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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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Maeo K, Nakaya Y, Mitsuda N, Ishiguro S. ACRE, a class of AP2/ERF transcription factors, activates the expression of sweet potato ß-amylase and sporamin genes through the sugar-responsible element CMSRE-1. PLANT MOLECULAR BIOLOGY 2024; 114:54. [PMID: 38714535 PMCID: PMC11076338 DOI: 10.1007/s11103-024-01450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/04/2024] [Indexed: 05/10/2024]
Abstract
Sugars, synthesized by photosynthesis in source organs, are loaded and utilized as an energy source and carbon skeleton in sink organs, and also known to be important signal molecules regulating gene expression in higher plants. The expression of genes coding for sporamin and β-amylase, the two most abundant proteins in storage roots of sweet potato, is coordinately induced by sugars. We previously reported on the identification of the carbohydrate metabolic signal-responsible element-1 (CMSRE-1) essential for the sugar-responsible expression of two genes. However, transcription factors that bind to this sequence have not been identified. In this study, we performed yeast one-hybrid screening using the sugar-responsible minimal promoter region of the ß-amylase gene as bait and a library composed only transcription factor cDNAs of Arabidopsis. Two clones, named Activator protein binding to CMSRE-1 (ACRE), encoding AP2/ERF transcription factors were isolated. ACRE showed transactivation activity of the sugar-responsible minimal promoter in a CMSRE-1-dependent manner in Arabidopsis protoplasts. Electric mobility shift assay (EMSA) using recombinant proteins and transient co-expression assay in Arabidopsis protoplasts revealed that ACRE could actually act to the CMSRE-1. Among the DEHYDRATION -RESPONSIVE ELEMENT BINDING FACTOR (DREB) subfamily, almost all homologs including ACRE, could act on the DRE, while only three ACREs could act to the CMSRE-1. Moreover, ACRE-homologs of Japanese morning glory also have the same property of DNA-binding preference and transactivation activity through the CMSRE-1. These findings suggested that ACRE plays an important role in the mechanism regulating the sugar-responsible gene expression through the CMSRE-1 conserved across plant species.
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Affiliation(s)
- Kenichiro Maeo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8601, Japan.
| | - Yuki Nakaya
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8601, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Sumie Ishiguro
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8601, Japan
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Khodaeiaminjan M, Gomes C, Pagano A, Kruszka D, Sulima P, Przyborowski JA, Krajewski P, Paiva JAP. Impacts of in-vitro zebularine treatment on genome-wide DNA methylation and transcriptomic profiles in Salix purpurea L. PHYSIOLOGIA PLANTARUM 2024; 176:e14403. [PMID: 38923551 DOI: 10.1111/ppl.14403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Renewable energy resources such as biomass are crucial for a sustainable global society. Trees are a major source of lignocellulosic biomass, which can vary in response to different environmental factors owing to epigenetic regulation, such as DNA C-methylation. To investigate the effects of DNA methylation on plant development and wood formation, and its impacts on gene expression, with a focus on secondary cell wall (SCW)-associated genes, Salix purpurea plantlets were cloned from buds derived from a single hybrid tree for both treatment and control conditions. For the treatment condition, buds were exposed to 50 μM zebularine in vitro and a combined strategy of whole-genome bisulfite sequencing (WGBS) and RNA-seq was employed to examine the methylome and transcriptome profiles of different tissues collected at various time points under both conditions. Transcriptomic and methylome data revealed that most of the promoter and gene body demethylation had no marked effects on the expression profiles of genes. Nevertheless, gene expression tended to decrease with the increased methylation levels of genes with highly methylated promoters. Results indicated that demethylation is less evident in centromeric regions and sex chromosomes. Promoters of secondary cell wall-associated genes, such as 4-coumarate-CoA ligase-like and Rac-like GTP-binding protein RHO, were differentially methylated in the secondary xylem samples collected from two-month potted treated plants compared to control samples. Our results provide novel insights into DNA methylation and gene expression landscapes and a basis for investigating the epigenetic regulation of wood formation in S. purpurea as a model plant for bioenergy species.
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Affiliation(s)
- Mortaza Khodaeiaminjan
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Carolina Gomes
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Andrea Pagano
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Dariusz Kruszka
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Paweł Sulima
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury, Olsztyn, Poland
| | - Jerzy Andrzej Przyborowski
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury, Olsztyn, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Jorge Almiro Pinto Paiva
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Sharma M, Tisarum R, Kohli RK, Batish DR, Cha-Um S, Singh HP. Inroads into saline-alkaline stress response in plants: unravelling morphological, physiological, biochemical, and molecular mechanisms. PLANTA 2024; 259:130. [PMID: 38647733 DOI: 10.1007/s00425-024-04368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/22/2024] [Indexed: 04/25/2024]
Abstract
MAIN CONCLUSION This article discusses the complex network of ion transporters, genes, microRNAs, and transcription factors that regulate crop tolerance to saline-alkaline stress. The framework aids scientists produce stress-tolerant crops for smart agriculture. Salinity and alkalinity are frequently coexisting abiotic limitations that have emerged as archetypal mediators of low yield in many semi-arid and arid regions throughout the world. Saline-alkaline stress, which occurs in an environment with high concentrations of salts and a high pH, negatively impacts plant metabolism to a greater extent than either stress alone. Of late, saline stress has been the focus of the majority of investigations, and saline-alkaline mixed studies are largely lacking. Therefore, a thorough understanding and integration of how plants and crops rewire metabolic pathways to repair damage caused by saline-alkaline stress is of particular interest. This review discusses the multitude of resistance mechanisms that plants develop to cope with saline-alkaline stress, including morphological and physiological adaptations as well as molecular regulation. We examine the role of various ion transporters, transcription factors (TFs), differentially expressed genes (DEGs), microRNAs (miRNAs), or quantitative trait loci (QTLs) activated under saline-alkaline stress in achieving opportunistic modes of growth, development, and survival. The review provides a background for understanding the transport of micronutrients, specifically iron (Fe), in conditions of iron deficiency produced by high pH. Additionally, it discusses the role of calcium in enhancing stress tolerance. The review highlights that to encourage biomolecular architects to reconsider molecular responses as auxiliary for developing tolerant crops and raising crop production, it is essential to (a) close the major gaps in our understanding of saline-alkaline resistance genes, (b) identify and take into account crop-specific responses, and (c) target stress-tolerant genes to specific crops.
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Affiliation(s)
- Mansi Sharma
- Department of Environment Studies, Panjab University, Chandigarh, 160 014, India
- Department of Environmental Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, 201310, Uttar Pradesh, India
| | - Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ravinder Kumar Kohli
- Department of Botany, Panjab University, Chandigarh, 160014, India
- Amity University, Mohali Campus, Sector 82A, Mohali, 140306, Punjab, India
| | - Daizy R Batish
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Harminder Pal Singh
- Department of Environment Studies, Panjab University, Chandigarh, 160 014, India.
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Park M, Shin SY, Moon H, Choi W, Shin C. Analysis of the global transcriptome and miRNAome associated with seed dormancy during seed maturation in rice (Oryza sativa L. cv. Nipponbare). BMC PLANT BIOLOGY 2024; 24:215. [PMID: 38532331 DOI: 10.1186/s12870-024-04928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Seed dormancy is a biological mechanism that prevents germination until favorable conditions for the subsequent generation of plants are encountered. Therefore, this mechanism must be effectively established during seed maturation. Studies investigating the transcriptome and miRNAome of rice embryos and endosperms at various maturation stages to evaluate seed dormancy are limited. This study aimed to compare the transcriptome and miRNAome of rice seeds during seed maturation. RESULTS Oryza sativa L. cv. Nipponbare seeds were sampled for embryos and endosperms at three maturation stages: 30, 45, and 60 days after heading (DAH). The pre-harvest sprouting (PHS) assay was conducted to assess the level of dormancy in the seeds at each maturation stage. At 60 DAH, the PHS rate was significantly increased compared to those at 30 and 45 DAH, indicating that the dormancy is broken during the later maturation stage (45 DAH to 60 DAH). However, the largest number of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified between 30 and 60 DAH in the embryo and endosperm, implying that the gradual changes in genes and miRNAs from 30 to 60 DAH may play a significant role in breaking seed dormancy. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses confirmed that DEGs related to plant hormones were most abundant in the embryo during 45 DAH to 60 DAH and 30 DAH to 60 DAH transitions. Alternatively, most of the DEGs in the endosperm were related to energy and abiotic stress. MapMan analysis and quantitative real-time polymerase chain reaction identified four newly profiled auxin-related genes (OsSAUR6/12/23/25) and one ethylene-related gene (OsERF087), which may be involved in seed dormancy during maturation. Additionally, miRNA target prediction (psRNATarget) and degradome dataset (TarDB) indicated a potential association between osa-miR531b and ethylene biosynthesis gene (OsACO4), along with osa-miR390-5p and the abscisic acid (ABA) exporter-related gene (OsMATE19) as factors involved in seed dormancy. CONCLUSIONS Analysis of the transcriptome and miRNAome of rice embryos and endosperms during seed maturation provided new insights into seed dormancy, particularly its relationship with plant hormones such as ABA, auxin, and ethylene.
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Affiliation(s)
- Minsu Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Yoon Shin
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongman Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Woochang Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea.
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Asiminicesei DM, Fertu DI, Gavrilescu M. Impact of Heavy Metal Pollution in the Environment on the Metabolic Profile of Medicinal Plants and Their Therapeutic Potential. PLANTS (BASEL, SWITZERLAND) 2024; 13:913. [PMID: 38592933 PMCID: PMC10976221 DOI: 10.3390/plants13060913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
The paper provides a comprehensive examination of heavy metal stress on medicinal plants, focusing on its impact on antioxidant capacity and biosynthetic pathways critical to their therapeutic potential. It explores the complex relationship between heavy metals and the physiological and biochemical responses of medicinal plants, highlighting how metal stress disrupts biosynthetic pathways, altering concentrations of secondary metabolites. This disruption may compromise the overall quality and efficacy of medicinal plants, requiring a holistic understanding of its cumulative impacts. Furthermore, the study discusses the potential of targeted genetic editing to enhance plant resilience against heavy metal stress by manipulating genes associated with antioxidant defenses. This approach represents a promising frontier in safeguarding medicinal plants in metal-contaminated environments. Additionally, the research investigates the role of phytohormone signaling in plant adaptive mechanisms to heavy metal stress, revealing its influence on biochemical and physiological responses, thereby adding complexity to plant adaptation. The study underscores the importance of innovative technologies and global cooperation in protecting medicinal plants' therapeutic potential and highlights the need for mitigation strategies to address heavy metal contamination effectively.
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Affiliation(s)
- Dana-Mihaela Asiminicesei
- Department of Environmental Engineering and Management, “Cristofor Simionescu” Faculty of Chemical Engineering and Environmental Protection, “Gheorghe Asachi” Technical University of Iasi, 73 Prof. D. Mangeron Blvd., 700050 Iasi, Romania;
| | - Daniela Ionela Fertu
- Department of Pharmaceutical Sciences, Faculty of Medicine and Pharmacy, “Dunarea de Jos” University of Galati, 35 Al. I. Cuza Street, 800002 Galati, Romania
| | - Maria Gavrilescu
- Department of Environmental Engineering and Management, “Cristofor Simionescu” Faculty of Chemical Engineering and Environmental Protection, “Gheorghe Asachi” Technical University of Iasi, 73 Prof. D. Mangeron Blvd., 700050 Iasi, Romania;
- Academy of Romanian Scientists, 3 Ilfov Street, 050044 Bucharest, Romania
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Yang L, Xu L, Guo J, Li A, Qi H, Wang J, Song S. SNAC1-OsERF103-OsSDG705 module mediates drought response in rice. THE NEW PHYTOLOGIST 2024; 241:2480-2494. [PMID: 38296835 DOI: 10.1111/nph.19552] [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: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Drought stress profoundly hampers both plant growth and crop yield. To combat this, plants have evolved intricate transcriptional regulation mechanisms as a pivotal strategy. Through a genetic screening with rice genome-scale mutagenesis pool under drought stress, we identified an APETALA2/Ethylene Responsive Factor, namely OsERF103, positively responds to drought tolerance in rice. Combining chromatin immunoprecipitation sequencing and RNA sequencing analyses, we pinpointed c. 1000 genes directly influenced by OsERF103. Further results revealed that OsERF103 interacts with Stress-responsive NAC1 (SNAC1), a positive regulator of drought tolerance in rice, to synergistically regulate the expression of key drought-related genes, such as OsbZIP23. Moreover, we found that OsERF103 recruits a Su(var)3-9,enhancer of zeste and trithorax-domain group protein 705, which encodes a histone 3 lysine 4 (H3K4)-specific methyltransferase to specifically affect the deposition of H3K4me3 at loci like OsbZIP23 and other genes linked to dehydration responses. Additionally, the natural alleles of OsERF103 are selected during the domestication of both indica and japonica rice varieties and exhibit significant geographic distribution. Collectively, our findings have unfurled a comprehensive mechanistic framework underlying the OsERF103-mediated cascade regulation of drought response. This discovery not only enhances our understanding of drought signaling but also presents a promising avenue for the genetic improvement of drought-tolerant rice cultivars.
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Affiliation(s)
- Lijia Yang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liang Xu
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiazhuo Guo
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Aipeng Li
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Haoyue Qi
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiaxuan Wang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiyong Song
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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Zhang J, Zhao H, Chen L, Lin J, Wang Z, Pan J, Yang F, Ni X, Wang Y, Wang Y, Li R, Pi E, Wang S. Multifaceted roles of WRKY transcription factors in abiotic stress and flavonoid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1303667. [PMID: 38169626 PMCID: PMC10758500 DOI: 10.3389/fpls.2023.1303667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Increasing biotic and abiotic stresses are seriously impeding the growth and yield of staple crops and threatening global food security. As one of the largest classes of regulators in vascular plants, WRKY transcription factors play critical roles governing flavonoid biosynthesis during stress responses. By binding major W-box cis-elements (TGACCA/T) in target promoters, WRKYs modulate diverse signaling pathways. In this review, we optimized existing WRKY phylogenetic trees by incorporating additional plant species with WRKY proteins implicated in stress tolerance and flavonoid regulation. Based on the improved frameworks and documented results, we aim to deduce unifying themes of distinct WRKY subfamilies governing specific stress responses and flavonoid metabolism. These analyses will generate experimentally testable hypotheses regarding the putative functions of uncharacterized WRKY homologs in tuning flavonoid accumulation to enhance stress resilience.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Younuskunju S, Mohamoud YA, Mathew LS, Mayer KFX, Suhre K, Malek JA. Genome-wide association of dry (Tamar) date palm fruit color. THE PLANT GENOME 2023; 16:e20373. [PMID: 37621134 DOI: 10.1002/tpg2.20373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 08/26/2023]
Abstract
Date palm (Phoenix dactylifera) fruit (dates) are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. Genetic studies of some date palm traits have been performed, including sex determination, sugar content, and fresh fruit color. In this study, we used genome sequences and image data of 199 dry dates (Tamar) collected from 14 countries to identify genetic loci associated with the color of this fruit stage. Here, we find loci across multiple linkage groups (LG) associated with dry fruit color phenotype. We recover both the previously identified VIRESCENS (VIR) genotype associated with fresh fruit yellow or red color and new associations with the lightness and darkness of dry fruit. This study will add resolution to our understanding of date color phenotype, especially at the most commercially important Tamar stage.
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Affiliation(s)
- Shameem Younuskunju
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Doha, Qatar
- School of Life Sciences, Technical University of Munich, Munich, Germany
| | | | - Lisa S Mathew
- Clinical Genomics Laboratory, Sidra Medicine, Doha, Qatar
| | - Klaus F X Mayer
- School of Life Sciences, Technical University of Munich, Munich, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, Munich, Germany
| | - Karsten Suhre
- Department of Physiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Joel A Malek
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
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Truong TTT, Chiu CC, Chen JY, Su PY, Nguyen TP, Trinh NN, Mimura T, Lee RH, Chang CH, Huang HJ. Uncovering molecular mechanisms involved in microbial volatile compounds-induced stomatal closure in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2023; 113:143-155. [PMID: 37985583 DOI: 10.1007/s11103-023-01379-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/18/2023] [Indexed: 11/22/2023]
Abstract
Microbial volatile compounds (mVCs) may cause stomatal closure to limit pathogen invasion as part of plant innate immune response. However, the mechanisms of mVC-induced stomatal closure remain unclear. In this study, we co-cultured Enterobacter aerogenes with Arabidopsis (Arabidopsis thaliana) seedlings without direct contact to initiate stomatal closure. Experiments using the reactive oxygen species (ROS)-sensitive fluorescent dye, H2DCF-DA, showed that mVCs from E. aerogenes enhanced ROS production in guard cells of wild-type plants. The involvement of ROS in stomatal closure was then demonstrated in an ROS production mutant (rbohD). In addition, we identified two stages of signal transduction during E. aerogenes VC-induced stomatal closure by comparing the response of wild-type Arabidopsis with a panel of mutants. In the early stage (3 h exposure), E. aerogenes VCs induced stomatal closure in wild-type and receptor-like kinase THESEUS1 mutant (the1-1) but not in rbohD, plant hormone-related mutants (nced3, erf4, jar1-1), or MAPK kinase mutants (mkk1 and mkk3). However, in the late stage (24 h exposure), E. aerogenes VCs induced stomatal closure in wild-type and rbohD but not in nced3, erf4, jar1-1, the1-1, mkk1 or mkk3. Taken together, our results suggest that E. aerogenes mVC-induced plant immune responses modulate stomatal closure in Arabidopsis by a multi-phase mechanism.
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Affiliation(s)
- Tu-Trinh Thi Truong
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
- Faculty of Technology, The University of Danang-Campus in Kontum, The University of Danang, Kon Tum City, 580000, Vietnam
| | - Chi-Chou Chiu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Jing-Yu Chen
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Pei-Yu Su
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Tri-Phuong Nguyen
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Ngoc-Nam Trinh
- Industrial University of Ho Chi Minh City, No. 12, Nguyen Van Bao, Ho Chi Minh City, Vietnam
| | - Tetsuro Mimura
- Kyoto University of Advanced Science, Kameoka, Kyoto, 621-8555, Japan
| | - Ruey-Hua Lee
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Ching-Han Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, No. 1, University Road, Tainan, 701, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan.
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, No. 1, University Road, Tainan, 701, Taiwan.
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan.
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11
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Dwiningsih Y, Thomas J, Kumar A, Gupta C, Gill N, Ruiz C, Alkahtani J, Baisakh N, Pereira A. QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population. Int J Mol Sci 2023; 24:15167. [PMID: 37894848 PMCID: PMC10606886 DOI: 10.3390/ijms242015167] [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: 07/31/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.
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Affiliation(s)
- Yheni Dwiningsih
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA;
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
| | - Charles Ruiz
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Jawaher Alkahtani
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Niranjan Baisakh
- Department of School of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
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12
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Aydinoglu F, Kuloglu A. Nicotiana benthamiana as a model plant host for Fusarium verticillioides to investigate RNA interference, cross-kingdom RNA exchange, and competitive endogenous RNA (ceRNA) network. Mol Biol Rep 2023; 50:8061-8072. [PMID: 37540455 DOI: 10.1007/s11033-023-08698-6] [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: 04/25/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Fusarium verticillioides is among the most devastating fungal pathogen of cereals. Therefore, it is crucial to employ effective and long-term strategies for managing F. verticillioides for sustainable agriculture. RNA interference (RNAi) being a natural defense mechanism of plants via regulation of gene expression, has emerged as a promising tool for eradicating pathogens. RNAi also operates between the host and pathogen through RNA exchange. RNAi interacts with competitive endogenous RNAs (ceRNAs) including long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA. Due to the lack of an elaborate model to investigate all these mechanisms, this study aimed to establish a Nicotiana benthamiana (Nb)-F. verticillioides (Fv) phyto-pathosystem as an experimental model. METHODS AND RESULTS Nb seedlings were inoculated with Fv, and the pathogenicity was monitored morphologically, microscopically, biochemically, and transcriptionally. To observe the role of RNAi and RNA-exchange in pathogenicity, Nb-miR172 and Nb-miR399 targeting Nb-lncRNA-IPS (Induced by Phosphate Starvation1) and Nb-AP2 (Apetala2) and Nb-PHO2 (phosphate over-accumulator) ceRNA network and Fv-V-ATPase (Vesicle-fusing ATPase) targeted by Nb-miR172 were investigated. As a result, epidermal cell density, leaf area, petiole length, and chlorophyll content were reduced while the density of stomata and trichome and phenolic content and the activity of ascorbate peroxidase (APX) and glutathione reductase (GR) were increased in response to Fv infection in Nb. The expression of AP2 and PHO2 were downregulated against Fv but no significant changes were detected in IPS, miR172, and miR399 expression. CONCLUSION These findings suggested the Fv-Nb phyto-pathosystem as a useful experimental model to reveal genetic regulations.
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Affiliation(s)
- Fatma Aydinoglu
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey.
| | - Aslihan Kuloglu
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
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13
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Yoon KN, Yoon YS, Hong HJ, Park JH, Song BS, Eun JB, Kim JK. Gamma irradiation delays tomato (Solanum lycopersicum) ripening by inducing transcriptional changes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:6640-6653. [PMID: 37267467 DOI: 10.1002/jsfa.12760] [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: 02/05/2023] [Revised: 05/02/2023] [Accepted: 06/02/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Tomato (Solanum lycopersicum) has a relatively short shelf life as a result of rapid ripening, limiting its transportability and marketability. Recently, gamma irradiation has emerged as a viable method for delaying tomato fruit ripening. Although few studies have shown that gamma irradiation delays the ripening of tomatoes, the underlying mechanism remains unknown. Therefore, the present study aimed to examine the effects of gamma irradiation on tomato fruit ripening and the underlying mechanisms using transcriptomics. RESULTS Following gamma irradiation, the total microbial count, weight loss, and decay rate of tomatoes significantly reduced during storage. Furthermore, the redness (a*), color change (∆E), and lycopene content of gamma-irradiated tomatoes decreased in a dose-dependent manner during storage. Moreover, gamma irradiation significantly upregulated the expression levels of genes associated with DNA, chloroplast, and oxidative damage repairs, whereas those of ethylene and auxin signaling-, ripening-, and cell wall metabolism-related, as well as carotenoid genes, were downregulated. CONCLUSION Gamma irradiation effectively delayed ripening by downregulating the expression of ripening-related genes and inhibiting microbial growth, which prevented decay and prolonged the shelf life of tomatoes. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ki-Nam Yoon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju, Republic of Korea
| | - Yeong-Seok Yoon
- Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup-si, Republic of Korea
| | - Hae-Jung Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
| | - Jong-Heum Park
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
| | - Beom-Seok Song
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
| | - Jong-Bang Eun
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju, Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea
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14
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Li L, Zhu Z, Liu J, Zhang Y, Lu Y, Zhao J, Xing H, Guo N. Transcription Factor GmERF105 Negatively Regulates Salt Stress Tolerance in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:3007. [PMID: 37631217 PMCID: PMC10459988 DOI: 10.3390/plants12163007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
The Ethylene Response Factor (ERF) transcription factors form a subfamily of the AP2/ERF family that is instrumental in mediating plant responses to diverse abiotic stressors. Herein, we present the isolation and characterization of the GmERF105 gene from Williams 82 (W82), which is rapidly induced by salt, drought, and abscisic acid (ABA) treatments in soybean. The GmERF105 protein contains an AP2 domain and localizes to the nucleus. GmERF105 was selectively bound to GCC-box by gel migration experiments. Under salt stress, overexpression of GmERF105 in Arabidopsis significantly reduced seed germination rate, fresh weight, and antioxidant enzyme activity; meanwhile, sodium ion content, malonic dialdehyde (MDA) content, and reactive oxygen species (ROS) levels were markedly elevated compared to the wild type. It was further found that the transcription levels of CSD1 and CDS2 of two SOD genes were reduced in OE lines. Furthermore, the GmERF105 transgenic plants displayed suppressed expression of stress response marker genes, including KIN1, LEA14, NCED3, RD29A, and COR15A/B, under salt treatment. Our findings suggest that GmERF105 can act as a negative regulator in plant salt tolerance pathways by affecting ROS scavenging systems and the transcription of stress response marker genes.
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Affiliation(s)
| | | | | | | | | | - Jinming Zhao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, MOE National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, Zhongshan Biological Breeding Laboratory, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (L.L.)
| | - Han Xing
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, MOE National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, Zhongshan Biological Breeding Laboratory, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (L.L.)
| | - Na Guo
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, MOE National Innovation Platform for Soybean Bio-Breeding Industry and Education Integration, Zhongshan Biological Breeding Laboratory, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (L.L.)
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15
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Di Giacomo M, Vega TA, Cambiaso V, Picardi LA, Rodríguez GR, Pereira da Costa JH. An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life. PLANTS (BASEL, SWITZERLAND) 2023; 12:2812. [PMID: 37570966 PMCID: PMC10421356 DOI: 10.3390/plants12152812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.
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Affiliation(s)
- Melisa Di Giacomo
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Tatiana Alejandra Vega
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Liliana Amelia Picardi
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
| | - Javier Hernán Pereira da Costa
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina; (M.D.G.); (T.A.V.); (V.C.); (G.R.R.)
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina;
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16
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Abulfaraj AA. Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat. Saudi J Biol Sci 2023; 30:103652. [PMID: 37206446 PMCID: PMC10189290 DOI: 10.1016/j.sjbs.2023.103652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/09/2023] [Indexed: 05/21/2023] Open
Abstract
The challenge of climate change makes it mandatory to improve tolerance to drought stress in bread wheat (Triticum aestivum) via biotechnological approaches. Drought stress experiment was conducted followed by RNA-Seq analysis for leaves of two wheat cultivars namely Giza 168 and Gemmiza 10 with contrasting genotypes. Expression patterns of the regulated stress-related genes and concordantly expressed TFs were detected, then, validated via qPCR for two loss-of-function mutants in Arabidopsis background harboring mutated genes analogue to those in wheat. Drought-stress related genes were searched for concordantly expressed TFs and a total of eight TFs were shown to coexpress with 14 stress-related genes. Among these genes, one TF belongs to the zinc finger protein CONSTANS family and proved via qPCR to drive expression of a gene encoding a speculative TF namely zinc transporter 3-like and two other stress related genes encoding tryptophan synthase alpha chain and asparagine synthetase. Known functions of the two TFs under drought stress complement those of the two concordantly expressed stress-related genes, thus, it is likely that they are related. This study highlights the possibility to utilize metabolic engineering approaches to decipher and incorporate existing regulatory frameworks under drought stress in future breeding programs of bread wheat.
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17
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Yang L, Wang X, Zhao F, Zhang X, Li W, Huang J, Pei X, Ren X, Liu Y, He K, Zhang F, Ma X, Yang D. Roles of S-Adenosylmethionine and Its Derivatives in Salt Tolerance of Cotton. Int J Mol Sci 2023; 24:ijms24119517. [PMID: 37298464 DOI: 10.3390/ijms24119517] [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: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Salinity is a major abiotic stress that restricts cotton growth and affects fiber yield and quality. Although studies on salt tolerance have achieved great progress in cotton since the completion of cotton genome sequencing, knowledge about how cotton copes with salt stress is still scant. S-adenosylmethionine (SAM) plays important roles in many organelles with the help of the SAM transporter, and it is also a synthetic precursor for substances such as ethylene (ET), polyamines (PAs), betaine, and lignin, which often accumulate in plants in response to stresses. This review focused on the biosynthesis and signal transduction pathways of ET and PAs. The current progress of ET and PAs in regulating plant growth and development under salt stress has been summarized. Moreover, we verified the function of a cotton SAM transporter and suggested that it can regulate salt stress response in cotton. At last, an improved regulatory pathway of ET and PAs under salt stress in cotton is proposed for the breeding of salt-tolerant varieties.
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Affiliation(s)
- Li Yang
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Fuyong Zhao
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Xianliang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Junsen Huang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiang Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
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18
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Matoušek J, Wüsthoff KP, Steger G. "Pathomorphogenic" Changes Caused by Citrus Bark Cracking Viroid and Transcription Factor TFIIIA-7ZF Variants Support Viroid Propagation in Tobacco. Int J Mol Sci 2023; 24:ijms24097790. [PMID: 37175498 PMCID: PMC10178017 DOI: 10.3390/ijms24097790] [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: 03/14/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Viroids are small, non-coding, pathogenic RNAs with the ability to disturb plant developmental processes. This dysregulation redirects the morphogenesis of plant organs, significantly impairing their functionality. Citrus bark cracking viroid (CBCVd) causes detrimental developmental distortions in infected hops (Humulus lupulus) and causes significant economic losses. CBCVd can infect cells and tissues of the model plant tobacco (Nicotiana tabacum), provided it is delivered via transgenesis. The levels of CBCVd in tobacco were enhanced in plant hybrids expressing CBCVd cDNAs and either the tobacco or hop variant of TFIIIA-7ZF, a viroid-mediated splicing derivative of transcription factor IIIA, which is important for viroid replication by DNA-dependent RNA polymerase II. The TFIIIA-7ZF variants can change the tobacco morphogenesis if expressed in leaves and shoots. In addition to the splitting of shoots, the "pathomorphogenic" network in hybrid plants expressing CBCVd and HlTFIIIA-7ZF induced leaf fusions and malformations. Moreover, CBCVd can dramatically change another morphogenesis into teratomic and petal-like tissues if propagated above some limit in young transgenic tobacco microspores and anthers. By comparative RNA profiling of transgenic tobacco shoots bearing TFIIIA-7ZFs and CBCVd-transformed/infected anthers, we found a differential expression of many genes at p < 0.05. As the main common factor showing the differential up-regulation in shoot and anther tissues, a LITTLE ZIPPER 2-like transcription factor was found. We propose that this factor, which can interact as a competitive inhibitor of the also dysregulated homeobox-leucin zipper family protein (HD-ZIPIII) in apical meristem, is essential for a network responsible for some morphological changes and modifications of plant degradome within shoot meristem regulation and secondary xylem differentiation.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Kevin P Wüsthoff
- Institut für Pysikalische Biologie, Heinrich Heine University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Gerhard Steger
- Institut für Pysikalische Biologie, Heinrich Heine University Düsseldorf, D-40204 Düsseldorf, Germany
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Akbari A, Ismaili A, Amirbakhtiar N, Pouresmael M, Shobbar ZS. Genome-wide transcriptional profiling provides clues to molecular mechanisms underlying cold tolerance in chickpea. Sci Rep 2023; 13:6279. [PMID: 37072529 PMCID: PMC10113226 DOI: 10.1038/s41598-023-33398-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Chickpea is an important food legume cultivated in several countries. A sudden drop in autumn temperature, freezing winter temperature, and late spring cold events result in significant losses in chickpea production. The current study used RNA sequencing of two cold tolerant (Saral) and sensitive (ILC533) Kabuli chickpea genotypes to identify cold tolerance-associated genes/pathways. A total of 200.85 million raw reads were acquired from the leaf samples by Illumina sequencing, and around 86% of the clean reads (199 million) were mapped to the chickpea reference genome. The results indicated that 3710 (1980 up- and 1730 down-regulated) and 3473 (1972 up- and 1501 down-regulated) genes were expressed differentially under cold stress in the tolerant and sensitive genotypes, respectively. According to the GO enrichment analysis of uniquely down-regulated genes under cold stress in ILC533, photosynthetic membrane, photosystem II, chloroplast part, and photosystem processes were enriched, revealing that the photosynthesis is severely sensitive to cold stress in this sensitive genotype. Many remarkable transcription factors (CaDREB1E, CaMYB4, CaNAC47, CaTCP4, and CaWRKY33), signaling/regulatory genes (CaCDPK4, CaPP2C6, CaMKK2, and CaHSFA3), and protective genes (CaCOR47, CaLEA3, and CaGST) were identified among the cold-responsive genes of the tolerant genotype. These findings would help improve cold tolerance across chickpea genotypes by molecular breeding or genetic engineering.
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Affiliation(s)
- Alireza Akbari
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Nazanin Amirbakhtiar
- Genetic Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Masoumeh Pouresmael
- Genetic Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization, Karaj, Iran.
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Su J, Song S, Wang Y, Zeng Y, Dong T, Ge X, Duan H. Genome-wide identification and expression analysis of DREB family genes in cotton. BMC PLANT BIOLOGY 2023; 23:169. [PMID: 36997878 PMCID: PMC10061749 DOI: 10.1186/s12870-023-04180-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome‑wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species. RESULTS In total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1-A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress. CONCLUSIONS Collectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response.
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Affiliation(s)
- Jiuchang Su
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shanglin Song
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yiting Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yunpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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Cheng C, An L, Li F, Ahmad W, Aslam M, Ul Haq MZ, Yan Y, Ahmad RM. Wide-Range Portrayal of AP2/ERF Transcription Factor Family in Maize ( Zea mays L.) Development and Stress Responses. Genes (Basel) 2023; 14:194. [PMID: 36672935 PMCID: PMC9859492 DOI: 10.3390/genes14010194] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
The APETALA2/Ethylene-Responsive Transcriptional Factors containing conservative AP2/ERF domains constituted a plant-specific transcription factor (TF) superfamily, called AP2/ERF. The configuration of the AP2/ERF superfamily in maize has remained unresolved. In this study, we identified the 229 AP2/ERF genes in the latest (B73 RefGen_v5) maize reference genome. Phylogenetic classification of the ZmAP2/ERF family members categorized it into five clades, including 27 AP2 (APETALA2), 5 RAV (Related to ABI3/VP), 89 DREB (dehydration responsive element binding), 105 ERF (ethylene responsive factors), and a soloist. The duplication events of the paralogous genes occurred from 1.724-25.855 MYA, a key route to maize evolution. Structural analysis reveals that they have more introns and few exons. The results showed that 32 ZmAP2/ERFs regulate biotic stresses, and 24 ZmAP2/ERFs are involved in responses towards abiotic stresses. Additionally, the expression analysis showed that DREB family members are involved in plant sex determination. The real-time quantitative expression profiling of ZmAP2/ERFs in the leaves of the maize inbred line B73 under ABA, JA, salt, drought, heat, and wounding stress revealed their specific expression patterns. Conclusively, this study unveiled the evolutionary pathway of ZmAP2/ERFs and its essential role in stress and developmental processes. The generated information will be useful for stress resilience maize breeding programs.
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Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Likun An
- College of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China
| | - Fangzhe Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wahaj Ahmad
- Institute of Soil and Environmental Sciences, COMSATS University Islamabad, Abbottabad 22020, Pakistan
| | - Muhammad Aslam
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Muhammad Zia Ul Haq
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Yuanxin Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ramala Masood Ahmad
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
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22
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Jia H, Zuo Q, Sadeghnezhad E, Zheng T, Chen X, Dong T, Fang J. HDAC19 recruits ERF4 to the MYB5a promoter and diminishes anthocyanin accumulation during grape ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:127-144. [PMID: 36423230 DOI: 10.1111/tpj.16040] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
DNA acetylation alters the expression of responsive genes during plant development. In grapes (Vitis vinifera), however, little is known about this regulatory mechanism. In the present study, 'Kyoho' grapes treated with trichostatin A (TSA, a deacetylase inhibitor) were used for transcriptome sequencing and quantitative proteomics analysis. We observed that acetylation was associated with anthocyanin accumulation and gene expression. Acetylation positively regulated phenylalanine metabolism and flavonoid biosynthesis pathways. Using omics analysis, we detected an increase in the levels of the AP2/EREBP transcription factor family after TSA treatment, indicating its association with acetylation-deacetylation dynamics in grapes. Furthermore, ethylene response factor 4 (ERF4) physically interacted with VvHDAC19, a histone deacetylase, which synergistically reduced the expression of target genes involved in anthocyanin biosynthesis owing to the binding of VvERF4 to the GCC-box cis-regulatory element in the VvMYB5a promoter. VvHDAC19 and VvERF4 also controlled anthocyanin biosynthesis and accumulation by regulating acetylation levels of histones H3 and H4. Therefore, alterations in histone modification can significantly regulate the expression of genes involved in anthocyanin biosynthesis and affect grape ripening.
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Affiliation(s)
- Haifeng Jia
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
- NJAU (Suqian) Academy of Protected Horticultures, Suqian, China
| | - Qianqian Zuo
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ehsan Sadeghnezhad
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ting Zheng
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Xueqin Chen
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - JinggGui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
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23
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Huh SU. Functional analysis of hot pepper ethylene responsive factor 1A in plant defense. PLANT SIGNALING & BEHAVIOR 2022; 17:2027137. [PMID: 35192782 PMCID: PMC9176226 DOI: 10.1080/15592324.2022.2027137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ethylene-responsive factors play important roles in the biotic and abiotic stresses. Only some ERF genes from Capsicum annuum have been characterized. In the study, the CaERF1A gene is characterized in response to biotic stress. CaERF1A transcripts were induced by various plant defense-related hormone treatments. Knockdown of CaERF1A in hot pepper plants are negatively affected Tobacco mosaic virus-P0-mediated hypersensitive response cell death, resulting in reduced gene expression of pathogenesis-related genes and ethylene and jasmonic acid synthesis-related gene. Overexpressing CaERF1A transgenic plants show enhanced resistance to fungal pathogen via regulating ethylene and jasmonic acid synthesis-related gene expression. Thus, CaERF1A is a positive regulator of plant defense by modulating ethylene and jasmonic acid synthesis-related gene expressions.
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Affiliation(s)
- Sung Un Huh
- Department of Biology, Kunsan National University, Gunsan, Republic of Korea
- CONTACT Sung Un Huh Department of Biology, Kunsan National University, Gunsan54150, Republic of Korea
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24
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Filyushin MA, Kochieva EZ, Shchennikova AV. ZmDREB2.9 Gene in Maize ( Zea mays L.): Genome-Wide Identification, Characterization, Expression, and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:3060. [PMID: 36432789 PMCID: PMC9694119 DOI: 10.3390/plants11223060] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Dehydration-responsive element-binding (DREB) transcription factors of the A2 subfamily play key roles in plant stress responses. In this study, we identified and characterized a new A2-type DREB gene, ZmDREB2.9, in the Zea mays cv. B73 genome and compared its expression profile with those of the known A2-type maize genes ZmDREB2.1-2.8. ZmDREB2.9 was mapped to chromosome 8, contained 18 predicted hormone- and stress-responsive cis-elements in the promoter, and had two splice isoforms: short ZmDREB2.9-S preferentially expressed in the leaves, embryos, and endosperm and long ZmDREB2.9-L expressed mostly in the male flowers, stamens, and ovaries. Phylogenetically, ZmDREB2.9 was closer to A. thaliana DREB2A than the other ZmDREB2 factors. ZmDREB2.9-S, ZmDREB2.2, and ZmDREB2.1/2A were upregulated in response to cold, drought, and abscisic acid and may play redundant roles in maize stress resistance. ZmDREB2.3, ZmDREB2.4, and ZmDREB2.6 were not expressed in seedlings and could be pseudogenes. ZmDREB2.7 and ZmDREB2.8 showed similar transcript accumulation in response to cold and abscisic acid and could be functionally redundant. Our results provide new data on Z. mays DREB2 factors, which can be used for further functional studies as well as in breeding programs to improve maize stress tolerance.
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25
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Chai Z, Fang J, Huang C, Huang R, Tan X, Chen B, Yao W, Zhang M. A novel transcription factor, ScAIL1, modulates plant defense responses by targeting DELLA and regulating gibberellin and jasmonic acid signaling in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6727-6743. [PMID: 35986920 DOI: 10.1093/jxb/erac339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
DELLA proteins are important repressors of gibberellin signaling, regulating plant development and defense responses through crosstalk with various phytohormones. Sugarcane ScGAI encodes a DELLA protein that regulates culm development. However, it is unclear which transcription factors mediate the transcription of ScGAI. Here, we identified two different ScGAI promoter sequences that cooperatively regulate ScGAI transcription. We also identified a nuclear-localized AP2 family transcription factor, ScAIL1, which inhibits the transcription of ScGAI by directly binding to two ScGAI promoters. ScAIL1 was expressed in all sugarcane tissues tested and was induced by gibberellin and various stressors, including NaCl, polyethylene glycol, and pathogenic fungi and bacteria. Overexpression of ScAIL1 in rice significantly improved resistance to bacterial blight and rice blast, while reducing growth and development. In addition, several genes associated with stress responses were significantly up-regulated in transgenic rice overexpressing ScAIL1. Endogenous phytohormone content and expression analysis further revealed that ScAIL1-overexpressing lines improved resistance to bacterial blight and rice blast instead of promoting growth, and that this response was associated with increased jasmonic acid synthesis and gibberellin inactivation. These results provide molecular evidence that the role of ScAIL1 in the plant defense response is related to jasmonic acid and gibberellin signaling.
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Affiliation(s)
- Zhe Chai
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
- College of Agricultural, Guangxi University, Nanning 530005, China
| | - Jinlan Fang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
- College of Agricultural, Guangxi University, Nanning 530005, China
| | - Cuilin Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Run Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Xuan Tan
- College of Agricultural, Guangxi University, Nanning 530005, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530005, China
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26
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Sun Y, Bai PP, Gu KJ, Yang SZ, Lin HY, Shi CG, Zhao YP. Dynamic transcriptome and network-based analysis of yellow leaf mutant Ginkgo biloba. BMC PLANT BIOLOGY 2022; 22:465. [PMID: 36171567 PMCID: PMC9520803 DOI: 10.1186/s12870-022-03854-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Golden leaf in autumn is a prominent feature of deciduous tree species like Ginkgo biloba L., a landscape tree widely cultivated worldwide. However, little was known about the molecular mechanisms of leaf yellowing, especially its dynamic regulatory network. Here, we performed a suite of comparative physiological and dynamic transcriptional analyses on the golden-leaf cultivar and the wild type (WT) ginkgo to investigate the underlying mechanisms of leaf yellowing across different seasons. RESULTS In the present study, we used the natural bud mutant cultivar with yellow leaves "Wannianjin" (YL) as materials. Physiological analysis revealed that higher ratios of chlorophyll a to chlorophyll b and carotenoid to chlorophyll b caused the leaf yellowing of YL. On the other hand, dynamic transcriptome analyses showed that genes related to chlorophyll metabolism played key a role in leaf coloration. Genes encoding non-yellow coloring 1 (NYC1), NYC1-like (NOL), and chlorophyllase (CLH) involved in the degradation of chlorophyll were up-regulated in spring. At the summer stage, down-regulated HEMA encoding glutamyl-tRNA reductase functioned in chlorophyll biosynthesis, while CLH involved in chlorophyll degradation was up-regulated, causing a lower chlorophyll accumulation. In carotenoid metabolism, genes encoding zeaxanthin epoxidase (ZEP) and 9-cis-epoxy carotenoid dioxygenase (NCED) showed significantly different expression levels in the WT and YL. Moreover, the weighted gene co-expression network analysis (WGCNA) suggested that the most associated transcriptional factor, which belongs to the AP2/ERF-ERF family, was engaged in regulating pigment metabolism. Furthermore, quantitative experiments validated the above results. CONCLUSIONS By comparing the golden-leaf cultivar and the wide type of ginkgo across three seasons, this study not only confirm the vital role of chlorophyll in leaf coloration of YL but also provided new insights into the seasonal transcriptome landscape and co-expression network. Our novel results pinpoint candidate genes for further wet-bench experiments in tree species.
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Affiliation(s)
- Yue Sun
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Pan-Pan Bai
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Kai-Jie Gu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | | | - Han-Yang Lin
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | | | - Yun-Peng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
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27
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Liu W, Zhao C, Liu L, Huang D, Ma C, Li R, Huang L. Genome-wide identification of the TGA gene family in kiwifruit (Actinidia chinensis spp.) and revealing its roles in response to Pseudomonas syringae pv. actinidiae (Psa) infection. Int J Biol Macromol 2022; 222:101-113. [PMID: 36150565 DOI: 10.1016/j.ijbiomac.2022.09.154] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022]
Abstract
Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is a destructive disease of kiwifruit worldwide. Functional genes in response to Psa infection are needed, as they could be utilized to control disease. TGACG-binding transcription factor (TGA), as an essential regulator, involved in the process of plant against pathogens. However, the function of TGA regulators has not been reported in kiwifruit. It is unclear that whether TGA genes play a role in response to Psa infection. Here, we performed genome-wide screening and identified 13 TGA genes in kiwifruit. Phylogenetic analysis showed that 13 members of the AcTGA gene family could be divided into five groups. AcTGA proteins were mainly located in the nucleus, and significant differences were identified in their 3D structures. Segmental duplications promoted the expansion of the AcTGA family. Additionally, RNA-Seq and qRT-PCR revealed that four genes (AcTGA01/06/07/09) were tissue-specific and responsive to hormones at different levels. Subcellular localization showed that four proteins located in the nucleus, and among them, three (AcTGA01/06/07) had transcriptional activation activity. Lastly, transient overexpression proved that these three genes (AcTGA01/06/07) potentially played a role in the resistance to kiwifruit canker. These results provided a theoretical basis for revealing TGA involved in kiwifruit regulation against Psa.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Chao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Lu Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Dong Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Chao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Rui Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling Shaanxi 712100, China.
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28
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Chen X, Xu X, Zhang S, Munir N, Zhu C, Zhang Z, Chen Y, Xuhan X, Lin Y, Lai Z. Genome-wide circular RNA profiling and competing endogenous RNA regulatory network analysis provide new insights into the molecular mechanisms underlying early somatic embryogenesis in Dimocarpus longan Lour. TREE PHYSIOLOGY 2022; 42:1876-1898. [PMID: 35313353 DOI: 10.1093/treephys/tpac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Circular RNAs (circRNAs) are widely involved in plant growth and development. However, the function of circRNAs in plant somatic embryogenesis (SE) remains elusive. Here, by using high-throughput sequencing, a total of 5029 circRNAs were identified in the three stages of longan (Dimocarpus longan Lour.) early SE. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed (DE) circRNA host genes were enriched in the 'non-homologous end-joining' (NHEJ) and 'butanoate metabolism' pathways. In addition, the reactive oxygen species (ROS) content during longan early SE was determined. The results indicated that ROS-induced DNA double-strand breaks may not depend on the NHEJ repair pathway. Correlation analyses of the levels of related metabolites (glutamate, γ-aminobutyrate and pyruvate) and the expression levels of circRNAs and their host genes involved in butanoate metabolism were performed. The results suggested that circRNAs may act as regulators of the expression of cognate mRNAs, thereby affecting the accumulation of related compounds. A competing endogenous RNA (ceRNA) network of DE circRNAs, DE mRNAs, DE long noncoding RNAs (lncRNAs) and DE microRNAs (miRNAs) was constructed. The results showed that the putative targets of the noncoding RNA (ncRNAs) were significantly enriched in the KEGG pathways 'mitogen-activated protein kinase signaling' and 'nitrogen metabolism'. Furthermore, the expression patterns of the candidate circRNAs, lncRNAs, miRNAs and mRNAs confirmed the negative correlation between miRNAs and ceRNAs. In addition, two circRNA overexpression vectors were constructed to further verify the ceRNA network correlations in longan early SE. Our study revealed the potential role of circRNAs in longan early SE, providing new insights into the intricate regulatory mechanism underlying plant SE.
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Affiliation(s)
- Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
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29
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Morey KJ, Peebles CAM. Hairy roots: An untapped potential for production of plant products. FRONTIERS IN PLANT SCIENCE 2022; 13:937095. [PMID: 35991443 PMCID: PMC9389236 DOI: 10.3389/fpls.2022.937095] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
While plants are an abundant source of valuable natural products, it is often challenging to produce those products for commercial application. Often organic synthesis is too expensive for a viable commercial product and the biosynthetic pathways are often so complex that transferring them to a microorganism is not trivial or feasible. For plants not suited to agricultural production of natural products, hairy root cultures offer an attractive option for a production platform which offers genetic and biochemical stability, fast growth, and a hormone free culture media. Advances in metabolic engineering and synthetic biology tools to engineer hairy roots along with bioreactor technology is to a point where commercial application of the technology will soon be realized. We discuss different applications of hairy roots. We also use a case study of the advancements in understanding of the terpenoid indole alkaloid pathway in Catharanthus roseus hairy roots to illustrate the advancements and challenges in pathway discovery and in pathway engineering.
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30
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Ren D, Wang T, Zhou G, Ren W, Duan X, Gao L, Chen J, Xu L, Zhu P. Ethylene Promotes Expression of the Appressorium- and Pathogenicity-Related Genes via GPCR- and MAPK-Dependent Manners in Colletotrichum gloeosporioides. J Fungi (Basel) 2022; 8:jof8060570. [PMID: 35736053 PMCID: PMC9224669 DOI: 10.3390/jof8060570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 01/27/2023] Open
Abstract
Ethylene (ET) represents a signal that can be sensed by plant pathogenic fungi to accelerate their spore germination and subsequent infection. However, the molecular mechanisms of responses to ET in fungi remain largely unclear. In this study, Colletotrichum gloeosporioides was investigated via transcriptomic analysis to reveal the genes that account for the ET-regulated fungal development and virulence. The results showed that ET promoted genes encoding for fungal melanin biosynthesis enzymes, extracellular hydrolases, and appressorium-associated structure proteins at 4 h after treatment. When the germination lasted until 24 h, ET induced multiple appressoria from every single spore, but downregulated most of the genes. Loss of selected ET responsive genes encoding for scytalone dehydratase (CgSCD1) and cerato-platanin virulence protein (CgCP1) were unable to alter ET sensitivity of C. gloeosporioides in vitro but attenuated the influence of ET on pathogenicity. Knockout of the G-protein-coupled receptors CgGPCR3-1/2 and the MAPK signaling pathway components CgMK1 and CgSte11 resulted in reduced ET sensitivity. Taken together, this study in C. gloeosporioides reports that ET can cause transcription changes in a large set of genes, which are mainly responsible for appressorium development and virulence expression, and these processes are dependent on the GPCR and MAPK pathways.
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Affiliation(s)
| | | | | | | | | | | | | | - Ling Xu
- Correspondence: (L.X.); (P.Z.); Tel.: +86-(021)-54341012 (L.X.); +86-(021)-24206574 (P.Z.)
| | - Pinkuan Zhu
- Correspondence: (L.X.); (P.Z.); Tel.: +86-(021)-54341012 (L.X.); +86-(021)-24206574 (P.Z.)
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Zafar MM, Rehman A, Razzaq A, Parvaiz A, Mustafa G, Sharif F, Mo H, Youlu Y, Shakeel A, Ren M. Genome-wide characterization and expression analysis of Erf gene family in cotton. BMC PLANT BIOLOGY 2022; 22:134. [PMID: 35317739 PMCID: PMC8939120 DOI: 10.1186/s12870-022-03521-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 03/04/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND AP2/ERF transcription factors are important in a variety of biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, little study has been done on cotton's AP2/ERF genes, although cotton is an essential fibre crop. We were able to examine the tissue and expression patterns of AP2/ERF genes in cotton on a genome-wide basis because of the recently published whole genome sequence of cotton. Genome-wide analysis of ERF gene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed. RESULTS A total of 118, 120, 213, 220 genes containing the sequence of single AP2 domain were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Synteny and collinearity analysis revealed that segmental duplications may have played crucial roles in the expansion of the cotton ERF gene family, as well as tandem duplications played a minor role. Cis-acting elements of the promoter sites of Ghi-ERFs genes predict the involvement in multiple hormone responses and abiotic stresses. Transcriptome and qRT-PCR analysis revealed that Ghi-ERF-2D.6, Ghi-ERF-12D.13, Ghi-ERF-6D.1, Ghi-ERF-7A.6 and Ghi-ERF-11D.5 are candidate genes against salinity tolerance in upland cotton. CONCLUSION Overwhelmingly, the present study paves the way to better understand the evolution of cotton ERF genes and lays a foundation for future investigation of ERF genes in improving salinity stress tolerance in cotton.
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Affiliation(s)
- Muhammad Mubashar Zafar
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture; Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture; Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Abdul Razzaq
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture; Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
- The Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Aqsa Parvaiz
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Ghulam Mustafa
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Faiza Sharif
- University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan
| | - Huijuan Mo
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture; Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Yuan Youlu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture; Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Amir Shakeel
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Maozhi Ren
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture; Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
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Regon P, Dey S, Rehman M, Pradhan AK, Chowra U, Tanti B, Talukdar AD, Panda SK. Transcriptomic Analysis Revealed Reactive Oxygen Species Scavenging Mechanisms Associated With Ferrous Iron Toxicity in Aromatic Keteki Joha Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:798580. [PMID: 35283928 PMCID: PMC8913046 DOI: 10.3389/fpls.2022.798580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Lowland acidic soils with water-logged regions are often affected by ferrous iron (Fe2+) toxicity, a major yield-limiting factor of rice production. Under severe Fe2+ toxicity, reactive oxygen species (ROS) are crucial, although molecular mechanisms and associated ROS homeostasis genes are still unknown. In this study, a comparative RNA-Seq based transcriptome analysis was conducted to understand the Fe2+ toxicity tolerance mechanism in aromatic Keteki Joha. About 69 Fe homeostasis related genes and their homologs were identified, where most of the genes were downregulated. Under severe Fe2+ toxicity, the biosynthesis of amino acids, RNA degradation, and glutathione metabolism were induced, whereas phenylpropanoid biosynthesis, photosynthesis, and fatty acid elongation were inhibited. The mitochondrial iron transporter (OsMIT), vacuolar iron transporter 2 (OsVIT2), ferritin (OsFER), vacuolar mugineic acid transporter (OsVMT), phenolic efflux zero1 (OsPEZ1), root meander curling (OsRMC), and nicotianamine synthase (OsNAS3) were upregulated in different tissues, suggesting the importance of Fe retention and sequestration for detoxification. However, several antioxidants, ROS scavenging genes and abiotic stress-responsive transcription factors indicate ROS homeostasis as one of the most important defense mechanisms under severe Fe2+ toxicity. Catalase (CAT), glutathione (GSH), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) were upregulated. Moreover, abiotic stress-responsive transcription factors, no apical meristem (NAC), myeloblastosis (MYB), auxin response factor (ARF), basic helix-loop-helix (bZIP), WRKY, and C2H2-zinc finger protein (C2H2-ZFP) were also upregulated. Accordingly, ROS homeostasis has been proposed as an essential defense mechanism under such conditions. Thus, the current study may enrich the understanding of Fe-homeostasis in rice.
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Affiliation(s)
- Preetom Regon
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Sangita Dey
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Mehzabin Rehman
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Amit Kumar Pradhan
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
- Department of Botany, Pragjyotish College, Guwahati, India
| | | | - Bhaben Tanti
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Sanjib Kumar Panda
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
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Bian X, Kim HS, Kwak SS, Zhang Q, Liu S, Ma P, Jia Z, Xie Y, Zhang P, Yu Y. Different Functions of IbRAP2.4, a Drought-Responsive AP2/ERF Transcription Factor, in Regulating Root Development Between Arabidopsis and Sweetpotato. FRONTIERS IN PLANT SCIENCE 2022; 13:820450. [PMID: 35154229 PMCID: PMC8826056 DOI: 10.3389/fpls.2022.820450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/04/2022] [Indexed: 06/09/2023]
Abstract
Plant root systems are essential for the uptake of water and nutrients from soil and are positively correlated to yield in many crops including the sweetpotato, Ipomoea batatas (L.) Lam. Here, we isolated and functionally characterized IbRAP2.4, a novel nuclear-localized gene encoding the AP2/ERF transcription factor, from sweetpotato. IbRAP2.4 was responsive to NaCl, PEG8000, ethylene, and Indole 3-acetic acid treatments. As revealed by electrophoretic mobility shift assay and dual luciferase assay, IbRAP2.4 could bind to both DRE and GCC-box elements and acted as a transcription activator. IbRAP2.4 overexpression significantly promoted lateral root formation and enhanced the drought tolerance in Arabidopsis thaliana, while it inhibited storage root formation in transgenic sweetpotato by comprehensively upregulating lignin biosynthesis pathway genes. Results suggested that IbRAP2.4 may be a useful potential target for further molecular breeding of high yielding sweetpotato.
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Affiliation(s)
- Xiaofeng Bian
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Qian Zhang
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Shuai Liu
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Peiyong Ma
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhaodong Jia
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yizhi Xie
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yang Yu
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Ma L, Wang Q, Zheng Y, Guo J, Yuan S, Fu A, Bai C, Zhao X, Zheng S, Wen C, Guo S, Gao L, Grierson D, Zuo J, Xu Y. Cucurbitaceae genome evolution, gene function and molecular breeding. HORTICULTURE RESEARCH 2022; 9:uhab057. [PMID: 35043161 PMCID: PMC8969062 DOI: 10.1093/hr/uhab057] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/28/2021] [Indexed: 05/07/2023]
Abstract
The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shufang Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shaogui Guo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yong Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Yang YN, Kim Y, Kim H, Kim SJ, Cho KM, Kim Y, Lee DS, Lee MH, Kim SY, Hong JC, Kwon SJ, Choi J, Park OK. The transcription factor ORA59 exhibits dual DNA binding specificity that differentially regulates ethylene- and jasmonic acid-induced genes in plant immunity. PLANT PHYSIOLOGY 2021; 187:2763-2784. [PMID: 34890461 PMCID: PMC8644270 DOI: 10.1093/plphys/kiab437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens in a synergistic and interdependent manner, while JA and ET also have independent roles in certain processes, e.g. in responses to wounding and flooding, respectively. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, of which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) GDSL LIPASE 1 (GLIP1) depends on ET for gene expression and pathogen resistance. Here, promoter analysis of GLIP1 revealed ERELEE4 as the critical cis-element for ET-responsive GLIP1 expression. In a yeast one-hybrid screening, ORA59 was isolated as a specific transcription factor that binds to the ERELEE4 element, in addition to the well-characterized GCC box. We found that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in gene promoters. Notably, ORA59 exhibited a differential preference for GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. JA and ET induced ORA59 phosphorylation, which was required for both activity and specificity of ORA59. Furthermore, RNA-seq and virus-induced gene silencing analyses led to the identification of ORA59 target genes of distinct functional categories in JA and ET pathways. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.
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Affiliation(s)
- Young Nam Yang
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Youngsung Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyeri Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Su Jin Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Kwang-Moon Cho
- Molecular Diagnosis Division, AccuGene, Incheon 22006, Korea
| | - Yerin Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Dong Sook Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Myoung-Hoon Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Soo Young Kim
- Department of Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Jong Chan Hong
- Division of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Sun Jae Kwon
- Molecular Diagnosis Division, AccuGene, Incheon 22006, Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Ohkmae K Park
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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Chen P, Li Z, Zhang D, Shen W, Xie Y, Zhang J, Jiang L, Li X, Shen X, Geng D, Wang L, Niu C, Bao C, Yan M, Li H, Li C, Yan Y, Zou Y, Micheletti D, Koot E, Ma F, Guan Q. Insights into the effect of human civilization on Malus evolution and domestication. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2206-2220. [PMID: 34161653 PMCID: PMC8541786 DOI: 10.1111/pbi.13648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 05/09/2023]
Abstract
The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA-like gene that underwent selection during domestication on 15th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB-ARC domain-containing gene was found to strongly affect anthocyanin accumulation using a genome-wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.
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Affiliation(s)
- Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Wenyun Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Lijuan Jiang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Liping Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Mingjia Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Haiyan Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Cuiying Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yangjun Zou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | | | - Emily Koot
- The New Zealand Institute for Plant and Food Research LimitedPalmerston NorthNew Zealand
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
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37
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Huang S, Ma Z, Hu L, Huang K, Zhang M, Zhang S, Jiang W, Wu T, Du X. Involvement of rice transcription factor OsERF19 in response to ABA and salt stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:22-30. [PMID: 34329842 DOI: 10.1016/j.plaphy.2021.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 05/24/2023]
Abstract
Soil salinity is a major environmental stressor that restricts the growth and yield of crops. Plants have evolved more complicated and precise mechanisms to cope with salt stress, as they cannot escape from harmful environments. In the current study we identified and characterized an AP2/ERF transcription factor in rice, OsERF19. The expression of OsERF19 was slightly repressed by salt stress or abscisic acid (ABA) treatment. OsERF19-overexpression (OsERF19-OX) plants displayed enhanced tolerance to salt stress and ABA hypersensitivity compared to wild type and control plants. Furthermore, OsLEA3, OsNHX1, OsHKT6, and OsOTS1 were upregulated in OsERF19-OX plants when the plants were subjected to salt stress. OsRAB21, OsNCED5, and OsP5CS1 were also upregulated in OsERF19-OX plants treated with ABA. Yeast one-hybrid and dual luciferase reporter assays demonstrated that OsERF19 directly targets the promoters of OsOTS1 and OsNCED5 and further increases their transcription. These results suggest that the transcription factor OsERF19 plays a positive role in salt stress and ABA responses in rice.
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Affiliation(s)
- Shuangzhan Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ziming Ma
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Lanjuan Hu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Kai Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mingxing Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Shihan Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wenzhu Jiang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Tao Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.
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Fraga OT, de Melo BP, Quadros IPS, Reis PAB, Fontes EPB. Senescence-Associated Glycine max ( Gm) NAC Genes: Integration of Natural and Stress-Induced Leaf Senescence. Int J Mol Sci 2021; 22:8287. [PMID: 34361053 PMCID: PMC8348617 DOI: 10.3390/ijms22158287] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/20/2021] [Accepted: 07/24/2021] [Indexed: 11/30/2022] Open
Abstract
Leaf senescence is a genetically regulated developmental process that can be triggered by a variety of internal and external signals, including hormones and environmental stimuli. Among the senescence-associated genes controlling leaf senescence, the transcriptional factors (TFs) comprise a functional class that is highly active at the onset and during the progression of leaf senescence. The plant-specific NAC (NAM, ATAF, and CUC) TFs are essential for controlling leaf senescence. Several members of Arabidopsis AtNAC-SAGs are well characterized as players in elucidated regulatory networks. However, only a few soybean members of this class display well-known functions; knowledge about their regulatory circuits is still rudimentary. Here, we describe the expression profile of soybean GmNAC-SAGs upregulated by natural senescence and their functional correlation with putative AtNAC-SAGs orthologs. The mechanisms and the regulatory gene networks underlying GmNAC081- and GmNAC030-positive regulation in leaf senescence are discussed. Furthermore, new insights into the role of GmNAC065 as a negative senescence regulator are presented, demonstrating extraordinary functional conservation with the Arabidopsis counterpart. Finally, we describe a regulatory circuit which integrates a stress-induced cell death program with developmental leaf senescence via the NRP-NAC-VPE signaling module.
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Affiliation(s)
- Otto Teixeira Fraga
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Bruno Paes de Melo
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- Embrapa Genetic Resources and Biotechnology, Brasília 70770.917, DF, Brazil
| | - Iana Pedro Silva Quadros
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Pedro Augusto Braga Reis
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
| | - Elizabeth Pacheco Batista Fontes
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil; (O.T.F.); (B.P.d.M.); (I.P.S.Q.); (P.A.B.R.)
- National Institute of Science and Technology in Plant-Pest Interactions, INCTIPP–BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570.000, MG, Brazil
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Chen L, Kashina A. Post-translational Modifications of the Protein Termini. Front Cell Dev Biol 2021; 9:719590. [PMID: 34395449 PMCID: PMC8358657 DOI: 10.3389/fcell.2021.719590] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTM) involve enzyme-mediated covalent addition of functional groups to proteins during or after synthesis. These modifications greatly increase biological complexity and are responsible for orders of magnitude change between the variety of proteins encoded in the genome and the variety of their biological functions. Many of these modifications occur at the protein termini, which contain reactive amino- and carboxy-groups of the polypeptide chain and often are pre-primed through the actions of cellular machinery to expose highly reactive residues. Such modifications have been known for decades, but only a few of them have been functionally characterized. The vast majority of eukaryotic proteins are N- and C-terminally modified by acetylation, arginylation, tyrosination, lipidation, and many others. Post-translational modifications of the protein termini have been linked to different normal and disease-related processes and constitute a rapidly emerging area of biological regulation. Here we highlight recent progress in our understanding of post-translational modifications of the protein termini and outline the role that these modifications play in vivo.
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Affiliation(s)
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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The Genetic Regulation of Secondary Metabolic Pathways in Response to Salinity and Drought as Abiotic Stresses. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11156668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Global development has generated a plethora of unfavorable and adverse environmental factors for the living organisms in the ecosystem. Plants are sessile organisms, and they are crucial to sustain life on earth. Since plants are sessile, they face a great number of environmental challenges related to abiotic stresses, such as temperature fluctuation, drought, salinity, flood and metal contamination. Salinity and drought are considered major abiotic stresses that negatively affect the plants’ growth and production of useful content. However, plants have evolved various molecular mechanisms to increase their tolerance to these environmental stresses. There is a whole complex system of communication (cross-talk) through massive signaling cascades that are activated and modulated in response to salinity and drought. Secondary metabolites are believed to play significant roles in the plant’s response and resistance to salinity and drought stress. Until recently, attempts to unravel the biosynthetic pathways were limited mainly due to the inadequate plant genomics resources. However, recent advancements in generating high-throughput “omics” datasets, computational tools and functional genomics approach integration have aided in the elucidation of biosynthetic pathways of many plant bioactive metabolites. This review gathers comprehensive knowledge of plants’ complex system that is involved in the response and resistance to salinity and water deficit stresses as abiotic stress. Additionally, it offers clues in determining the genes involved in this complex and measures its activity. It covers basic information regarding the signaling molecules involved in salinity and drought resistance and how plant hormones regulate the cross-talking mechanism with emphasis on transcriptional activity. Moreover, it discusses many studies that illustrate the relationship between salinity and drought and secondary metabolite production. Furthermore, several transcriptome analysis research papers of medicinal plants are illustrated. The aim of this review is to be a key for any researcher that is aspiring to study the relationship between salinity and drought stresses and secondary metabolite production at the transcriptome and transcription level.
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Leitão ST, Santos C, Araújo SDS, Rubiales D, Vaz Patto MC. Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit. HORTICULTURE RESEARCH 2021; 8:149. [PMID: 34193847 PMCID: PMC8245569 DOI: 10.1038/s41438-021-00583-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.), one of the most consumed food legumes worldwide, is threatened by two main constraints that are found frequently together in nature, water deficit (WD) and fusarium wilt (Fop). To understand the shared and unique responses of common bean to Fop and WD, we analyzed the transcriptomic changes and phenotypic responses in two accessions, one resistant and one susceptible to both stresses, exposed to single and combined stresses. Physiological responses (photosynthetic performance and pigments quantification) and disease progression were also assessed. The combined FopWD imposition negatively affected the photosynthetic performance and increased the susceptible accession disease symptoms. The susceptible accession revealed a higher level of transcriptional changes than the resistant one, and WD single stress triggered the highest transcriptional changes. While 89 differentially expressed genes were identified exclusively in combined stresses for the susceptible accession, 35 were identified in the resistant one. These genes belong mainly to "stress", "signaling", "cell wall", "hormone metabolism", and "secondary metabolism" functional categories. Among the up-regulated genes with higher expression in the resistant accession, the cysteine-rich secretory, antigen 5 and Pr-1 (CAP) superfamily protein, a ribulose bisphosphate carboxylase family protein, and a chitinase A seem promising targets for multiple stress breeding.
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Affiliation(s)
- Susana T Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3 - Technology and Innovation Campus, Centre Bio R&D Unit, Lagares da Beira, Portugal
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Xiao S, Hu Q, Zhang X, Si H, Liu S, Chen L, Chen K, Berne S, Yuan D, Lindsey K, Zhang X, Zhu L. Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4721-4743. [PMID: 33928361 DOI: 10.1093/jxb/erab186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Salicylic acid (SA) and brassinosteroids (BRs) are well known to regulate diverse processes of plant development and stress responses, but the mechanisms by which these phytohormones mediate the growth and defense trade-off are largely unclear. In addition, little is known about the roles of DEHYDRATION RESPONSIVE ELEMENT BINDING transcription factors, especially in biotic stress and plant growth. Here, we identified a cotton (Gossypium hirsutum) APETALA2/ETHYLENE RESPONSIVE FACTOR gene GhTINY2 that is strongly induced by Verticillium dahliae. Overexpression of GhTINY2 in cotton and Arabidopsis enhanced tolerance to V. dahliae, while knockdown of expression increased the susceptibility of cotton to the pathogen. GhTINY2 was found to promote SA accumulation and SA signaling transduction by directly activating expression of WRKY51. Moreover, GhTINY2-overexpressing cotton and Arabidopsis showed retardation of growth, increased sensitivity to inhibitors of BR biosynthesis, down-regulation of several BR-induced genes, and up-regulation of BR-repressed genes, while GhTINY2-RNAi cotton showed the opposite effects. We further determined that GhTINY2 negatively regulates BR signaling by interacting with BRASSINAZOLE-RESISTANT 1 (BZR1) and restraining its transcriptional activation of the expression of INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19). These findings indicate that GhTINY2 fine-tunes the trade-off between immunity and growth via indirect crosstalk between WRKY51-mediated SA biosynthesis and BZR1-IAA19-regulated BR signaling.
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Affiliation(s)
- Shenghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan 430000, Hubei, China
| | - Xiaojun Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Huan Si
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Shiming Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Kun Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Sabina Berne
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Genome editing for resistance against plant pests and pathogens. Transgenic Res 2021; 30:427-459. [PMID: 34143358 DOI: 10.1007/s11248-021-00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.
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Massel K, Lam Y, Wong ACS, Hickey LT, Borrell AK, Godwin ID. Hotter, drier, CRISPR: the latest edit on climate change. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1691-1709. [PMID: 33420514 DOI: 10.1007/s00122-020-03764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/30/2020] [Indexed: 05/23/2023]
Abstract
Integrating CRISPR/Cas9 genome editing into modern breeding programs for crop improvement in cereals. Global climate trends in many agricultural regions have been rapidly changing over the past decades, and major advances in global food systems are required to ensure food security in the face of these emerging challenges. With increasing climate instability due to warmer temperatures and rising CO2 levels, the productivity of global agriculture will continue to be negatively impacted. To combat these growing concerns, creative approaches will be required, utilising all the tools available to produce more robust and tolerant crops with increased quality and yields under more extreme conditions. The integration of genome editing and transgenics into current breeding strategies is one promising solution to accelerate genetic gains through targeted genetic modifications, producing crops that can overcome the shifting climate realities. This review focuses on how revolutionary genome editing tools can be directly implemented into breeding programs for cereal crop improvement to rapidly counteract many of the issues affecting agriculture production in the years to come.
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Affiliation(s)
- Karen Massel
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Yasmine Lam
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Albert C S Wong
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Andrew K Borrell
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian D Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
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Plant Transcription Factors Involved in Drought and Associated Stresses. Int J Mol Sci 2021; 22:ijms22115662. [PMID: 34073446 PMCID: PMC8199153 DOI: 10.3390/ijms22115662] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.
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Zeng D, Teixeira da Silva JA, Zhang M, Yu Z, Si C, Zhao C, Dai G, He C, Duan J. Genome-Wide Identification and Analysis of the APETALA2 (AP2) Transcription Factor in Dendrobium officinale. Int J Mol Sci 2021; 22:5221. [PMID: 34069261 PMCID: PMC8156592 DOI: 10.3390/ijms22105221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022] Open
Abstract
The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 DoAP2 TFs that were identified from the D. officinale genome and named DoAP2-1 to DoAP2-14 were divided into three clades: euAP2, euANT, and basalANT. The promoters of all DoAP2 genes contained cis-regulatory elements related to plant development and also responsive to plant hormones and stress. qRT-PCR analysis showed the abundant expression of DoAP2-2, DoAP2-5, DoAP2-7, DoAP2-8 and DoAP2-12 genes in protocorm-like bodies (PLBs), while DoAP2-3, DoAP2-4, DoAP2-6, DoAP2-9, DoAP2-10 and DoAP2-11 expression was strong in plantlets. In addition, the expression of some DoAP2 genes was down-regulated during flower development. These results suggest that DoAP2 genes may play roles in plant regeneration and flower development in D. officinale. Four DoAP2 genes (DoAP2-1 from euAP2, DoAP2-2 from euANT, and DoAP2-6 and DoAP2-11 from basal ANT) were selected for further analyses. The transcriptional activation of DoAP2-1, DoAP2-2, DoAP2-6 and DoAP2-11 proteins, which were localized in the nucleus of Arabidopsis thaliana mesophyll protoplasts, was further analyzed by a dual-luciferase reporter gene system in Nicotiana benthamiana leaves. Our data showed that pBD-DoAP2-1, pBD-DoAP2-2, pBD-DoAP2-6 and pBD-DoAP2-11 significantly repressed the expression of the LUC reporter compared with the negative control (pBD), suggesting that these DoAP2 proteins may act as transcriptional repressors in the nucleus of plant cells. Our findings on AP2 genes in D. officinale shed light on the function of AP2 genes in this orchid and other plant species.
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Affiliation(s)
- Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | | | - Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Conghui Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Guangyi Dai
- Opening Public Laboratory, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Juan Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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Testone G, Sobolev AP, Mele G, Nicolodi C, Gonnella M, Arnesi G, Biancari T, Giannino D. Leaf nutrient content and transcriptomic analyses of endive (Cichorium endivia) stressed by downpour-induced waterlog reveal a gene network regulating kestose and inulin contents. HORTICULTURE RESEARCH 2021; 8:92. [PMID: 33931617 PMCID: PMC8087766 DOI: 10.1038/s41438-021-00513-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/08/2021] [Accepted: 02/24/2021] [Indexed: 05/03/2023]
Abstract
Endive (Cichorium endivia L.), a vegetable consumed as fresh or packaged salads, is mostly cultivated outdoors and known to be sensitive to waterlogging in terms of yield and quality. Phenotypic, metabolic and transcriptomic analyses were used to study variations in curly- ('Domari', 'Myrna') and smooth-leafed ('Flester', 'Confiance') cultivars grown in short-term waterlog due to rainfall excess before harvest. After recording loss of head weights in all cultivars (6-35%), which was minimal in 'Flester', NMR untargeted profiling revealed variations as influenced by genotype, environment and interactions, and included drop of total carbohydrates (6-50%) and polyols (3-37%), gain of organic acids (2-30%) and phenylpropanoids (98-560%), and cultivar-specific fluctuations of amino acids (-37 to +15%). The analysis of differentially expressed genes showed GO term enrichment consistent with waterlog stress and included the carbohydrate metabolic process. The loss of sucrose, kestose and inulin recurred in all cultivars and the sucrose-inulin route was investigated by covering over 50 genes of sucrose branch and key inulin synthesis (fructosyltransferases) and catabolism (fructan exohydrolases) genes. The lowered expression of a sucrose gene subset together with that of SUCROSE:SUCROSE-1-FRUCTOSYLTRANSFERASE (1-SST) may have accounted for sucrose and kestose contents drop in the leaves of waterlogged plants. Two anti-correlated modules harbouring candidate hub-genes, including 1-SST, were identified by weighted gene correlation network analysis, and proposed to control positively and negatively kestose levels. In silico analysis further pointed at transcription factors of GATA, DOF, WRKY types as putative regulators of 1-SST.
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Affiliation(s)
- Giulio Testone
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300 - 00015 Monterotondo, Rome, Italy
| | - Anatoly Petrovich Sobolev
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300 - 00015 Monterotondo, Rome, Italy
| | - Giovanni Mele
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300 - 00015 Monterotondo, Rome, Italy
| | - Chiara Nicolodi
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300 - 00015 Monterotondo, Rome, Italy
| | - Maria Gonnella
- Institute of Sciences of Food Production, CNR. Via G. Amendola 122/O - 70126, Bari, Italy
| | - Giuseppe Arnesi
- Enza Zaden Italia, Strada Statale Aurelia km. 96.400 - 01016 Tarquinia, Viterbo, Italy
| | - Tiziano Biancari
- Enza Zaden Italia, Strada Statale Aurelia km. 96.400 - 01016 Tarquinia, Viterbo, Italy
| | - Donato Giannino
- Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300 - 00015 Monterotondo, Rome, Italy.
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Zhang J, Zhang P, Huo X, Gao Y, Chen Y, Song Z, Wang F, Zhang J. Comparative Phenotypic and Transcriptomic Analysis Reveals Key Responses of Upland Cotton to Salinity Stress During Postgermination. FRONTIERS IN PLANT SCIENCE 2021; 12:639104. [PMID: 33927736 PMCID: PMC8076740 DOI: 10.3389/fpls.2021.639104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/19/2021] [Indexed: 06/01/2023]
Abstract
To understand the molecular mechanisms of salinity tolerance during seed germination and post-germination stages, this study characterized phenotypic and transcriptome responses of two cotton cultivars during salinity stress. The two cultivars were salt-tolerant (ST) LMY37 and salt-sensitive (SS) ZM12, with the former exhibiting higher germination rate, growth, and primary-root fresh weight under salinity stress. Transcriptomic comparison revealed that up-regulation of differentially expressed genes (DEGs) was the main characteristic of transcriptional regulation in ST, while SS DEGs were mainly down-regulated. GO and KEGG analyses uncovered both common and specific responses in ST and SS. Common processes, such as reactive oxygen species (ROS) metabolism and cell wall biosynthesis, may be general responses to salinity in cotton. In contrast, DEGs involved in MAPK-signaling pathway activated by ROS, carotenoid biosynthesis pathway and cysteine and methionine metabolism pathway [producing the precursors of stress hormone abscisic acid (ABA) and ethylene (ET), respectively] as well as stress tolerance related transcription factor genes, showed significant expression differences between ST and SS. These differences might be the molecular basis leading to contrasting salinity tolerance. Silencing of GhERF12, an ethylene response factor gene, caused higher salinity sensitivity and increased ROS accumulation after salinity stress. In addition, peroxidase (POD) and superoxide dismutase (SOD) activity obviously declined after silencing GhERF12. These results suggest that GhERF12 is involved in salinity tolerance during early development. This study provides a novel and comprehensive perspective to understand key mechanisms of salinity tolerance and explores candidate genes that may be useful in developing stress-tolerant crops through biotechnology.
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Affiliation(s)
- Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
| | - Pei Zhang
- Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xuehan Huo
- Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yang Gao
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
| | - Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
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TaAP2-15, An AP2/ERF Transcription Factor, Is Positively Involved in Wheat Resistance to Puccinia striiformis f. sp. tritici. Int J Mol Sci 2021; 22:ijms22042080. [PMID: 33669850 PMCID: PMC7923241 DOI: 10.3390/ijms22042080] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/25/2022] Open
Abstract
AP2 transcription factors play a crucial role in plant development and reproductive growth, as well as response to biotic and abiotic stress. However, the role of TaAP2-15, in the interaction between wheat and the stripe fungus, Puccinia striiformis f. sp. tritici (Pst), remains elusive. In this study, we isolated TaAP2-15 and characterized its function during the interaction. TaAP2-15 was localized in the nucleus of wheat and N. benthamiana. Silencing of TaAP2-15 by barley stripe mosaic virus (BSMV)-mediated VIGS (virus-induced gene silencing) increased the susceptibility of wheat to Pst accompanied by enhanced growth of the pathogen (number of haustoria, haustorial mother cells and hyphal length). We confirmed by quantitative real-time PCR that the transcript levels of pathogenesis-related genes (TaPR1 and TaPR2) were down-regulated, while reactive oxygen species (ROS)-scavenging genes (TaCAT3 and TaFSOD3D) were induced accompanied by reduced accumulation of H2O2. Furthermore, we found that TaAP2-15 interacted with a zinc finger protein (TaRZFP34) that is a homolog of OsRZFP34 in rice. Together our findings demonstrate that TaAP2-15 is positively involved in resistance of wheat to the stripe rust fungus and provides new insights into the roles of AP2 in the host-pathogen interaction.
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Sakeh NM, Abdullah SNA, Bahari MNA, Azzeme AM, Shaharuddin NA, Idris AS. EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense. BMC PLANT BIOLOGY 2021; 21:59. [PMID: 33482731 PMCID: PMC7825162 DOI: 10.1186/s12870-020-02812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Hemibiotrophic pathogen such as the fungal pathogen Ganoderma boninense that is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic phase at early interaction which switched to necrotrophic phase at a later stage of infection. RESULTS The present report is a continuing study from our previous published transcriptomic profiling of oil palm seedlings against G. boninense. We focused on identifying differentially expressed genes (DEGs) encoding transcription factors (TFs) from the same RNA-seq data; resulting in 106 upregulated and 108 downregulated TFs being identified. The DEGs are involved in four established defense-related pathways responsible for cell wall modification, reactive oxygen species (ROS)-mediated signaling, programmed cell death (PCD) and plant innate immunity. We discovered upregulation of JUNGBRUNNEN 1 (EgJUB1) during the fungal biotrophic phase while Ethylene Responsive Factor 113 (EgERF113) demonstrated prominent upregulation when the palm switches to defense against necrotrophic phase. EgJUB1 was shown to have a binding activity to a 19 bp palindromic SNBE1 element, WNNYBTNNNNNNNAMGNHW found in the promoter region of co-expressing EgHSFC-2b. Further in silico analysis of promoter regions revealed co-expression of EgJUB1 with TFs containing SNBE1 element with single nucleotide change at either the 5th or 18th position. Meanwhile, EgERF113 binds to both GCC and DRE/CRT elements promoting plasticity in upregulating the downstream defense-related genes. Both TFs were proven to be nuclear-localized based on subcellular localization experiment using onion epidermal cells. CONCLUSION Our findings demonstrated unprecedented transcriptional reprogramming of specific TFs potentially to enable regulation of a specific set of genes during different infection phases of this hemibiotrophic fungal pathogen. The results propose the intricacy of oil palm defense response in orchestrating EgJUB1 during biotrophic and EgERF113 during the subsequent transition to the necrotrophic phase. Binding of EgJUB1 to SNBE motif instead of NACBS while EgERF113 to GCC-box and DRE/CRT motifs is unconventional and not normally associated with pathogen infection. Identification of these phase-specific oil palm TFs is important in designing strategies to tackle or attenuate the progress of infection.
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Affiliation(s)
- Nurshafika Mohd Sakeh
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
| | | | - Azzreena Mohamad Azzeme
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Abu Seman Idris
- Ganoderma and Diseases Research for Oil Palm Unit, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
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