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Liu B, Xu C, He Q, Zhang K, Qi S, Jin Z, Cheng W, Ding Z, Chen D, Zhao X, Zhang W, Zhang K, Li K. Membralin is required for maize development and defines a branch of the endoplasmic reticulum-associated degradation pathway in plants. Proc Natl Acad Sci U S A 2024; 121:e2406090121. [PMID: 38865274 PMCID: PMC11194580 DOI: 10.1073/pnas.2406090121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/15/2024] [Indexed: 06/14/2024] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) plays key roles in controlling protein levels and quality in eukaryotes. The Ring Finger Protein 185 (RNF185)/membralin ubiquitin ligase complex was recently identified as a branch in mammals and is essential for neuronal function, but its function in plant development is unknown. Here, we report the map-based cloning and characterization of Narrow Leaf and Dwarfism 1 (NLD1), which encodes the ER membrane-localized protein membralin and specifically interacts with maize homologs of RNF185 and related components. The nld1 mutant shows defective leaf and root development due to reduced cell number. The defects of nld1 were largely restored by expressing membralin genes from Arabidopsis thaliana and mice, highlighting the conserved roles of membralin proteins in animals and plants. The excessive accumulation of β-hydroxy β-methylglutaryl-CoA reductase in nld1 indicates that the enzyme is a membralin-mediated ERAD target. The activation of bZIP60 mRNA splicing-related unfolded protein response signaling and marker gene expression in nld1, as well as DNA fragment and cell viability assays, indicate that membralin deficiency induces ER stress and cell death in maize, thereby affecting organogenesis. Our findings uncover the conserved, indispensable role of the membralin-mediated branch of the ERAD pathway in plants. In addition, ZmNLD1 contributes to plant architecture in a dose-dependent manner, which can serve as a potential target for genetic engineering to shape ideal plant architecture, thereby enhancing high-density maize yields.
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Affiliation(s)
- Baiyu Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
| | - Changzheng Xu
- School of Life Sciences, Southwest University, Chongqing400715, China
| | - Qiuxia He
- Science and Technology Service Platform, Qilu University of Technology (Shandong Academy of Sciences), Jinan250103, China
| | - Ke Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
| | - Shoumei Qi
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
| | - Zhe Jin
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
| | - Wen Cheng
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
| | - Zhaohua Ding
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
| | - Donghua Chen
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong271018, China
| | - Wei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
| | - Kewei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
| | - Kunpeng Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao266237, China
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2
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Li J, Zhang W, Lu Q, Sun J, Cheng C, Huang S, Li S, Li Q, Zhang W, Zhou C, Liu B, Xiang F. GmDFB1, an ARM-repeat superfamily protein, regulates floral organ identity through repressing siRNA- and miRNA-mediated gene silencing in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38860597 DOI: 10.1111/jipb.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 05/04/2024] [Indexed: 06/12/2024]
Abstract
The development of flowers in soybean (Glycine max) is essential for determining the yield potential of the plant. Gene silencing pathways are involved in modulating flower development, but their full elucidation is still incomplete. Here, we conducted a forward genetic screen and identified an abnormal flower mutant, deformed floral bud1-1 (Gmdfb1-1), in soybean. We mapped and identified the causal gene, which encodes a member of the armadillo (ARM)-repeat superfamily. Using small RNA sequencing (sRNA-seq), we found an abnormal accumulation of small interfering RNAs (siRNAs) and microRNA (miRNAs) in the Gmdfb1 mutants. We further demonstrated that GmDFB1 interacts with the RNA exosome cofactor SUPER KILLER7 (GmSKI7). Additionally, GmDFB1 interacts with the PIWI domain of ARGONAUTE 1 (GmAGO1) to inhibit the cleavage efficiency on the target genes of sRNAs. The enhanced gene silencing mediated by siRNA and miRNA in the Gmdfb1 mutants leads to the downregulation of their target genes associated with flower development. This study revealed the crucial role of GmDFB1 in regulating floral organ identity in soybean probably by participating in two distinct gene silencing pathways.
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Affiliation(s)
- Jie Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wenxiao Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qing Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Jiaqi Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chuang Cheng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shiyu Huang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qiang Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wei Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bin Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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3
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Shu L, Li L, Jiang YQ, Yan J. Advances in membrane-tethered NAC transcription factors in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112034. [PMID: 38365003 DOI: 10.1016/j.plantsci.2024.112034] [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: 10/24/2023] [Revised: 02/08/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Transcription factors are central components in cell signal transduction networks and are critical regulators for gene expression. It is estimated that approximately 10% of all transcription factors are membrane-tethered. MTFs (membrane-bound transcription factors) are latent transcription factors that are inherently anchored in the cellular membrane in a dormant form. When plants encounter environmental stimuli, they will be released from the membrane by intramembrane proteases or by the ubiquitin proteasome pathway and then were translocated to the nucleus. The capacity to instantly activate dormant transcription factors is a critical strategy for modulating diverse cellular functions in response to external or internal signals, which provides an important transcriptional regulatory network in response to sudden stimulus and improves plant survival. NTLs (NTM1-like) are a small subset of NAC (NAM, ATAF1/2, CUC2) transcription factors, which contain a conserved NAC domain at the N-terminus and a transmembrane domain at the C-terminus. In the past two decades, several NTLs have been identified from several species, and most of them are involved in both development and stress response. In this review, we review the reports and findings on NTLs in plants and highlight the mechanism of their nuclear import as well as their functions in regulating plant growth and stress response.
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Affiliation(s)
- Lin Shu
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan province 450002, China
| | - Longhui Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan province 450002, China
| | - Yuan-Qing Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi province 712100, China
| | - Jingli Yan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan province 450002, China.
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4
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Marathe S, Grotewold E, Otegui MS. Should I stay or should I go? Trafficking of plant extra-nuclear transcription factors. THE PLANT CELL 2024; 36:1524-1539. [PMID: 38163635 PMCID: PMC11062434 DOI: 10.1093/plcell/koad277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 01/03/2024]
Abstract
At the heart of all biological processes lies the control of nuclear gene expression, which is primarily achieved through the action of transcription factors (TFs) that generally contain a nuclear localization signal (NLS) to facilitate their transport into the nucleus. However, some TFs reside in the cytoplasm in a transcriptionally inactive state and only enter the nucleus in response to specific signals, which in plants include biotic or abiotic stresses. These extra-nuclear TFs can be found in the cytosol or associated with various membrane systems, including the endoplasmic reticulum and plasma membrane. They may be integral proteins with transmembrane domains or associate peripherally with the lipid bilayer via acylation or membrane-binding domains. Although over 30 plant TFs, most of them involved in stress responses, have been experimentally shown to reside outside the nucleus, computational predictions suggest that this number is much larger. Understanding how extra-nuclear TFs are trafficked into the nucleus is essential for reconstructing transcriptional regulatory networks that govern major cellular pathways in response to biotic and abiotic signals. Here, we provide a perspective on what is known on plant extranuclear-nuclear TF retention, nuclear trafficking, and the post-translational modifications that ultimately enable them to regulate gene expression upon entering the nucleus.
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Affiliation(s)
- Sarika Marathe
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
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5
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Shen L, Yang S, Zhao E, Xia X, Yang X. StoMYB41 positively regulates the Solanum torvum response to Verticillium dahliae in an ABA dependent manner. Int J Biol Macromol 2024; 263:130072. [PMID: 38346615 DOI: 10.1016/j.ijbiomac.2024.130072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 02/26/2024]
Abstract
MYB transcription factor despite their solid involvement in growth are potent regulator of plant stress response. Herein, we identified a MYB gene named as StoMYB41 in a wild eggplant species Solanum torvum. The expression level of StoMYB41 was higher in root than the tissues including stem, leaf, and seed. It induced significantly by Verticillium dahliae inoculation. StoMYB41 was localized in the nucleus and exhibited transcriptional activation activity. Silencing of StoMYB41 enhanced susceptibility of Solanum torvum against Verticillium dahliae, accompanied by higher disease index. The significant down-regulation of resistance marker gene StoABR1 comparing to the control plants was recorded in the silenced plants. Moreover, transient expression of StoMYB41 could trigger intense hypersensitive reaction mimic cell death, darker DAB and trypan blue staining, higher ion leakage, and induced the expression levels of StoABR1 and NbDEF1 in the leaves of Solanum torvum and Nicotiana benthamiana. Taken together, our data indicate that StoMYB41 acts as a positive regulator in Solanum torvum against Verticillium wilt.
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Affiliation(s)
- Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
| | - Shixin Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Enpeng Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xin Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
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6
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Xiao G, Wang M, Li X, Jiang Z, Zhang H, Gao D, Zhang B, Xia G, Wang M. TaCHP encoding C1-domain protein stably enhances wheat yield in saline-alkaline fields. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:169-171. [PMID: 38146667 DOI: 10.1111/jipb.13605] [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: 09/27/2023] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 12/27/2023]
Abstract
Overexpression of the zinc finger gene TaCHP stably enhanced wheat yield in saline-alkaline conditions in a multi-year, three-site field trial, and the genetic variations in its promoter contribute to saline-alkaline tolerance of wheat accessions. TaCHP and its tolerant haplotype have great potential for molecular breeding of stress-tolerant wheat.
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Affiliation(s)
- Guilian Xiao
- The Key Laboratory of Plant Development and Environment Adaptation Biology Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Minqin Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Xiaomeng Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Zhengning Jiang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China
| | - Hongjian Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Derong Gao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China
| | - Boqiao Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environment Adaptation Biology Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
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7
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Zhang W, Zhi W, Qiao H, Huang J, Li S, Lu Q, Wang N, Li Q, Zhou Q, Sun J, Bai Y, Zheng X, Bai M, Van Breusegem F, Xiang F. H2O2-dependent oxidation of the transcription factor GmNTL1 promotes salt tolerance in soybean. THE PLANT CELL 2023; 36:112-135. [PMID: 37770034 PMCID: PMC10734621 DOI: 10.1093/plcell/koad250] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Reactive oxygen species (ROS) play an essential role in plant growth and responses to environmental stresses. Plant cells sense and transduce ROS signaling directly via hydrogen peroxide (H2O2)-mediated posttranslational modifications (PTMs) on protein cysteine residues. Here, we show that the H2O2-mediated cysteine oxidation of NAC WITH TRANS-MEMBRANE MOTIF1-LIKE 1 (GmNTL1) in soybean (Glycine max) during salt stress promotes its release from the endoplasmic reticulum (ER) membrane and translocation to the nucleus. We further show that an oxidative posttranslational modification on GmNTL1 residue Cys-247 steers downstream amplification of ROS production by binding to and activating the promoters of RESPIRATORY BURST OXIDASE HOMOLOG B (GmRbohB) genes, thereby creating a feed-forward loop to fine-tune GmNTL1 activity. In addition, oxidation of GmNTL1 Cys-247 directly promotes the expression of CATION H+ EXCHANGER 1 (GmCHX1)/SALT TOLERANCE-ASSOCIATED GENE ON CHROMOSOME 3 (GmSALT3) and Na+/H+ Antiporter 1 (GmNHX1). Accordingly, transgenic overexpression of GmNTL1 in soybean increases the H2O2 levels and K+/Na+ ratio in the cell, promotes salt tolerance, and increases yield under salt stress, while an RNA interference-mediated knockdown of GmNTL1 elicits the opposite effects. Our results reveal that the salt-induced oxidation of GmNTL1 promotes its relocation and transcriptional activity through an H2O2-mediated posttranslational modification on cysteine that improves resilience of soybean against salt stress.
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Affiliation(s)
- Wenxiao Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Wenjiao Zhi
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Hong Qiao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Qing Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Nan Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Qiang Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Qian Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Jiaqi Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Yuting Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Xiaojian Zheng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Mingyi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
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8
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Zhang Z, Jin S, Tian H, Wang Z, Jiang R, Liu C, Xin D, Wu X, Chen Q, Zhu R. Identifying the Soybean microRNAs Related to Phytophthora sojae Based on RNA Sequencing and Bioinformatics Analysis. Int J Mol Sci 2023; 24:ijms24108546. [PMID: 37239903 DOI: 10.3390/ijms24108546] [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: 03/19/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Phytophthora root rot in soybeans is caused by a pathogen called Phytophthora sojae (P. sojae), which results in a significant decrease in soybean production within affected regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a key post-transcriptional regulatory role in eukaryotes. In this paper, the miRNAs that respond to P. sojae were analyzed from the gene level to complement the study of molecular resistance mechanisms in soybean. The study utilized high-throughput sequencing of soybean data to predict miRNAs that respond to P. sojae, analyze their specific functions, and verify regulatory relationships using qRT-PCR. The results showed that the miRNAs in soybean respond to P. sojae infection. MiRNAs can be transcribed independently, suggesting the presence of transcription factor binding sites in the promoter regions. Additionally, we performed an evolutionary analysis on conserved miRNAs that respond to P. sojae. Finally, we investigated the regulatory relationships among miRNAs, genes, and transcription factors, and identified five regulatory patterns. These findings lay the groundwork for future studies on the evolution of miRNAs responsive to P. sojae.
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Affiliation(s)
- Zhanguo Zhang
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- National Research Center of Soybean Engineering and Technology, Harbin 150030, China
| | - Song Jin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Huilin Tian
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Zhihao Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Rui Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Rongsheng Zhu
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
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Rai N, Rai KK, Singh MK, Singh J, Kaushik P. Investigating NAC Transcription Factor Role in Redox Homeostasis in Solanum lycopersicum L.: Bioinformatics, Physiological and Expression Analysis under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:2930. [PMID: 36365384 PMCID: PMC9654907 DOI: 10.3390/plants11212930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
NAC transcription factors regulate stress-defence pathways and developmental processes in crop plants. However, their detailed functional characterization in tomatoes needs to be investigated comprehensively. In the present study, tomato hybrids subjected to 60 and 80 days of drought stress conditions showed a significant increase in membrane damage and reduced relative water, chlorophyll and proline content. However, hybrids viz., VRTH-16-3 and VRTH-17-68 showed superior growth under drought stress, as they were marked with low electrolytic leakage, enhanced relative water content, proline content and an enhanced activity of enzymatic antioxidants, along with the upregulation of NAC and other stress-defence pathway genes. Candidate gene(s) exhibiting maximum expression in all the hybrids under drought stress were subjected to detailed in silico characterization to provide significant insight into its structural and functional classification. The homology modelling and superimposition analysis of predicted tomato NAC protein showed that similar amino acid residues were involved in forming the conserved WKAT domain. DNA docking discovered that the SlNAC1 protein becomes activated and exerts a stress-defence response after the possible interaction of conserved DNA elements using Pro72, Asn73, Trp81, Lys82, Ala83, Thr84, Gly85, Thr86 and Asp87 residues. A protein-protein interaction analysis identified ten functional partners involved in the induction of stress-defence tolerance.
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Affiliation(s)
- Nagendra Rai
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
| | - Krishna Kumar Rai
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, UP, India
| | - Manish Kumar Singh
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
| | - Jagdish Singh
- Indian Institute of Vegetable Research (IIVR), Varanasi 221305, UP, India
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
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10
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De Backer J, Van Breusegem F, De Clercq I. Proteolytic Activation of Plant Membrane-Bound Transcription Factors. FRONTIERS IN PLANT SCIENCE 2022; 13:927746. [PMID: 35774815 PMCID: PMC9237531 DOI: 10.3389/fpls.2022.927746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/23/2022] [Indexed: 06/03/2023]
Abstract
Due to the presence of a transmembrane domain, the subcellular mobility plan of membrane-bound or membrane-tethered transcription factors (MB-TFs) differs from that of their cytosolic counterparts. The MB-TFs are mostly locked in (sub)cellular membranes, until they are released by a proteolytic cleavage event or when the transmembrane domain (TMD) is omitted from the transcript due to alternative splicing. Here, we review the current knowledge on the proteolytic activation mechanisms of MB-TFs in plants, with a particular focus on regulated intramembrane proteolysis (RIP), and discuss the analogy with the proteolytic cleavage of MB-TFs in animal systems. We present a comprehensive inventory of all known and predicted MB-TFs in the model plant Arabidopsis thaliana and examine their experimentally determined or anticipated subcellular localizations and membrane topologies. We predict proteolytically activated MB-TFs by the mapping of protease recognition sequences and structural features that facilitate RIP in and around the TMD, based on data from metazoan intramembrane proteases. Finally, the MB-TF functions in plant responses to environmental stresses and in plant development are considered and novel functions for still uncharacterized MB-TFs are forecasted by means of a regulatory network-based approach.
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Affiliation(s)
- Jonas De Backer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
| | - Inge De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgium
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11
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A Rice R2R3-Type MYB Transcription Factor OsFLP Positively Regulates Drought Stress Response via OsNAC. Int J Mol Sci 2022; 23:ijms23115873. [PMID: 35682553 PMCID: PMC9180394 DOI: 10.3390/ijms23115873] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/18/2022] [Accepted: 05/22/2022] [Indexed: 11/17/2022] Open
Abstract
Abiotic stresses adversely affect plant growth and the yield of crops worldwide. R2R3-MYB transcriptional factors have been found to be vital for plants to confer stress response. In Arabidopsis, FOUR LIPS (FLP, MYB124) and its paralogous MYB88 function redundantly regulated the symmetric division of guard mother cells (GMCs) and abiotic stress response. Here, OsFLP was identified as an R2R3-MYB transcriptional activator and localized in the nucleus. OsFLP was transiently induced by drought, salt stress and abscisic acid (ABA). Overexpression of OsFLP showed enhanced tolerance to drought and salt stresses. The stomatal density in OsFLP-OE plants was not changed, whereas the stomatal closure was sensitive to ABA treatment compared to wild-type plants. In contrast, OsFLP-RNAi plants had abnormal stomata and were sensitive to drought. Moreover, the transcripts of stomatal closure-related genes DST and peroxidase 24 precursor, which are identified as downstream of OsNAC1, were inhibited in OsFLP-RNAi plants. The yeast-one-hybrid assay indicated that OsFLP can specifically bind and positively regulate OsNAC1 and OsNAC6. Meanwhile, stress response genes, such as OsLEA3 and OsDREB2A, were up-regulated in OsFLP-OE plants. These findings suggested that OsFLP positively participates in drought stress, mainly through regulating regulators' transcripts of OsNAC1 and OsNAC6.
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12
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Norero NS, Rey Burusco MF, D’Ippólito S, Décima Oneto CA, Massa GA, Castellote MA, Feingold SE, Guevara MG. Genome-Wide Analyses of Aspartic Proteases on Potato Genome ( Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040544. [PMID: 35214878 PMCID: PMC8875628 DOI: 10.3390/plants11040544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/04/2021] [Accepted: 01/06/2022] [Indexed: 05/11/2023]
Abstract
Aspartic proteases are proteolytic enzymes widely distributed in living organisms and viruses. Although they have been extensively studied in many plant species, they are poorly described in potatoes. The present study aimed to identify and characterize S. tuberosum aspartic proteases. Gene structure, chromosome and protein domain organization, phylogeny, and subcellular predicted localization were analyzed and integrated with RNAseq data from different tissues, organs, and conditions focused on abiotic stress. Sixty-two aspartic protease genes were retrieved from the potato genome, distributed in 12 chromosomes. A high number of intronless genes and segmental and tandem duplications were detected. Phylogenetic analysis revealed eight StAP groups, named from StAPI to StAPVIII, that were differentiated into typical (StAPI), nucellin-like (StAPIIIa), and atypical aspartic proteases (StAPII, StAPIIIb to StAPVIII). RNAseq data analyses showed that gene expression was consistent with the presence of cis-acting regulatory elements on StAP promoter regions related to water deficit. The study presents the first identification and characterization of 62 aspartic protease genes and proteins on the potato genome and provides the baseline material for functional gene determinations and potato breeding programs, including gene editing mediated by CRISPR.
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Affiliation(s)
- Natalia Sigrid Norero
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - María Florencia Rey Burusco
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
- Faculty of Agricultural Sciences, University National of Mar del Plata, Balcarce B7620, Argentina
| | - Sebastián D’Ippólito
- Institute of Biological Research, University of Mar del Plata (IIB-UNMdP), Mar del Plata B7600, Argentina;
- National Scientific and Technical Research Council, Argentina (CONICET), Buenos Aires C1499, Argentina
| | - Cecilia Andrea Décima Oneto
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - Gabriela Alejandra Massa
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
- Faculty of Agricultural Sciences, University National of Mar del Plata, Balcarce B7620, Argentina
| | - Martín Alfredo Castellote
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - Sergio Enrique Feingold
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - María Gabriela Guevara
- Institute of Biological Research, University of Mar del Plata (IIB-UNMdP), Mar del Plata B7600, Argentina;
- National Scientific and Technical Research Council, Argentina (CONICET), Buenos Aires C1499, Argentina
- Correspondence: or
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13
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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14
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Lin Y, Liu G, Xue Y, Guo X, Luo J, Pan Y, Chen K, Tian J, Liang C. Functional Characterization of Aluminum (Al)-Responsive Membrane-Bound NAC Transcription Factors in Soybean Roots. Int J Mol Sci 2021; 22:12854. [PMID: 34884659 PMCID: PMC8657865 DOI: 10.3390/ijms222312854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
The membrane-bound NAC transcription (NTL) factors have been demonstrated to participate in the regulation of plant development and the responses to multiple environmental stresses. This study is aimed to functionally characterize soybean NTL transcription factors in response to Al-toxicity, which is largely uncharacterized. The qRT-PCR assays in the present study found that thirteen out of fifteen GmNTL genes in the soybean genome were up-regulated by Al toxicity. However, among the Al-up-regulated GmNTLs selected from six duplicate gene pairs, only overexpressing GmNTL1, GmNTL4, and GmNTL10 could confer Arabidopsis Al resistance. Further comprehensive functional characterization of GmNTL4 showed that the expression of this gene in response to Al stress depended on root tissues, as well as the Al concentration and period of Al treatment. Overexpression of GmNTL4 conferred Al tolerance of transgenic Arabidopsis in long-term (48 and 72 h) Al treatments. Moreover, RNA-seq assay identified 517 DEGs regulated by GmNTL4 in Arabidopsis responsive to Al stress, which included MATEs, ALMTs, PMEs, and XTHs. These results suggest that the function of GmNTLs in Al responses is divergent, and GmNTL4 might confer Al resistance partially by regulating the expression of genes involved in organic acid efflux and cell wall modification.
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Affiliation(s)
- Yan Lin
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Guoxuan Liu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Yingbing Xue
- Department of Resources and Environmental Sciences, College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China;
| | - Xueqiong Guo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Jikai Luo
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Yaoliang Pan
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Kang Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (G.L.); (X.G.); (J.L.); (Y.P.); (K.C.); (J.T.)
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15
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Wang T, Dong Q, Wang W, Chen S, Cheng Y, Tian H, Li X, Hussain S, Wang L, Gong L, Wang S. Evolution of AITR family genes in cotton and their functions in abiotic stress tolerance. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23 Suppl 1:58-68. [PMID: 33202099 DOI: 10.1111/plb.13218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/11/2020] [Indexed: 05/18/2023]
Abstract
Abiotic stresses are major environmental factors inhibiting plant growth and development. AITRs (ABA-induced transcription repressors) are a novel family of transcription factors regulating ABA (abscisic acid) signalling and plant responses to abiotic stresses in Arabidopsis. However, the composition and evolution history of AITRs and their roles in the cotton genus are largely unknown. A total of 12 putative AITRs genes were identified in cultivated tetraploid cotton, Gossypium hirsutum. Phylogenetic analysis of GhAITRs in these tetraploid cottons and their closely related species implicate ancient genome-wide duplication occurring after speciation of Gossypium, and Theobroma could generate duplicates of GhAITRs. Duplicated GhAITRs were stably inherited following diploid speciation and further allotetraploidy in Gossypium. Homologous GhAITRs shared common expression patterns in response to ABA, drought and salinity treatments, and drought tolerance induced in transgenic Arabidopsis plants expressing GhAITR-A1. Together, our findings reveal that duplicates in the GhAITRs gene family were achieved by whole genome duplication rather than three individual duplication events, and that GhAITRs function as transcription repressors and are involved in the regulation of plant responses to ABA and drought stress. These results provide insights towards the improvement of abiotic stress tolerance in cotton using GhAITRs.
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Affiliation(s)
- T Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Q Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - W Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - S Chen
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Y Cheng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - H Tian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - X Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - S Hussain
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - L Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
| | - L Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - S Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
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16
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Jiao Z, Du H, Chen S, Huang W, Ge L. LAZY Gene Family in Plant Gravitropism. FRONTIERS IN PLANT SCIENCE 2021; 11:606241. [PMID: 33613583 PMCID: PMC7893674 DOI: 10.3389/fpls.2020.606241] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/01/2020] [Indexed: 05/26/2023]
Abstract
Adapting to the omnipresent gravitational field was a fundamental basis driving the flourishing of terrestrial plants on the Earth. Plants have evolved a remarkable capability that not only allows them to live and develop within the Earth's gravity field, but it also enables them to use the gravity vector to guide the growth of roots and shoots, in a process known as gravitropism. Triggered by gravistimulation, plant gravitropism is a highly complex, multistep process that requires many organelles and players to function in an intricate coordinated way. Although this process has been studied for several 100 years, much remains unclear, particularly the early events that trigger the relocation of the auxin efflux carrier PIN-FORMED (PIN) proteins, which presumably leads to the asymmetrical redistribution of auxin. In the past decade, the LAZY gene family has been identified as a crucial player that ensures the proper redistribution of auxin and a normal tropic response for both roots and shoots upon gravistimulation. LAZY proteins appear to be participating in the early steps of gravity signaling, as the mutation of LAZY genes consistently leads to altered auxin redistribution in multiple plant species. The identification and characterization of the LAZY gene family have significantly advanced our understanding of plant gravitropism, and opened new frontiers of investigation into the novel molecular details of the early events of gravitropism. Here we review current knowledge of the LAZY gene family and the mechanism modulated by LAZY proteins for controlling both roots and shoots gravitropism. We also discuss the evolutionary significance and conservation of the LAZY gene family in plants.
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Affiliation(s)
- Zhicheng Jiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Huan Du
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Shu Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, China
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17
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Yuan S, Ke D, Li R, Li X, Wang L, Chen H, Zhang C, Huang Y, Chen L, Hao Q, Yang H, Cao D, Chen S, Guo W, Shan Z, Yang Z, Zhang X, Qiu D, Guan Y, Zhou X. Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis. BMC PLANT BIOLOGY 2020; 20:517. [PMID: 33183238 PMCID: PMC7659060 DOI: 10.1186/s12870-020-02725-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood. RESULTS In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development. CONCLUSIONS Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence.
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Affiliation(s)
- Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Danxia Ke
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Rong Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiangyong Li
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Lei Wang
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuefeng Guan
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China.
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18
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Liu W, Zhang Y, Li W, Lin Y, Wang C, Xu R, Zhang L. Genome-wide characterization and expression analysis of soybean trihelix gene family. PeerJ 2020; 8:e8753. [PMID: 32206450 PMCID: PMC7075366 DOI: 10.7717/peerj.8753] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/14/2020] [Indexed: 01/10/2023] Open
Abstract
Trihelix transcription factors play multiple roles in plant growth, development and various stress responses. In this study, we identified 71 trihelix family genes in the soybean genome. These trihelix genes were located at 19 out of 20 soybean chromosomes unevenly and were classified into six distinct subfamilies: GT-1, GT-2, GTγ, SIP1, SH4 and GTδ. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Thirteen segmental duplicated gene pairs were identified and all of them experienced a strong purifying selective pressure during evolution. Various stress-responsive cis-elements presented in the promoters of soybean trihelix genes, suggesting that the trihelix genes might respond to the environmental stresses in soybean. The expression analysis suggests that trihelix genes are involved in diverse functions during soybean development, flood or salinity tolerance, and plant immunity. Our results provide genomic information of the soybean trihelix genes and a basis for further characterizing their roles in response to environmental stresses.
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Affiliation(s)
- Wei Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Yanwei Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Yanhui Lin
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Caijie Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Lifeng Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
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Liu Z, Fu M, Li H, Chen Y, Wang L, Liu R. Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt. PeerJ 2019; 7:e7995. [PMID: 31720116 PMCID: PMC6839521 DOI: 10.7717/peerj.7995] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/07/2019] [Indexed: 11/30/2022] Open
Abstract
As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.
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Affiliation(s)
- Zhanji Liu
- 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
| | - Mingchuan Fu
- 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
| | - Hao Li
- 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
| | - Yizhen 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
| | - Liguo 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
| | - Renzhong Liu
- 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
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Li S, Wang N, Ji D, Zhang W, Wang Y, Yu Y, Zhao S, Lyu M, You J, Zhang Y, Wang L, Wang X, Liu Z, Tong J, Xiao L, Bai MY, Xiang F. A GmSIN1/GmNCED3s/GmRbohBs Feed-Forward Loop Acts as a Signal Amplifier That Regulates Root Growth in Soybean Exposed to Salt Stress. THE PLANT CELL 2019; 31:2107-2130. [PMID: 31227558 PMCID: PMC6751118 DOI: 10.1105/tpc.18.00662] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 05/07/2019] [Accepted: 06/17/2019] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) and reactive oxygen species (ROS) act as key signaling molecules in the plant response to salt stress; however, how these signals are transduced and amplified remains unclear. Here, a soybean (Glycine max) salinity-induced NAM/ATAF1/2/CUC2 (NAC) transcription factor encoded by SALT INDUCED NAC1 (GmSIN1) was shown to be a key component of this process. Overexpression of GmSIN1 in soybean promoted root growth and salt tolerance and increased yield under salt stress; RNA interference-mediated knockdown of GmSIN1 had the opposite effect. The rapid induction of GmSIN1 in response to salinity required ABA and ROS, and the effect of GmSIN1 on root elongation and salt tolerance was achieved by boosting cellular ABA and ROS contents. GmSIN1 upregulated 9-cis-epoxycarotenoid dioxygenase coding genes in soybean (GmNCED3s, associated with ABA synthesis) and Respiratory burst oxidase homolog B genes in soybean (GmRbohBs, associated with ROS generation) by binding to their promoters at a site that has not been described to date. Together, GmSIN1, GmNCED3s, and GmRbohBs constitute a positive feed-forward system that enables the rapid accumulation of ABA and ROS, effectively amplifying the initial salt stress signal. These findings suggest that the combined modulation of ABA and ROS contents enhances soybean salt tolerance.
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Affiliation(s)
- Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Nan Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Dandan Ji
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Wenxiao Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Ying Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Yanchong Yu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Shizhen Zhao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Menghua Lyu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Juanjuan You
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Yangyang Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Luli Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Xiaofang Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Zhenhua Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic China
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Cao S, Guo M, Wang C, Xu W, Shi T, Tong G, Zhen C, Cheng H, Yang C, Elsheery NI, Cheng Y. Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation. BMC PLANT BIOLOGY 2019; 19:276. [PMID: 31234799 PMCID: PMC6591973 DOI: 10.1186/s12870-019-1865-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/03/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined. RESULTS A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAPpromoter::GUS techniques, the activities of PtAP66 promoters were observed only in fiber cells, not in the vessels of stems as the xylem and leaf veins developed in the transgenic Populus tree, and strong GUS signals were detected in interfascicular fiber cells, roots, anthers and sepals of PtAP17promoter::GUS transgenic plants. Intensive GUS activities in various secondary tissues implied that PtAP66 and PtAP17 could function in wood formation. In addition, most of the PtAP proteins were predicted to contain N- and (or) O-glycosylation sites, and the integration of PNGase F digestion and western blotting revealed that the PtAP17 and PtAP66 proteins were N-glycosylated in Populus. CONCLUSIONS Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.
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Affiliation(s)
- Shenquan Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Mengjie Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Chong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Wenjing Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Tianyuan Shi
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Guimin Tong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Cheng Zhen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Hao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | | | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
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Zhang L, Zhao T, Sun X, Wang Y, Du C, Zhu Z, Gichuki DK, Wang Q, Li S, Xin H. Overexpression of VaWRKY12, a transcription factor from Vitis amurensis with increased nuclear localization under low temperature, enhances cold tolerance of plants. PLANT MOLECULAR BIOLOGY 2019; 100:95-110. [PMID: 0 DOI: 10.1007/s11103-019-00846-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 02/18/2019] [Indexed: 05/23/2023]
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23
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Cao J. Molecular Evolution of the Vacuolar Iron Transporter ( VIT) Family Genes in 14 Plant Species. Genes (Basel) 2019; 10:E144. [PMID: 30769903 PMCID: PMC6409731 DOI: 10.3390/genes10020144] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/14/2022] Open
Abstract
The vacuolar iron transporter (VIT) proteins are involved in the storage and transport of iron. However, the evolution of this gene family in plants is unknown. In this study, I first identified 114 VIT genes in 14 plant species and classified these genes into seven groups by phylogenetic analysis. Conserved gene organization and motif distribution implied conserved function in each group. I also found that tandem duplication, segmental duplication and transposition contributed to the expansion of this gene family. Additionally, several positive selection sites were identified. Divergent expression patterns of soybean VIT genes were further investigated in different development stages and under iron stress. Functional network analysis exhibited 211 physical or functional interactions. The results will provide the basis for further functional studies of the VIT genes in plants.
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Affiliation(s)
- Jun Cao
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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24
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Liu M, Ma Z, Sun W, Huang L, Wu Q, Tang Z, Bu T, Li C, Chen H. Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum). BMC Genomics 2019; 20:113. [PMID: 30727951 PMCID: PMC6366116 DOI: 10.1186/s12864-019-5500-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/30/2019] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, there is no comprehensive study on the NAC genes of Tartary buckwheat (Fagopyrum tataricum), a large group of extensively cultivated medicinal and edible plants. The recently published Tartary buckwheat genome permits us to explore all the FtNAC genes on a genome-wide basis. RESULTS In the present study, 80 NAC (FtNAC) genes of Tartary buckwheat were obtained and named uniformly according to their distribution on chromosomes. Phylogenetic analysis of NAC proteins in both Tartary buckwheat and Arabidopsis showed that the FtNAC proteins are widely distributed in 15 subgroups with one subgroup unclassified. Gene structure analysis found that multitudinous FtNAC genes contained three exons, indicating that the structural diversity in Tartary buckwheat NAC genes is relatively low. Some duplication genes of FtNAC have a conserved structure that was different from others, indicating that these genes may have a variety of functions. By observing gene expression, we found that FtNAC genes showed abundant differences in expression levels in various tissues and at different stages of fruit development. CONCLUSIONS In this research, 80 NAC genes were identified in Tartary buckwheat, and their phylogenetic relationships, gene structures, duplication, global expression and potential roles in Tartary buckwheat development were studied. Comprehensive analysis will be useful for a follow-up study of functional characteristics of FtNAC genes and for the development of high-quality Tartary buckwheat varieties.
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Affiliation(s)
- Moyang Liu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zhaotang Ma
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Li Huang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zizhong Tang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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25
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He K, Zhao X, Chi X, Wang Y, Jia C, Zhang H, Zhou G, Hu R. A novel Miscanthus NAC transcription factor MlNAC10 enhances drought and salinity tolerance in transgenic Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2019; 233:84-93. [PMID: 30623878 DOI: 10.1016/j.jplph.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 05/11/2023]
Abstract
NAC (NAM, ATAF1/2 and CUC2) proteins are key regulators of various plant stress tolerances. However, knowledge of NAC genes remains largely unknown in Miscanthus. Here, we characterized a novel NAC gene MlNAC10 from M. lutarioriparius than plays a role in abiotic stress tolerance. MlNAC10 encodes a nuclear-localized protein with a C-terminal transactivation domain, and has a specific binding affinity to the NAC recognition sequence (NACRS). Ectopic expression of MlNAC10 in Arabidopsis led to increased sensitivity to abscisic acid (ABA) at early seedling growth stages. In addition, the proline content was significantly increased and the reactive oxygen species (ROS) scavenging capability was significantly enhanced in MlNAC10 overexpression lines under ABA treatment. Moreover, the drought and salt stress tolerance was significantly improved in MlNAC10 overexpression lines. Consistently, the activities of three antioxidant enzymes, namely catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), were dramatically stimulated in the overexpression lines compared to the wild type (WT). Correspondingly, the accumulation of ROS was dramatically decreased and malondialdehyde (MDA) was accumulated at a much lower level in the transgenic lines. Meanwhile, the expression of six abiotic stress-related genes was dramatically stimulated in the overexpression lines in comparison to the WT. Together, our results demonstrated that MlNAC10 acts as an important regulator of drought and salinity stress tolerance by stimulating antioxidant enzymes and alleviating ROS damage via the ABA signaling pathway.
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Affiliation(s)
- Kang He
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xun Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xiaoyuan Chi
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Yiping Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunlin Jia
- Shandong Institute of Agricultural Sustainable Development, Jinan 250100, China
| | - Hongpeng Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Gongke Zhou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Ruibo Hu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
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Sun H, Hu M, Li J, Chen L, Li M, Zhang S, Zhang X, Yang X. Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton. BMC PLANT BIOLOGY 2018; 18:150. [PMID: 30041622 PMCID: PMC6057059 DOI: 10.1186/s12870-018-1367-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 07/17/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Transcription factors operate as important switches of transcription networks, and NAC (NAM, ATAF, and CUC) transcription factors are a plant-specific family involved in multiple biological processes. However, this gene family has not been systematically characterized in cotton. RESULTS Here we identify a large number of genes with conservative NAC domains in four cotton species, with 147 found in Gossypium arboreum, 149 in G. raimondii, 267 in G. barbadense and 283 in G. hirsutum. Predicted membrane-bound NAC genes were also identified. Phylogenetic analysis showed that cotton NAC proteins clustered into seven subfamilies and homologous protein pairs showed similar characteristics. Evolutionary property analysis revealed that purifying selection of NAC genes occurred between diploid and polyploid cotton species, and variation analysis showed GhNAC genes may have been subjected to selection and domestication. NAC proteins showed extensive transactivation and this was dependent on the C-terminus. Some development and stress related cis-elements were enriched in the promoters of GhNAC genes. Comprehensive expression analysis indicated that 38 GhNAC genes were candidates for involvement in fiber development, and 120 in stress responses. Gene co-expression network analysis revealed relationships between fiber-associated NAC genes and secondary cell wall (SCW) biosynthesis genes. CONCLUSIONS NAC genes were identified in diploid and tetraploid cotton, revealing new insights into their evolution, variation and homology relationships. Transcriptome analysis and co-expression network indicated roles for GhNAC genes in cotton fiber development and stress response, and NAC genes may prove useful in molecular breeding programmes.
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Affiliation(s)
- Heng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Meiling Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Lin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Meng Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Shuqin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
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Mathew IE, Agarwal P. May the Fittest Protein Evolve: Favoring the Plant-Specific Origin and Expansion of NAC Transcription Factors. Bioessays 2018; 40:e1800018. [PMID: 29938806 DOI: 10.1002/bies.201800018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/26/2018] [Indexed: 12/12/2022]
Abstract
Plant-specific NAC transcription factors (TFs) evolve during the transition from aquatic to terrestrial plant life and are amplified to become one of the biggest TF families. This is because they regulate genes involved in water conductance and cell support. They also control flower and fruit formation. The review presented here focuses on various properties, regulatory intricacies, and developmental roles of NAC family members. Processes controlled by NACs depend majorly on their transcriptional properties. NACs can function as both activators and/or repressors. Additionally, their homo/hetero dimerization abilities can also affect DNA binding and activation properties. The active protein levels are dependent on the regulatory cascades. Because NACs regulate both development and stress responses in plants, in-depth knowledge about them has the potential to help guide future crop improvement studies.
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Affiliation(s)
- Iny Elizebeth Mathew
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Zhang Y, Li D, Wang Y, Zhou R, Wang L, Zhang Y, Yu J, Gong H, You J, Zhang X. Genome-wide identification and comprehensive analysis of the NAC transcription factor family in Sesamum indicum. PLoS One 2018; 13:e0199262. [PMID: 29927997 PMCID: PMC6013105 DOI: 10.1371/journal.pone.0199262] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/04/2018] [Indexed: 12/31/2022] Open
Abstract
The NAM, ATAF1/2, and CUC2 (NAC) family constitutes a large family of plant-specific transcription factors, involved in many aspects of physiological processes and a variety of abiotic stresses. There is little information concerning the NAC family in Sesamum indicum. In this study, 87 sesame NAC genes were identified and phylogenetically clustered into 12 groups with Arabidopsis NAC genes. A total of 83 SiNAC genes were distributed non-randomly on the 16 linkage groups in sesame. Four and 49 SiNACs were found to be tandemly and segmentally duplicated, respectively. Expression profiles of SiNAC genes in different tissues (root, stem, leaf, flower, seed, and capsule) and in response to drought and waterlogging stresses by using RNA-seq data demonstrated that 23 genes were highly expressed in all tissues, 18 and 31 SiNACs respond strongly to drought and waterlogging stresses, respectively. In addition, the expression of 30 SiNAC genes distributed in different subgroups was analyzed with quantitative real-time RT-PCR under cold, osmotic, and salt stresses, revealed that their expression patterns vary in response to abiotic stresses. SiNAC genes displayed diverse expression patterns among the different tissues and stress treatments, suggested that their contribution to plant growth and development in sesame and multiple stress resistance in sesame. In this study, NAC transcription factors were analyzed in sesame and some specific candidate SiNAC genes in response to abiotic stress for functional study were identified. This study provides valuable information to deepen our understanding of the abiotic stress responses by NAC transcription factors in sesame.
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Affiliation(s)
- Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yanyan Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huihui Gong
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (XZ); (JY)
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (XZ); (JY)
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Wagner S, Van Aken O, Elsässer M, Schwarzländer M. Mitochondrial Energy Signaling and Its Role in the Low-Oxygen Stress Response of Plants. PLANT PHYSIOLOGY 2018; 176:1156-1170. [PMID: 29298823 PMCID: PMC5813528 DOI: 10.1104/pp.17.01387] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 05/07/2023]
Abstract
Cellular responses to low-oxygen stress and to respiratory inhibitors share common mitochondrial energy signaling pathways.
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Affiliation(s)
- Stephan Wagner
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
| | | | - Marlene Elsässer
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
- Institute for Cellular and Molecular Botany (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
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Li W, Li X, Chao J, Zhang Z, Wang W, Guo Y. NAC Family Transcription Factors in Tobacco and Their Potential Role in Regulating Leaf Senescence. FRONTIERS IN PLANT SCIENCE 2018; 9:1900. [PMID: 30622549 PMCID: PMC6308388 DOI: 10.3389/fpls.2018.01900] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/07/2018] [Indexed: 05/20/2023]
Abstract
The NAC family is one of the largest families of plant-specific transcription factors (TFs) and NAC proteins play important regulatory roles in a variety of developmental and stress response processes in plants. Members of the NAC family TFs have been shown to be important regulators of leaf senescence in a number of plant species. Here we report the identification of the NAC family in tobacco (Nicotiana tabacum) and characterization of the potential role of some of the tobacco NAC TFs in regulating leaf senescence. A total of 154 NAC genes (NtNACs) were identified and clustered together with the Arabidopsis NAC family into fifteen groups (a-o). Transcriptome data analysis followed by qRT-PCR validation showed that the majority of the senescence-up-regulated NtNACs fall into subgroups NAC-b and f. A number of known senescence regulators from Arabidopsis also belong to these two subgroups. Among these senescence-up-regulated NtNACs, NtNAC080, a close homolog of AtNAP, is a positive regulator of leaf senescence. Overexpression of NtNAC080 caused early senescence in Arabidopsis leaves and NtNAC080 mutation induced by Cas9/gRNA in tobacco led to delayed leaf senescence.
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Melo BP, Fraga OT, Silva JCF, Ferreira DO, Brustolini OJB, Carpinetti PA, Machado JPB, Reis PAB, Fontes EPB. Revisiting the Soybean GmNAC Superfamily. FRONTIERS IN PLANT SCIENCE 2018; 9:1864. [PMID: 30619426 PMCID: PMC6305603 DOI: 10.3389/fpls.2018.01864] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/04/2018] [Indexed: 05/07/2023]
Abstract
The NAC (NAM, ATAF, and CUC) genes encode transcription factors involved with the control of plant morph-physiology and stress responses. The release of the last soybean (Glycine max) genome assembly (Wm82.a2.v1) raised the possibility that new NAC genes would be present in the soybean genome. Here, we interrogated the last version of the soybean genome against a conserved NAC domain structure. Our analysis identified 32 putative novel NAC genes, updating the superfamily to 180 gene members. We also organized the genes in 15 phylogenetic subfamilies, which showed a perfect correlation among sequence conservation, expression profile, and function of orthologous Arabidopsis thaliana genes and NAC soybean genes. To validate our in silico analyses, we monitored the stress-mediated gene expression profiles of eight new NAC-genes by qRT-PCR and monitored the GmNAC senescence-associated genes by RNA-seq. Among ER stress, osmotic stress and salicylic acid treatment, all the novel tested GmNAC genes responded to at least one type of stress, displaying a complex expression profile under different kinetics and extension of the response. Furthermore, we showed that 40% of the GmNACs were differentially regulated by natural leaf senescence, including eight (8) newly identified GmNACs. The developmental and stress-responsive expression profiles of the novel NAC genes fitted perfectly with their phylogenetic subfamily. Finally, we examined two uncharacterized senescence-associated proteins, GmNAC065 and GmNAC085, and a novel, previously unidentified, NAC protein, GmNAC177, and showed that they are nuclear localized, and except for GmNAC065, they display transactivation activity in yeast. Consistent with a role in leaf senescence, transient expression of GmNAC065 and GmNAC085 induces the appearance of hallmarks of leaf senescence, including chlorophyll loss, leaf yellowing, lipid peroxidation and accumulation of H2O2. GmNAC177 was clustered to an uncharacterized subfamily but in close proximity to the TIP subfamily. Accordingly, it was rapidly induced by ER stress and by salicylic acid under late kinetic response and promoted cell death in planta. Collectively, our data further substantiated the notion that the GmNAC genes display functional and expression profiles consistent with their phylogenetic relatedness and established a complete framework of the soybean NAC superfamily as a foundation for future analyses.
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Affiliation(s)
- Bruno P. Melo
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otto T. Fraga
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - José Cleydson F. Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Dalton O. Ferreira
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otávio J. B. Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Paola A. Carpinetti
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Pedro A. B. Reis
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elizabeth P. B. Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
- *Correspondence: Elizabeth P. B. Fontes
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Song J, Zhou Y, Zhang J, Zhang K. Structural, expression and evolutionary analysis of the non-specific phospholipase C gene family in Gossypium hirsutum. BMC Genomics 2017; 18:979. [PMID: 29258435 PMCID: PMC5738194 DOI: 10.1186/s12864-017-4370-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nonspecific phospholipase C (NPC), which belongs to a phospholipase C subtype, is a class of phospholipases that hydrolyzes the primary membrane phospholipids, such as phosphatidylcholine, to yield sn-1, 2-diacylglycerol and a phosphorylated head-group. NPC plays multiple physiological roles in lipid metabolism and signaling in plants. To fully understand the putative roles of NPC genes in upland cotton, we cloned NPC genes from Gossypium hirsutum and carried out structural, expression and evolutionary analysis. RESULTS Eleven NPC genes were cloned from G. hirsutum, which were found on chromosomes scaffold269.1, D03, A07, D07, A08, D11, and scaffold3511_A13. All GhNPCs had typical phosphoesterase domains and have hydrolase activity that acts on ester bonds. GhNPCs were annotated as phospholipase C, which was involved in glycerophospholipid metabolism, ether lipid metabolism, and biosynthesis of secondary metabolites. These GhNPCs showed differential expression patterns in distinct plant tissues and in response to various types of stress (low-phosphate, salt, drought, and abscisic acid). They also had different types and numbers of cis-element. GhNPCs could be classified into four subfamilies. Four pairs of GhNPCs were generated by whole-genome duplication and they underwent purifying selection. CONCLUSIONS Our results suggested that GhNPCs are involved in regulating key abiotic stress responses and ABA signaling transduction, and they may have various functional roles for different members under complex abiotic stress conditions. Functional divergence may be the evolutionary driving force for the retention of four pairs of duplicate NPCs. Our analysis provides a solid foundation for the further functional characterization of the GhNPC gene family, and leads to potential applications in the genetic improvement of cotton cultivars.
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Affiliation(s)
- Jiuling Song
- Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Yonghe Zhou
- School of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Juren Zhang
- Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Kewei Zhang
- Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Science, Shandong University, Jinan, Shandong, China.
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miRNA mediated regulation of NAC transcription factors in plant development and environment stress response. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Tian H, Wang X, Guo H, Cheng Y, Hou C, Chen JG, Wang S. NTL8 Regulates Trichome Formation in Arabidopsis by Directly Activating R3 MYB Genes TRY and TCL1. PLANT PHYSIOLOGY 2017; 174:2363-2375. [PMID: 28649093 PMCID: PMC5543959 DOI: 10.1104/pp.17.00510] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/19/2017] [Indexed: 05/17/2023]
Abstract
The NAM, ATAF1/2, and CUC (NAC) are plant-specific transcription factors that regulate multiple aspects of plant growth and development and plant response to environmental stimuli. We report here the identification of NTM1-LIKE8 (NTL8), a membrane-associated NAC transcription factor, as a novel regulator of trichome formation in Arabidopsis (Arabidopsis thaliana). From an activation-tagged Arabidopsis population, we identified a dominant, gain-of-function mutant with glabrous inflorescence stem. By using plasmid rescue and RT-PCR analyses, we found that NTL8 was tagged; thus, the mutant was named ntl8-1 Dominant (ntl8-1D). Recapitulation experiment further confirmed that the phenotype observed in the ntl8-1D mutant was caused by elevated expression of NTL8 Quantitative RT-PCR results showed that the expression level of the single-repeat R3 MYB genes TRIPTYCHON (TRY) and TRICHOMELESS1 (TCL1) was elevated in the ntl8-1D mutant. Genetic analyses demonstrated that NTL8 acts upstream of TRY and TCL1 in the regulation of trichome formation. When recruited to the promoter region of the reporter gene Gal4:GUS by a fused GAL4 DNA-binding domain, NTL8 activated the expression of the reporter gene. Chromatin immunoprecipitation results indicated that TRY and TCL1 are direct targets of NTL8. However, NTL8 did not interact with SQUAMOSA PROMOTER BINDING PROTEIN LIKE9, another transcription factor that regulates the expression of TRY and TCL1, in yeast and plant cells. Taken together, our results suggest that NTL8 negatively regulates trichome formation in Arabidopsis by directly activating the expression of TRY and TCL1.
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Affiliation(s)
- Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Xianling Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Hongyan Guo
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Yuxin Cheng
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Chunjiang Hou
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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Shiriga K, Sharma R, Kumar K, Yadav SK, Hossain F, Thirunavukkarasu N. Genome-wide identification and expression pattern of drought-responsive members of the NAC family in maize. Meta Gene 2014; 2:407-417. [PMID: 25606426 DOI: 10.1007/s00344-019-09984-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/09/2014] [Accepted: 05/03/2014] [Indexed: 05/28/2023] Open
Abstract
NAC proteins are plant-specific transcription factors (TFs). Although they play a pivotal role in regulating distinct biological processes, TFs in maize are yet to be investigated comprehensively. Within the maize genome, we identified 152 putative NAC domain-encoding genes (ZmNACs), including eight membrane-bound members, by systematic sequence analysis and physically mapped them onto ten chromosomes of maize. In silico analysis of the ZmNACs and comparison with similar genes in other plants such as Arabidopsis, rice, and soybean, revealed a similar NAC sequence architecture. Phylogenetically, the ZmNACs were arranged into six distinct subgroups (I-VI) possessing conserved motifs. Phylogenetic analysis using stress-related NAC TFs from Arabidopsis, rice, and soybean as seeding sequences identified 24 of the 152 ZmNACs (all from Group II) as putative stress-responsive genes, including one dehydration-responsive ZmSNAC1 gene reported earlier. One drought-tolerant genotype (HKI577) and one susceptible genotype (PC13T-3) were used for studying the expression pattern of the NAC genes during drought stress. qRT-PCR based expression profiles of 11 genes predicted to be related to stress confirmed strong differential gene expression during drought stress. Phylogenetic analyses revealed that ZmNAC18, ZmNAC51, ZmNAC145, and ZmNAC72, which were up-regulated in the tolerant genotype and down-regulated in the susceptible genotype, belonged to the same group to which also belong other drought-responsive genes, namely SNAC1, OsNAC6, ANAC019, and ANAC055, which act as a transcriptional activator and are strongly induced under stress from various abiotic sources. Differentially expressed ZmNAC genes, alone or in combination with each other or with other type(s) of TFs, may control the general cellular machinery and regulate stress-responsive downstream genes. Alternatively, they may serve as a platform to regulate a broad set of genes, which are subsequently fine-tuned by specific regulators. This genome-wide identification and expression profiling opens new avenues for systematic functional analysis of new members of the NAC gene family, which may be exploited in developing lines that are better adapted to drought.
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Affiliation(s)
- Kaliyugam Shiriga
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India ; School of Life Sciences, Singhania University, Rajasthan 333515, India
| | - Rinku Sharma
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Krishan Kumar
- School of Life Sciences, Singhania University, Rajasthan 333515, India
| | - Shiv Kumar Yadav
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Firoz Hossain
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
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