zheng W, Huang D, Wang Q, Yang J, Liu C, Li C, Gong X, Li C, Ma F, Mao K. Overexpression of MdVQ37 reduces drought tolerance by altering leaf anatomy and SA homeostasis in transgenic apple. TREE PHYSIOLOGY 2022; 42:160-174. [PMID: 34328189 DOI: 10.1093/treephys/tpab098] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Drought stress is an environmental factor that seriously threatens plant growth, development and yield. VQ proteins are transcriptional regulators that have been reported to be involved in plant growth, development and the responses to biotic and abiotic stressors. However, the relationship between VQ proteins and drought stress has not been well documented in plants. In this study, overexpressing the apple VQ motif-containing protein (MdVQ37) gene in apple plants markedly reduced the tolerance to drought. Physiological and biochemical studies further demonstrated lower enzymatic activities and decreased photosynthetic capacity in transgenic lines compared with wild-type (WT) plants under drought stress. Ultrastructural analysis of leaves showed that the leaves and palisade tissues from the transgenic lines were significantly thinner than those from WT plants. Salicylic acid (SA) analysis indicated that overexpression of MdVQ37 increased the accumulation of 2,5-DHBA by up-regulating the expression of the SA catabolic gene, which ultimately resulted to a significant reduction in endogenous SA content and the disruption of the SA-dependent signaling pathway under drought stress. Applying SA partially increased the survival rate of the transgenic lines under drought stress. These results demonstrate that the regulatory function of apple MdVQ37 is implicated in drought stress, through a change in leaf development and SA homeostasis. This study provides novel insight into understanding the multiple functions of VQ proteins.
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Affiliation(s)
- Qinglong Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Dingyue Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Wenqian Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Dong Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Qian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Jie Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Changhai Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Cuiying Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, P.R. China
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Tang Y, Li H, Liu C, He Y, Wang H, Zhao T, Xu X, Li J, Yang H, Jiang J. CRISPR-Cas9-mediated mutagenesis of the SlSRM1-like gene leads to abnormal leaf development in tomatoes. BMC PLANT BIOLOGY 2022; 22:13. [PMID: 34979927 PMCID: PMC8722279 DOI: 10.1186/s12870-021-03397-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Leaves, which are the most important organs of plants, can not only fix carbon sources through photosynthesis, but also absorb nutrients through transpiration. Leaf development directly determines the growth, flowering and fruiting of plants. There are many factors that affect leaf development, such as the growth environment, gene expression, and hormone synthesis. In this study, tomatoes were used to study the role of the transcription factor Solanum lycopersicum salt-related MYB1-like (SlSRM1-like) in the development of tomato leaves. RESULTS Loss-of-function of the SlSRM1-like gene mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) resulted in abnormal tomato leaf morphology, including thinner leaves, wrinkled edges, raised veins, disordered edge veins, and left and right asymmetry. An analysis of the transcription levels of genes related to leaf development revealed that the expression of these genes was significantly altered in the SlSRM1-like mutants (SlSRM1-like-Ms). Moreover, the SlSRM1-like gene was expressed at higher transcription levels in young tissues than in old tissues, and its expression was also induced in response to auxin. In addition, the transcription levels of genes related to the auxin pathway, which regulates tomato growth and development, were severely affected in the SlSRM1-like-Ms. Therefore, it is hypothesized that the SlSRM1-like gene functions in the regulation of tomato leaf development through the auxin-related pathway. CONCLUSIONS In this study, we successfully knocked out the SlSRM1-like gene in the tomato variety Ailsa Craig using CRISPR technology and found that knockout of the SlSRM1-like gene resulted in abnormal development of tomato leaves. Further research indicated that SlSRM1-like regulated tomato leaf development through auxin-related pathways. The results provide an important reference for the functional study of other SRM1-like genes in plants and provide new insights into the regulation of leaf development in tomato and other plants.
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Affiliation(s)
- Yao Tang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Huijia Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Chunxin Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Yuqing He
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Hexuan Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Huanhuan Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
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Yamada Y, Sato F. Transcription Factors in Alkaloid Engineering. Biomolecules 2021; 11:1719. [PMID: 34827717 PMCID: PMC8615522 DOI: 10.3390/biom11111719] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Plants produce a large variety of low-molecular-weight and specialized secondary compounds. Among them, nitrogen-containing alkaloids are the most biologically active and are often used in the pharmaceutical industry. Although alkaloid chemistry has been intensively investigated, characterization of alkaloid biosynthesis, including biosynthetic enzyme genes and their regulation, especially the transcription factors involved, has been relatively delayed, since only a limited number of plant species produce these specific types of alkaloids in a tissue/cell-specific or developmental-specific manner. Recent advances in molecular biology technologies, such as RNA sequencing, co-expression analysis of transcripts and metabolites, and functional characterization of genes using recombinant technology and cutting-edge technology for metabolite identification, have enabled a more detailed characterization of alkaloid pathways. Thus, transcriptional regulation of alkaloid biosynthesis by transcription factors, such as basic helix-loop-helix (bHLH), APETALA2/ethylene-responsive factor (AP2/ERF), and WRKY, is well elucidated. In addition, jasmonate signaling, an important cue in alkaloid biosynthesis, and its cascade, interaction of transcription factors, and post-transcriptional regulation are also characterized and show cell/tissue-specific or developmental regulation. Furthermore, current sequencing technology provides more information on the genome structure of alkaloid-producing plants with large and complex genomes, for genome-wide characterization. Based on the latest information, we discuss the application of transcription factors in alkaloid engineering.
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Affiliation(s)
- Yasuyuki Yamada
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Fumihiko Sato
- Department of Plant Gene and Totipotency, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- Graduate School of Science, Osaka Prefecture University, Sakai 599-8531, Japan
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Thakur T, Gandass N, Mittal K, Jamwal P, Muthamilarasan M, Salvi P. A rapid, efficient, and low-cost BiFC protocol and its application in studying in vivo interaction of seed-specific transcription factors, RISBZ and RPBF. Funct Integr Genomics 2021; 21:593-603. [PMID: 34436705 DOI: 10.1007/s10142-021-00801-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 10/20/2022]
Abstract
Proteins regulate cellular and biological processes in all living organisms. More than 80% of the proteins interact with one another to perform their respective functions; therefore, studying the protein-protein-interaction has gained attention in functional characterization studies. Bimolecular fluorescence complement (BiFC) assay is widely adopted to determine the physical interaction of two proteins in vivo. Here, we developed a simple, yet effective BiFC assay for protein-protein-interaction using transient Agrobacterium-mediated-transformation of onion epidermal cells by taking case study of Rice-P-box-Binding-Factor (RPBF) and rice-seed-specific-bZIP (RISBZ) in vivo interaction. Our result revealed that both the proteins, i.e., RISBZ and RPBF, interacted in the nucleus and cytosol. These two transcription factors are known for their coordinate/synergistic regulation of seed-protein content via concurrent binding to the promoter region of the seed storage protein (SSP) encoding genes. We further validated our results with BiFC assay in Nicotiana by agroinfiltration method, which exhibited similar results as Agrobacterium-mediated-transformation of onion epidermal cells. We also examined the subcellular localization of RISBZ and RPBF to assess the efficacy of the protocol. The subcellular localization and BiFC assay presented here is quite easy-to-follow, reliable, and reproducible, which can be completed within 2-3 days without using costly instruments and technologies that demand a high skill set.
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Affiliation(s)
- Tanika Thakur
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Nishu Gandass
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Kajal Mittal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Pallavi Jamwal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Prafull Salvi
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India.
- DST-INSPIRE Faculty, Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, India.
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Shan D, Wang C, Song H, Bai Y, Zhang H, Hu Z, Wang L, Shi K, Zheng X, Yan T, Sun Y, Zhu Y, Zhang T, Zhou Z, Guo Y, Kong J. The MdMEK2-MdMPK6-MdWRKY17 pathway stabilizes chlorophyll levels by directly regulating MdSUFB in apple under drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:814-828. [PMID: 34469599 DOI: 10.1111/tpj.15480] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Drought stress severely limits plant growth and production in apple (Malus domestica Borkh.). To breed water-deficit-tolerant apple cultivars that maintain high yields under slight or moderate drought stress, it is important to uncover the mechanisms underlying the transcriptional regulation of chlorophyll metabolism in apple. To explore this mechanism, we generated transgenic 'Gala3' apple plants with overexpression or knockdown of MdWRKY17, which encodes a transcription factor whose expression is significantly induced by water deficit. Under moderate drought stress, we observed significantly higher chlorophyll contents and photosynthesis rates in overexpression transgenic plants than in controls, whereas these were dramatically lower in the knockdown lines. MdWRKY17 directly regulates MdSUFB expression, as demonstrated by in vitro and in vivo experiments. MdSUFB, a key component of the sulfur mobilization (SUF) system that assembles Fe-S clusters, is essential for inhibiting chlorophyll degradation and stabilizing electron transport during photosynthesis, leading to higher chlorophyll levels in transgenic apple plants overexpressing MdWRKY17. The activated MdMEK2-MdMPK6 cascade by water-deficit stress fine-tunes the MdWRKY17-MdSUFB pathway by phosphorylating MdWRKY17 under water-deficit stress. This fine-tuning of the MdWRKY17-MdSUFB regulatory pathway is important for balancing plant survival and yield losses (chlorophyll degradation and reduced photosynthesis) under slight or moderate drought stress. The phosphorylation by MdMEK2-MdMPK6 activates the MdWRKY17-MdSUFB pathway at S66 (identified by LC-MS), as demonstrated by in vitro and in vivo experiments. Our findings reveal that the MdMEK2-MdMPK6-MdWRKY17-MdSUFB pathway stabilizes chlorophyll levels under moderate drought stress, which could facilitate the breeding of apple varieties that maintain high yields under drought stress.
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Affiliation(s)
- Dongqian Shan
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Chanyu Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Handong Song
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yixue Bai
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Haixia Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zehui Hu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lin Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Kun Shi
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaodong Zheng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Tianci Yan
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yanzhao Sun
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yunpeng Zhu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Tong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhaoyang Zhou
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jin Kong
- College of Horticulture, China Agricultural University, Beijing, 100193, China
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Li J, Fan R, Wu B, Ji X, Hao C. Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper ( Piper nigrum L.). Genes (Basel) 2021; 12:genes12111740. [PMID: 34828347 PMCID: PMC8625754 DOI: 10.3390/genes12111740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Black pepper (Piper nigrum L.), is dubbed "the King of Spices". However, the lack of genic knowledge has limited the understanding of its physiological processes and hindered the development of its molecular breeding. The SBP-box gene family is an important family in plant development and integrates multiple physiological processes. Here, we made a genome-wide identification of the pepper SBP-box gene family to provide evolutionary and functional information about this conserved transcription factor. In total, 34 SBP genes were identified in pepper. All these pepper SBP genes were clustered into eight groups, and one pepper group was not found in Arabidopsis thaliana. Segment duplications played the most important role in the expansion process of pepper SBP genes, and all these duplications were subjected to purifying selection. Half of pepper SBP genes were found miR156 target sites, and 17 miR156s were predicted. The tissue expression analysis revealed the differential expression of pepper SBP genes. Eleven SBP genes were found in four co-expression networks, and the GO enrichment further provides a functional prediction for pepper SBP genes. This study lays a foundation for further studies of pepper and provides a valuable reference for functional mining of pepper SBP genes.
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Affiliation(s)
- Jing Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Xunzhi Ji
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; (J.L.); (R.F.); (B.W.); (X.J.)
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning 571533, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulatioin for Tropical Spice and Beverage Crops, Wanning 571533, China
- Academician Sim Soonliang of Hainan Province Research Station, Wanning 571533, China
- Correspondence:
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Emerging roles of NAC transcription factor in medicinal plants: progress and prospects. 3 Biotech 2021; 11:425. [PMID: 34567930 DOI: 10.1007/s13205-021-02970-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022] Open
Abstract
Transcriptional factors act as mediators in regulating stress response in plants from signal perception to processing the directed gene expression. WRKY, MYB, AP2/ERF, etc. are some of the major families of transcription factors known to mediate stress mechanisms in plants by regulating the production of secondary metabolites. NAC domain-containing proteins are among these large transcription factors families in plants. These proteins play impulsive roles in plant growth, development, and various abiotic as well as biotic stresses. They are involved in regulating the different signaling pathways of plant hormones that direct a plant's immunity against pathogens, thereby affecting their immune responses. However, their role in stress regulation or defence mechanism in plants through the secondary metabolite biosynthesis pathway is studied for very few cases. Emerging concern over the requirement of medicinal plants for the production of biocompatible drugs and antibiotics, the study of these vast, affecting proteins should be focused to improve their qualitative and quantitative production further. In medicinal plants, phytochemicals and secondary metabolites are the major biochemicals that impose antimicrobial and other medicinal properties in these plants. This review compiles the NAC transcription factors reported in selected medicinal plants and their possible roles in different mechanisms. Further, the comprehensive understanding of the molecular mechanism, genetic engineering, and regulation responses of NAC TFs in medicinal plants, can lead to improvement in stress response, immunity, and production of usable secondary metabolites.
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Dong Q, Duan D, Zheng W, Huang D, Wang Q, Li X, Mao K, Ma F. MdVQ37 overexpression reduces basal thermotolerance in transgenic apple by affecting transcription factor activity and salicylic acid homeostasis. HORTICULTURE RESEARCH 2021; 8:220. [PMID: 34593787 PMCID: PMC8484266 DOI: 10.1038/s41438-021-00655-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/09/2021] [Accepted: 06/18/2021] [Indexed: 06/01/2023]
Abstract
High temperature (HT) is one of the most important environmental stress factors and seriously threatens plant growth, development, and production. VQ motif-containing proteins are transcriptional regulators that have been reported to regulate plant growth and developmental processes, including responses to biotic and abiotic stresses. However, the relationships between VQ motif-containing proteins and HT stress have not been studied in depth in plants. In this study, transgenic apple (Malus domestica) plants overexpressing the apple VQ motif-containing protein-coding gene (MdVQ37) were exposed to HT stress, and the transgenic lines exhibited a heat-sensitive phenotype. In addition, physiological and biochemical studies revealed that, compared with WT plants, transgenic lines had lower enzymatic activity and photosynthetic capacity and lower amounts of nonenzymatic antioxidant system metabolites under HT stress. Transcriptome analysis revealed 1379 genes whose expression differed between the transgenic lines and WT plants. GO and KEGG pathway analyses showed that transcription factor activity and plant hormone signaling pathways were differentially influenced and enriched in the transgenic lines. Salicylic acid (SA) content analysis indicated that overexpression of MdVQ37 reduced the content of endogenous SA by regulating the expression of SA catabolism-related genes, which ultimately resulted in disruption of the SA-dependent signaling pathway under HT stress. The application of SA slightly increased the survival rate of the transgenic lines under HT stress. Taken together, our results indicate that apple MdVQ37 has a regulatory function in basal thermotolerance by modulating the activity of transcription factors and SA homeostasis. Overall, this study provides novel insights that improve our understanding of the various functions of VQ motif-containing proteins.
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Affiliation(s)
- Qinglong Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - Dingyue Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - Wenqian Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - Dong Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - Qian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - Xiaoran Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China.
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China.
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Sun S, Wang B, Jiang Q, Li Z, Jia S, Wang Y, Guo H. Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch ( Betula platyphylla). PeerJ 2021; 9:e11938. [PMID: 34513325 PMCID: PMC8395574 DOI: 10.7717/peerj.11938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/19/2021] [Indexed: 01/23/2023] Open
Abstract
Background DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear. Methods The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results. Results A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17 were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.
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Affiliation(s)
- Shilin Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Bo Wang
- Department of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, Heilongjiang, China
| | - Qi Jiang
- Department of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, Heilongjiang, China
| | - Zhuoran Li
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Site Jia
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Huiyan Guo
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
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Perea-García A, Andrés-Bordería A, Huijser P, Peñarrubia L. The Copper-microRNA Pathway Is Integrated with Developmental and Environmental Stress Responses in Arabidopsis thaliana. Int J Mol Sci 2021; 22:9547. [PMID: 34502449 PMCID: PMC8430956 DOI: 10.3390/ijms22179547] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
As an essential nutrient, copper (Cu) scarcity causes a decrease in agricultural production. Cu deficiency responses include the induction of several microRNAs, known as Cu-miRNAs, which are responsible for degrading mRNAs from abundant and dispensable cuproproteins to economize copper when scarce. Cu-miRNAs, such as miR398 and miR408 are conserved, as well as the signal transduction pathway to induce them under Cu deficiency. The Arabidopsis thaliana SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family member SPL7 binds to the cis-regulatory motifs present in the promoter regions of genes expressed under Cu deficiency, including Cu-miRNAs. The expression of several other SPL transcription factor family members is regulated by miR156. This regulatory miR156-SPL module plays a crucial role in developmental phase transitions while integrating internal and external cues. Here, we show that Cu deficiency also affects miR156 expression and that SPL3 overexpressing plants, resistant to miR156 regulation, show a severe decrease in SPL7-mediated Cu deficiency responses. These include the expression of Cu-miRNAs and their targets and is probably due to competition between SPL7 and miR156-regulated SPL3 in binding to cis-regulatory elements in Cu-miRNA promoters. Thus, the conserved SPL7-mediated Cu-miRNA pathway could generally be affected by the miR156-SPL module, thereby underscoring the integration of the Cu-miRNA pathway with developmental and environmental stress responses in Arabidopsis thaliana.
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Affiliation(s)
- Ana Perea-García
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Valencia, Spain; (A.P.-G.); (A.A.-B.)
| | - Amparo Andrés-Bordería
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Valencia, Spain; (A.P.-G.); (A.A.-B.)
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;
| | - Lola Peñarrubia
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Valencia, Spain; (A.P.-G.); (A.A.-B.)
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