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Xi R, Liu H, Chen Y, Zhuang H, Han H, Wang H, Wang Q, Li N. Genome-Wide Characterization of Tomato FAD Gene Family and Expression Analysis under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:3818. [PMID: 38005715 PMCID: PMC10675527 DOI: 10.3390/plants12223818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023]
Abstract
The fatty acid desaturase (FAD) gene family plays a crucial regulatory role in the resistance process of plant biomembranes. To understand the role of FADs in tomato growth and development, this study identified and analyzed the tomato FAD gene family based on bioinformatics analysis methods. In this study, 26 SlFADs were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the SlFAD gene family was divided into six branches, and the exon-intron composition and conserved motifs of SlFADs clustered in the same branch were quite conservative. Several hormone and stress response elements in the SlFAD promoter suggest that the expression of SlFAD members is subject to complex regulation; the construction of a tomato FAD protein interaction network found that SlFAD proteins have apparent synergistic effects with SPA and GPAT proteins. qRT-PCR verification results show that SlFAD participates in the expression of tomato root, stem, and leaf tissues; SlFAD8 is mainly highly expressed in leaves; SlFAD9 plays a vital role in response to salt stress; and SlFAB5 regulates all stages of fruit development under the action of exogenous hormones. In summary, this study provides a basis for a systematic understanding of the SlFAD gene family. It provides a theoretical basis for in-depth research on the functional characteristics of tomato SlFAD genes.
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Affiliation(s)
- Rui Xi
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Huifang Liu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Yijia Chen
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hongmei Zhuang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Hongwei Han
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Hao Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Qiang Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
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Waheed S, Liang F, Zhang M, He D, Zeng L. High-Throughput Sequencing Reveals Novel microRNAs Involved in the Continuous Flowering Trait of Longan ( Dimocarpus longan Lour.). Int J Mol Sci 2022; 23:15565. [PMID: 36555206 PMCID: PMC9779457 DOI: 10.3390/ijms232415565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
A major determinant of fruit production in longan (Dimocarpus longan Lour.) is the difficulty of blossoming. In this study, high-throughput microRNA sequencing (miRNA-Seq) was carried out to compare differentially expressed miRNAs (DEmiRNAs) and their target genes between a continuous flowering cultivar 'Sijimi' (SJ), and a unique cultivar 'Lidongben' (LD), which blossoms only once in the season. Over the course of our study, 1662 known miRNAs and 235 novel miRNAs were identified and 13,334 genes were predicted to be the target of 1868 miRNAs. One conserved miRNA and 29 new novel miRNAs were identified as differently expressed; among them, 16 were upregulated and 14 were downregulated. Through the KEGG pathway and cluster analysis of DEmiRNA target genes, three critical regulatory pathways, plant-pathogen interaction, plant hormone signal transduction, and photosynthesis-antenna protein, were discovered to be strongly associated with the continuous flowering trait of the SJ. The integrated correlation analysis of DEmiRNAs and their target mRNAs revealed fourteen important flowering-related genes, including COP1-like, Casein kinase II, and TCP20. These fourteen flowering-related genes were targeted by five miRNAs, which were novel-miR137, novel-miR76, novel-miR101, novel-miR37, and csi-miR3954, suggesting these miRNAs might play vital regulatory roles in flower regulation in longan. Furthermore, novel-miR137 was cloned based on small RNA sequencing data analysis. The pSAK277-miR137 transgenic Arabidopsis plants showed delayed flowering phenotypes. This study provides new insight into molecular regulation mechanisms of longan flowering.
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Affiliation(s)
| | | | | | | | - Lihui Zeng
- Institute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Stafen CF, Kleine-Vehn J, Maraschin FDS. Signaling events for photomorphogenic root development. TRENDS IN PLANT SCIENCE 2022; 27:1266-1282. [PMID: 36057533 DOI: 10.1016/j.tplants.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.
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Affiliation(s)
- Cássia Fernanda Stafen
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Jürgen Kleine-Vehn
- Institute of Biology II, Chair of Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Felipe Dos Santos Maraschin
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Botânica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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Iqbal Z, Iqbal MS, Hashem A, Abd_Allah EF, Ansari MI. Plant Defense Responses to Biotic Stress and Its Interplay With Fluctuating Dark/Light Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:631810. [PMID: 33763093 PMCID: PMC7982811 DOI: 10.3389/fpls.2021.631810] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/08/2021] [Indexed: 05/24/2023]
Abstract
Plants are subjected to a plethora of environmental cues that cause extreme losses to crop productivity. Due to fluctuating environmental conditions, plants encounter difficulties in attaining full genetic potential for growth and reproduction. One such environmental condition is the recurrent attack on plants by herbivores and microbial pathogens. To surmount such attacks, plants have developed a complex array of defense mechanisms. The defense mechanism can be either preformed, where toxic secondary metabolites are stored; or can be inducible, where defense is activated upon detection of an attack. Plants sense biotic stress conditions, activate the regulatory or transcriptional machinery, and eventually generate an appropriate response. Plant defense against pathogen attack is well understood, but the interplay and impact of different signals to generate defense responses against biotic stress still remain elusive. The impact of light and dark signals on biotic stress response is one such area to comprehend. Light and dark alterations not only regulate defense mechanisms impacting plant development and biochemistry but also bestow resistance against invading pathogens. The interaction between plant defense and dark/light environment activates a signaling cascade. This signaling cascade acts as a connecting link between perception of biotic stress, dark/light environment, and generation of an appropriate physiological or biochemical response. The present review highlights molecular responses arising from dark/light fluctuations vis-à-vis elicitation of defense mechanisms in plants.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | | | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Bhatia C, Gaddam SR, Pandey A, Trivedi PK. COP1 mediates light-dependent regulation of flavonol biosynthesis through HY5 in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110760. [PMID: 33487344 DOI: 10.1016/j.plantsci.2020.110760] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 05/25/2023]
Abstract
Flavonols, a class of flavonoids, accumulate as protective agents in response to various stresses. Among various environmental stimuli, light is one of the factors regulating flavonol production. MYB12/11/111, members of the R2R3 MYBs family, regulates spatio-temporal flavonol accumulation in Arabidopsis. Although various studies indicate at the involvement of an E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5) in flavonoid biosynthesis in response to UV-B, the regulatory roles of these components under visible light are yet to be investigated. Here, we demonstrate that flavonol accumulation in Arabidopsis is light-regulated. Furthermore, our analysis suggests that MYB12 is a HY5-dependent light-inducible gene and plays a key role in the activation of the flavonol biosynthesis in response to light. Our results indicate the involvement of COP1 in the dark-dependent repression of MYB12 expression and flavonol accumulation. In addition, results also suggest that the effect of COP1 on MYB12 is indirect and is mediated through HY5, a direct transcriptional activator of the MYB12. Together these findings indicate that COP1 acts as a master negative regulator of flavonol biosynthesis in the dark.
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Affiliation(s)
- Chitra Bhatia
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Subhash Reddy Gaddam
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Prabodh Kumar Trivedi
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Favero DS, Lambolez A, Sugimoto K. Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:392-420. [PMID: 32986276 DOI: 10.1111/tpj.14996] [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: 07/16/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.
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Affiliation(s)
- David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Alice Lambolez
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
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Kathare PK, Xu X, Nguyen A, Huq E. A COP1-PIF-HEC regulatory module fine-tunes photomorphogenesis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:113-123. [PMID: 32652745 PMCID: PMC7959245 DOI: 10.1111/tpj.14908] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/30/2020] [Accepted: 06/22/2020] [Indexed: 05/23/2023]
Abstract
Light responses mediated by the photoreceptors play crucial roles in regulating different aspects of plant growth and development. An E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)1/SUPPRESSOR OF PHYA (SPA), one of the central repressors of photomorphogenesis, is critical for maintaining skotomorphogenesis. It targets several positive regulators of photomorphogenesis for degradation in darkness. Recently, we revealed that basic helix-loop-helix factors, HECATEs (HECs), function as positive regulators of photomorphogenesis by directly interacting and antagonizing the activity of another group of repressors called PHYTOCHROME-INTERACTING FACTORs (PIFs). It was also shown that HECs are partially degraded in the dark through the ubiquitin/26S proteasome pathway. However, the underlying mechanism of HEC degradation in the dark is still unclear. Here, we show that HECs also interact with both COP1 and SPA proteins in darkness, and that HEC2 is directly targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway. Moreover, COP1-mediated polyubiquitylation and degradation of HEC2 are enhanced by PIF1. Therefore, the ubiquitylation and subsequent degradation of HECs are significantly reduced in both cop1 and pif mutants. Consistent with this, the hec mutants partially suppress photomorphogenic phenotypes of both cop1 and pifQ mutants. Collectively, our work reveals that the COP1/SPA-mediated ubiquitylation and degradation of HECs contributes to the coordination of skoto/photomorphogenic development in plants.
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Affiliation(s)
| | | | | | - Enamul Huq
- Corresponding author: Enamul Huq, University of Texas at Austin, NHB 2.616, Stop A5000, 100 E. 24 St., Austin, TX 78712. Tel: 512-471-9848, Fax: 512-471-1218,
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Martínez-Garcia JF, Monte E. The International Symposium on Plant Photobiology 2019: a bright and colourful experience. PHYSIOLOGIA PLANTARUM 2020; 169:297-300. [PMID: 32602159 DOI: 10.1111/ppl.13127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Light is a key resource for plants as it fuels photosynthesis. It also provides essential information about their habitat. Thus, light tracking is of great importance to plants throughout their life cycle. To gain information about their light environment, plants possess light receptors that cover the perception of the complete light spectrum, including light invisible to the human eye (far-red and ultra-violet light). The information sensed by these photoreceptors is utilized for optimal growth during day-night cycles and in sub-optimal light conditions, such as shaded areas and high-light sun flecks. Plant photobiology research focuses on the perception of light by plants, their developmental adaptations to a changing light environment and the mechanistic and genetic basis of these adaptations. The International Symposium on Plant Photobiology (ISPP) is a biannual meeting where the world's leaders, as well as upcoming talents in the field, gather to share their latest results and discuss future directions. The past edition was held between June 3 and 8 of 2019 in the beautiful PRBB research park building on the seafront of the city of Barcelona (Spain). The ISPP2019 was organized by a gender-balanced committee formed by two junior (Lot Gommers and Jordi Moreno-Romero) and two senior researchers (Jamie F. Martínez-Garcia and Elena Monte).
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Affiliation(s)
- Jaime F Martínez-Garcia
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València, Spain
| | - Elena Monte
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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