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Imani Asl E, Soorni A, Mehrabi R. Genome-wide characterization, functional analysis, and expression profiling of the Aux/IAA gene family in spinach. BMC Genomics 2024; 25:567. [PMID: 38840073 PMCID: PMC11155116 DOI: 10.1186/s12864-024-10467-z] [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: 01/14/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The auxin/indole-3-acetic acid (Aux/IAA) gene family is a crucial element of the auxin signaling pathway, significantly influencing plant growth and development. Hence, we conducted a comprehensive investigation of Aux/IAAs gene family using the Sp75 and Monoe-Viroflay genomes in spinach. RESULTS A total of 24 definitive Aux/IAA genes were identified, exhibiting diverse attributes in terms of amino acid length, molecular weight, and isoelectric points. This diversity underscores potential specific roles within the family, such as growth regulation and stress response. Structural analysis revealed significant variations in gene length and molecular weight. These variations indicate distinct roles within the Aux/IAA gene family. Chromosomal distribution analysis exhibited a dispersed pattern, with chromosomes 4 and 1 hosting the highest and lowest numbers of Aux/IAA genes, respectively. Phylogenetic analysis grouped the identified genes into distinct clades, revealing potential evolutionary relationships. Notably, the phylogenetic tree highlighted specific gene clusters suggesting shared genetic ancestry and potential functional synergies within spinach. Expression analysis under NAA treatment unveiled gene-specific and time-dependent responses, with certain genes exhibiting distinct temporal expression patterns. Specifically, SpoIAA5 displayed a substantial increase at 2 h post-NAA treatment, while SpoIAA7 and SpoIAA9 demonstrated continuous rises, peaking at the 4-hour time point. CONCLUSIONS These observations indicate a complex interplay of gene-specific and temporal regulation in response to auxin. Moreover, the comparison with other plant species emphasized both shared characteristics and unique features in Aux/IAA gene numbers, providing insights into the evolutionary dynamics of this gene family. This comprehensive characterization of Aux/IAA genes in spinach not only establishes the foundation for understanding their specific functions in spinach development but also provides a valuable resource for experimental validation and further exploration of their roles in the intricate network of auxin signaling pathways.
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Affiliation(s)
- Erfan Imani Asl
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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2
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Feng S, Li N, Chen H, Liu Z, Li C, Zhou R, Zhang Y, Cao R, Ma X, Song X. Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants. MOLECULAR HORTICULTURE 2024; 4:13. [PMID: 38589963 PMCID: PMC11003162 DOI: 10.1186/s43897-024-00090-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/03/2024] [Indexed: 04/10/2024]
Abstract
The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.
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Affiliation(s)
- Shuyan Feng
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Nan Li
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Huilong Chen
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhuo Liu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Chunjin Li
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus, 8200, Denmark
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
- College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066600, China.
| | - Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
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Hakeem MK, Elangovan S, Rafi M, George S, Shah I, Amiri KMA. Advancing Antibiotic Residue Analysis: LC-MS/MS Methodology for Ticarcillin Degradation Products in Tomato Leaves. Antibiotics (Basel) 2024; 13:133. [PMID: 38391519 PMCID: PMC10886401 DOI: 10.3390/antibiotics13020133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
The indiscriminate use of antibiotics in agriculture has raised concerns about antibiotic residues in food products, necessitating robust analytical methods for detection and quantification. In this study, our primary aim was to develop a robust and advanced liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology specifically designed for the accurate quantification of ticarcillin degradation products in tomato leaves. The choice of ticarcillin as the target analyte stems from its frequent use in agriculture and the potential formation of degradation products, which can pose a threat to food safety. The use of tomatoes as the target sample matrix in this study is justified by their significance in human diets, their widespread cultivation, and their suitability as a model for assessing antibiotic residue dynamics in diverse agricultural environments. By optimizing the MS/MS parameters, the study successfully demonstrates the practicality and reliability of the employed LC-MS/MS method in accurately assessing ticarcillin degradation product (Thiophene-2-Acetic acid and Thiophene-3-Acetic acid) levels. The chromatographic separation was achieved using a specialized column, ensuring high resolution and sensitivity in detecting analytes. Multiple reaction monitoring (MRM) data acquisition was employed to enhance the selectivity and accuracy of the analysis. The developed method exhibited excellent linearity and precision, meeting the stringent requirements for antibiotic residue analysis in complex matrices. Key outcomes of this study include the successful identification and quantification of ticarcillin and its degradation products in tomato leaves, providing crucial insights into the fate of this antibiotic in agricultural settings. The methodology's applicability was further demonstrated by analyzing real-world samples, highlighting its potential for routine monitoring and ensuring food safety compliance. In summary, our study constitutes a noteworthy advancement in the domain of antibiotic residue analysis, offering a reliable method for quantifying ticarcillin degradation products in tomato leaves. The optimized parameters and MRM-based LC-MS/MS approach enhance the precision and sensitivity of the analysis, opening up opportunities for further studies in the assessment of antibiotic residues in agricultural ecosystems.
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Affiliation(s)
- Muhammad K Hakeem
- Department of Chemistry, College of Science, United Arab Emirates University (UAEU), Al-Ain P.O. Box 15551, United Arab Emirates
| | - Sampathkumar Elangovan
- Department of Chemistry, College of Science, United Arab Emirates University (UAEU), Al-Ain P.O. Box 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Suja George
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University (UAEU), Al-Ain P.O. Box 15551, United Arab Emirates
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Wakeman A, Bennett T. Auxins and grass shoot architecture: how the most important hormone makes the most important plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6975-6988. [PMID: 37474124 PMCID: PMC10690731 DOI: 10.1093/jxb/erad288] [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: 03/05/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023]
Abstract
Cereals are a group of grasses cultivated by humans for their grain. It is from these cereal grains that the majority of all calories consumed by humans are derived. The production of these grains is the result of the development of a series of hierarchical reproductive structures that form the distinct shoot architecture of the grasses. Being spatiotemporally complex, the coordination of grass shoot development is tightly controlled by a network of genes and signals, including the key phytohormone auxin. Hormonal manipulation has therefore been identified as a promising potential approach to increasing cereal crop yields and therefore ultimately global food security. Recent work translating the substantial body of auxin research from model plants into cereal crop species is revealing the contribution of auxin biosynthesis, transport, and signalling to the development of grass shoot architecture. This review discusses this still-maturing knowledge base and examines the possibility that changes in auxin biology could have been a causative agent in the evolution of differences in shoot architecture between key grass species, or could underpin the future selective breeding of cereal crops.
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Affiliation(s)
- Alex Wakeman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Tom Bennett
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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Wang M, Feng G, Yang Z, Wu J, Liu B, Xu X, Nie G, Huang L, Zhang X. Genome-Wide Characterization of the Aux/IAA Gene Family in Orchardgrass and a Functional Analysis of DgIAA21 in Responding to Drought Stress. Int J Mol Sci 2023; 24:16184. [PMID: 38003372 PMCID: PMC10671735 DOI: 10.3390/ijms242216184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Drought stress is an important factor that reduces plant biomass production and quality. As one of the most important economic forage grasses, orchardgrass (Dactylis glomerata) has high drought tolerance. Auxin/indole-3-acetic acid (Aux/IAA) is one of the early responsive gene families of auxin and plays a key role in the response to drought stress. However, the characteristics of the Aux/IAA gene family in orchardgrass and their potential function in responding to drought stress remain unclear. Here, 30 Aux/IAA members were identified in orchardgrass. Segmental duplication may be an important driving force in the evolution of the Aux/IAA gene family in orchardgrass. Some Aux/IAA genes were induced by IAA, drought, salt, and temperature stresses, implying that these genes may play important roles in responding to abiotic stresses. Heterologous expression in yeast revealed that DgIAA21 can reduce drought tolerance. Similarly, the overexpression of DgIAA21 also reduced drought tolerance in transgenic Arabidopsis, which was supported by lower total chlorophyll content and relative water content as well as higher relative electrolyte leakage and malondialdehyde content (MDA) than Col-0 plants under drought conditions. The results of this study provided valuable insight into the function of DgIAAs in response to drought stress, which can be further used to improve forage grass breeding programs.
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Affiliation(s)
| | | | | | | | | | | | | | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.W.); (G.F.); (Z.Y.)
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.W.); (G.F.); (Z.Y.)
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6
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Si C, Zeng D, da Silva JAT, Qiu S, Duan J, Bai S, He C. Genome-wide identification of Aux/IAA and ARF gene families reveal their potential roles in flower opening of Dendrobium officinale. BMC Genomics 2023; 24:199. [PMID: 37055721 PMCID: PMC10099678 DOI: 10.1186/s12864-023-09263-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/21/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND The auxin indole-3-acetic acid (IAA) is a vital phytohormone that influences plant growth and development. Our previous work showed that IAA content decreased during flower development in the medicinally important orchid Dendrobium officinale, while Aux/IAA genes were downregulated. However, little information about auxin-responsive genes and their roles in D. officinale flower development exists. RESULTS This study validated 14 DoIAA and 26 DoARF early auxin-responsive genes in the D. officinale genome. A phylogenetic analysis classified the DoIAA genes into two subgroups. An analysis of cis-regulatory elements indicated that they were related by phytohormones and abiotic stresses. Gene expression profiles were tissue-specific. Most DoIAA genes (except for DoIAA7) were sensitive to IAA (10 μmol/L) and were downregulated during flower development. Four DoIAA proteins (DoIAA1, DoIAA6, DoIAA10 and DoIAA13) were mainly localized in the nucleus. A yeast two-hybrid assay showed that these four DoIAA proteins interacted with three DoARF proteins (DoARF2, DoARF17, DoARF23). CONCLUSIONS The structure and molecular functions of early auxin-responsive genes in D. officinale were investigated. The DoIAA-DoARF interaction may play an important role in flower development via the auxin signaling pathway.
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Affiliation(s)
- Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Shengxiang Qiu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Song Bai
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
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7
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Yang Z, Dong D, Qi Z, Jia C, Han L, Chao Y. Genome-wide identification, expression analysis, and transcriptome analysis of the IAA gene family in Zoysia japonica. Mol Biol Rep 2023; 50:4385-4394. [PMID: 36961632 DOI: 10.1007/s11033-022-08154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/23/2022] [Indexed: 03/25/2023]
Abstract
BACKGROUND AUX/IAA is an essential signaling molecule and has great physiological importance in various plants, but its function in Zoysia japonica remains unknown. METHODS AND RESULTS Genome-wide identification and analysis of AUX/IAA genes used bioinformatics methods to investigate the ZjIAA genes' expression of exogenous IAA hydroponics treatment for 2 h by qRT-PCR, control and exogenous IAA treated zoysia were subjected to transcriptome sequencing. ZjIAAs were distributed across the 13 subfamilies by phylogenetic analysis with Oryza sativa and Arabidopsis thaliana. Multiple sequence alignment revealed that the majority of genes were non-canonical ZjIAAs with incomplete domain. The optimal growth concentration of the IAA hormone was 0.05 mM, and the qRT-PCR analysis revealed that eight ZjIAAs were differentially expressed, with seven genes considerably upregulating and one gene significantly downregulating. The result of transcriptome sequencing revealed that 515 differentially expressed genes (DEGs) were identified, with 344 upregulated genes and 171 downregulated genes. A total of 18 genes were annotated as involved in the plant hormone signal transduction pathway. And 8 ZjIAAs exhibited distinct expressions, 7 upregulated, and only one downregulated, according to the qRT-PCR study. CONCLUSIONS Genome-wide identification and analysis increased the understanding of the evolution and function of the IAA family in zoysia. DEGs of control and treatment with 0.05 mM exogenous IAA hormone were investigated by transcriptome sequencing. ZjIAAs had substantial variations in the expression of associated genes, with the majority of genes upregulated and 18 genes implicated in plant hormone signal transduction.
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Affiliation(s)
- Zhuoxiong Yang
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Di Dong
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Zewen Qi
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Chenyan Jia
- Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd, Hohhot, 010010, Inner Mongolia, China
| | - Liebao Han
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
| | - Yuehui Chao
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
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Chaudhary C, Sharma N, Khurana P. Genome-wide identification of Aux/IAA and ARF gene families in bread wheat (Triticum aestivum L.). PROTOPLASMA 2023; 260:257-270. [PMID: 35606614 DOI: 10.1007/s00709-022-01773-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/11/2022] [Indexed: 05/12/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important food crops in the world. Somatic embryogenesis is an event that is triggered by the presence of auxin hormone for the induction of somatic cells to get converted to embryonic cells. Somatic embryogenesis represents the most important process of totipotency of plants. The role of auxins is widely understood during various stages of embryogenesis including polarity establishment, de-differentiation, re-differentiations, and morphogenesis. Many of the Aux/IAAs and ARFs which are part of auxin signaling components have been identified to play various roles during embryogenesis. In this analysis, the Aux/IAAs and ARFs of T. aestivum have been analyzed at the genome-scale; their structure, function, and evolutionary relatedness were determined. Several Aux/IAAs and ARFs components of T. aestivum have been found to exclusively regulate axis formation, meristem commitment, and other re-differentiation processes by differential expression studies.
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Affiliation(s)
- Chanderkant Chaudhary
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Nikita Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Genome-Wide Identification and Expression Analysis of the Aux/IAA Gene Family of the Drumstick Tree ( Moringa oleifera Lam.) Reveals Regulatory Effects on Shoot Regeneration. Int J Mol Sci 2022; 23:ijms232415729. [PMID: 36555370 PMCID: PMC9779525 DOI: 10.3390/ijms232415729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Auxin plays a critical role in organogenesis in plants. The classical auxin signaling pathway holds that auxin initiates downstream signal transduction by degrading Aux/IAA transcription repressors that interact with ARF transcription factors. In this study, 23 MoIAA genes were identified in the drumstick tree genome. All MoIAA genes were located within five subfamilies based on phylogenetic evolution analysis; the gene characteristics and promoter cis-elements were also analyzed. The protein interaction network between the MoIAAs with MoARFs was complex. The MoIAA gene family responded positively to NAA treatment, exhibiting different patterns and degrees, notably for MoIAA1, MoIAA7 and MoIAA13. The three genes expressed and functioned in the nucleus; only the intact encoding protein of MoIAA13 exhibited transcriptional activation activity. The shoot regeneration capacity in the 35S::MoIAA13-OE transgenic line was considerably lower than in the wild type. These results establish a foundation for further research on MoIAA gene function and provide useful information for improved tissue culture efficiency and molecular breeding of M. oleifera.
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Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism. Proc Natl Acad Sci U S A 2022; 119:e2201350119. [PMID: 35881796 PMCID: PMC9351459 DOI: 10.1073/pnas.2201350119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The growth angle roots adopt are critical for capturing soil resources, such as nutrients and water. Despite its agronomic importance, few regulatory genes have been identified in crops. Here we identify the root angle regulatory gene ENHANCED GRAVITROPISM 1 (EGT1) in barley. Strikingly, mutants lacking EGT1 exhibit a steeper angle in every root class. EGT1 appears to function as a component of an antigravitropic offset mechanism that regulates tissue stiffness, which impacts final root growth angle. EGT1 is a hot spot for selection as natural allelic variation within a conserved Tubby domain that is linked with steeper root angle. Analogous EGT1-dependent regulation of root angle in wheat demonstrates broad significance of EGT1 for trait improvement in cereal crops. Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus antigravitropic offset (AGO) mechanisms. Here we report a root angle regulatory gene termed ENHANCED GRAVITROPISM1 (EGT1) that encodes a putative AGO component, whose loss-of-function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes an F-box and Tubby domain-containing protein that is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wild-type. Transcript profiling revealed Hvegt1 roots deregulate reactive oxygen species (ROS) homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shows that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic force microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wild-type. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery’s known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.
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Gao Y, Quan S, Lyu B, Tian T, Liu Z, Nie Z, Qi S, Jia J, Shu J, Groot E, Wu J, Wang Y. Barley transcription factor HvNLP2 mediates nitrate signaling and affects nitrogen use efficiency. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:770-783. [PMID: 34050753 DOI: 10.1093/jxb/erab245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Plants have evolved complex mechanisms to adapt to the changing nitrogen levels in the environment. In Arabidopsis, more than a dozen nitrate signaling regulatory genes have been characterized, including the NODULE INCEPTION-LIKE PROTEIN (AtNLP) genes, which play essential roles in nitrate signaling. However, whether NLP genes in the Triticeae crops are involved in nitrate regulation and nitrogen use efficiency (NUE) remains unknown. Here, we isolated a barley (Hordeum vulgare L.) mutant, hvnlp2-1, from a TILLING (Targeting Local Lesions IN Genomes) population and constructed two RNAi lines, hvnlp2-2 and hvnlp2-3, to study the function of HvNLP2. The expression of the nitrate-responsive genes was substantially inhibited after nitrate treatment in the hvnlp2 mutants, indicating that HvNLP2 controls nitrate signaling. Nitrate content was significantly higher in the hvnlp2 mutants, which may result from the decreased assimilation of nitrogen caused by reduced nitrate reductase activity and expression of nitrate assimilatory genes. HvNLP2 is localized to the nucleus in the presence of nitrate. Further investigation showed that HvNLP2 binds to and activates the nitrate-responsive cis-elements. Moreover, hvnlp2 exhibited reduced biomass, seed yield, and NUE. Therefore, HvNLP2 controls nitrate signaling and plays an important role in NUE.
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Affiliation(s)
- Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Bo Lyu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Tian Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zhiguang Liu
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zhentian Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jingbo Jia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jing Shu
- College of Agriculture Science and Technology, Shandong Agriculture and Engineering University, Jinan, Shandong, China
| | - Edwin Groot
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
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Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant. Genes (Basel) 2021; 13:genes13010024. [PMID: 35052364 PMCID: PMC8775021 DOI: 10.3390/genes13010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.
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Melino VJ, Plett DC, Bendre P, Thomsen HC, Zeisler-Diehl VV, Schreiber L, Kronzucker HJ. Nitrogen depletion enhances endodermal suberization without restricting transporter-mediated root NO 3- influx. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153334. [PMID: 33373827 DOI: 10.1016/j.jplph.2020.153334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/21/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Roots vary their permeability to aid radial transport of solutes towards xylem vessels in response to nutritional cues. Nitrogen (N) depletion was previously shown to induce early suberization of endodermal cell walls and reduce hydraulic conductivity of barley roots suggesting reduced apoplastic transport of ions (Armand et al., 2019). Suberization may also limit transcellular ion movement by blocking access to transporters (Barberon et al., 2016). The aim of this study was to confirm that N depletion induced suberization in the roots of barley and demonstrate that this was a specific effect in response to NO3- depletion. Furthermore, in roots with early and enhanced suberization, we assessed their ability for transporter-mediated NO3- influx. N depletion induced lateral root elongation and early and enhanced endodermal suberization of the seminal root of each genotype. Both root to shoot NO3- translocation and net N uptake was half that of plants supplied with steady-state NO3-. Genes with predicted functions in suberin synthesis (HvHORST) and NO3- transport (HvNRT2.2) were induced under N-deplete conditions. N-deplete roots had a higher capacity for high-affinity NO3- influx in early suberized roots than under optimal NO3-. In conclusion, NO3- depletion induced early and enhanced suberization in the roots of barley, however, suberization did not restrict transcellular NO3- transport.
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Affiliation(s)
- V J Melino
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, 3010, Australia; Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - D C Plett
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, 3010, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia.
| | - P Bendre
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - H C Thomsen
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia; Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark.
| | - V V Zeisler-Diehl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, 53115, Bonn, Germany.
| | - L Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, 53115, Bonn, Germany.
| | - H J Kronzucker
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, 3010, Australia; Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Li T, Pan W, Yuan Y, Liu Y, Li Y, Wu X, Wang F, Cui L. Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:684619. [PMID: 34335653 PMCID: PMC8319850 DOI: 10.3389/fpls.2021.684619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/23/2021] [Indexed: 05/17/2023]
Abstract
Plant mitochondrial transcription termination factor (mTERF) family regulates organellar gene expression (OGE) and is functionally characterized in diverse species. However, limited data are available about its functions in the agriculturally important cereal barley (Hordeum vulgare L.). In this study, we identified 60 mTERFs in the barley genome (HvmTERFs) through a comprehensive search against the most updated barley reference genome, Morex V2. Then, phylogenetic analysis categorized these genes into nine subfamilies, with approximately half of the HvmTERFs belonging to subfamily IX. Members within the same subfamily generally possessed conserved motif composition and exon-intron structure. Both segmental and tandem duplication contributed to the expansion of HvmTERFs, and the duplicated gene pairs were subjected to strong purifying selection. Expression analysis suggested that many HvmTERFs may play important roles in barley development (e.g., seedlings, leaves, and developing inflorescences) and abiotic stresses (e.g., cold, salt, and metal ion), and HvmTERF21 and HvmTERF23 were significant induced by various abiotic stresses and/or phytohormone treatment. Finally, the nucleotide diversity was decreased by only 4.5% for HvmTERFs during the process of barley domestication. Collectively, this is the first report to characterize HvmTERFs, which will not only provide important insights into further evolutionary studies but also contribute to a better understanding of the potential functions of HvmTERFs and ultimately will be useful in future gene functional studies.
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Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Yiyuan Yuan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Ying Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaoyu Wu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Fei Wang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Licao Cui
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Su Y, He H, Wang P, Ma Z, Mao J, Chen B. Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in apple (Malus domestica). Gene 2020; 768:145302. [PMID: 33181252 DOI: 10.1016/j.gene.2020.145302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/18/2022]
Abstract
Auxin is a necessary phytohormone for fruit development, accompanying the whole process of fruit growth and development. The Aux/IAA gene family is one of the early auxin-responsive gene families. At present, there were few reports involved in Aux/IAA genes in the fruit, especially in apple. In our study, we identified 42 MdAux/IAAs, phylogenetic analysis showed that Aux/IAA proteins from apple, tomato, and strawberry were clustered into 5 groups, 42 MdAux/IAAs randomly distributed on 13 chromosomes. Additionally, a comprehensive analysis of Aux/IAA gene family was completed, including gene structures, conserved motifs, phylogenetic analysis, chromosome mapping, orthologous identification, selection pressure analyses, synteny analysis, and protein interaction. We also tested the expression of MdAux/IAAs in different tissues and fruit development stages using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), we found that the most members of Aux/IAA showed higher expression in seeds compared within stem and leaves, indicating they may play a role in regulating fruit development. We also declared that the expression of Aux/IAA gene was not consistent in the pericarp and seeds at the same developmental stage, 3 MdAux/IAAs of the pericarp were upregulated over 20-fold at 90 d and 5 MdAux/IAAs of the seeds were upregulated over 40-fold at 90 d. It was MdAux/IAA23 that showed extreme up-regulated expression in both pericarp and seeds. This study proved that the Aux/IAA gene families may perform a different function in apple fruit development and ripening, more importantly, it provided a foundation for further exploring the biological function of these MdAux/IAAs.
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Affiliation(s)
- Yanli Su
- Department of Horticulture, Gansu Agricultural University, Lanzhou 730000, China
| | - Honghong He
- Department of Horticulture, Gansu Agricultural University, Lanzhou 730000, China
| | - Ping Wang
- Department of Horticulture, Gansu Agricultural University, Lanzhou 730000, China
| | - Zonghuan Ma
- Department of Horticulture, Gansu Agricultural University, Lanzhou 730000, China
| | - Juan Mao
- Department of Horticulture, Gansu Agricultural University, Lanzhou 730000, China
| | - Baihong Chen
- Department of Horticulture, Gansu Agricultural University, Lanzhou 730000, China.
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