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Abd-Hamid NA, Ismail I. An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling. JOURNAL OF PLANT PHYSIOLOGY 2024; 300:154299. [PMID: 38936241 DOI: 10.1016/j.jplph.2024.154299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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2
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Morton M, Fiene G, Ahmed HI, Rey E, Abrouk M, Angel Y, Johansen K, Saber NO, Malbeteau Y, Al-Mashharawi S, Ziliani MG, Aragon B, Oakey H, Berger B, Brien C, Krattinger SG, Mousa MAA, McCabe MF, Negrão S, Tester M, Julkowska MM. Deciphering salt stress responses in Solanum pimpinellifolium through high-throughput phenotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38970620 DOI: 10.1111/tpj.16894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 06/03/2024] [Indexed: 07/08/2024]
Abstract
Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium diversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance in S. pimpinellifolium and lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.
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Affiliation(s)
- Mitchell Morton
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gabriele Fiene
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Elodie Rey
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yoseline Angel
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, Maryland, USA
| | - Kasper Johansen
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Noha O Saber
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yoann Malbeteau
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Samir Al-Mashharawi
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Matteo G Ziliani
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Hydrosat S.à r.l., 9 Rue du Laboratoire, Luxembourg City, 1911, Luxembourg
| | - Bruno Aragon
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Helena Oakey
- Robinson Institute, University of Adelaide, Adelaide, Australia
| | - Bettina Berger
- Australian Plant Phenomics Facility, University of Adelaide, Urrbrae, Australia
| | - Chris Brien
- Australian Plant Phenomics Facility, University of Adelaide, Urrbrae, Australia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Magdi A A Mousa
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah, 80208, Saudi Arabia
- Department of Vegetable Crops, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Matthew F McCabe
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Sónia Negrão
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- University College, Dublin, Republic of Ireland
| | - Mark Tester
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Magdalena M Julkowska
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Boyce Thompson Institute, Ithaca, New York, USA
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3
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Ahrens CW, Murray K, Mazanec RA, Ferguson S, Jones A, Tissue DT, Byrne M, Borevitz JO, Rymer PD. Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla. BMC Genomics 2024; 25:640. [PMID: 38937661 PMCID: PMC11209971 DOI: 10.1186/s12864-024-10531-8] [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: 09/15/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. RESULTS We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. CONCLUSIONS Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
- Cesar Australia, Brunswick, VIC, 3058, Australia.
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Richard A Mazanec
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Scott Ferguson
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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Zhao Y, Zhong X, Xu G, Zhu X, Shi Y, Liu M, Wang R, Kang H, You X, Ning Y, Wang G, Wang X. The F-box protein OsFBX156 positively regulates rice defence against the blast fungus Magnaporthe oryzae by mediating ubiquitination-dependent degradation of OsHSP71.1. MOLECULAR PLANT PATHOLOGY 2024; 25:e13459. [PMID: 38808386 PMCID: PMC11134189 DOI: 10.1111/mpp.13459] [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: 12/27/2023] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 05/30/2024]
Abstract
F-box protein is a subunit of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which plays a critical role in regulating different pathways in plant immunity. In this study, we identified the rice (Oryza sativa) F-box protein OsFBX156, which targets the heat shock protein 70 (OsHSP71.1) to regulate resistance to the rice blast fungus Magnaporthe oryzae. Overexpression of OsFBX156 or knockout of OsHSP71.1 in rice resulted in the elevation of pathogenesis-related (PR) genes and an induction burst of reactive oxygen species (ROS) after flg22 and chitin treatments, thereby enhancing resistance to M. oryzae. Furthermore, OsFBX156 can promote the degradation of OsHSP71.1 through the 26S proteasome pathway. This study sheds lights on a novel mechanism wherein the F-box protein OsFBX156 targets OsHSP71.1 for degradation to promote ROS production and PR gene expression, thereby positively regulating rice innate immunity.
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Affiliation(s)
- Yudan Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Xionghui Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Ministry of AgricultureBeijingChina
| | - Guojuan Xu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoying Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yanlong Shi
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Minghao Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Ruyi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoman You
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Guo‐Liang Wang
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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Afonnikova SD, Kiseleva AA, Fedyaeva AV, Komyshev EG, Koval VS, Afonnikov DA, Salina EA. Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1309. [PMID: 38794380 PMCID: PMC11126043 DOI: 10.3390/plants13101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs AX-95172164 (chromosome 1B) and AX-158544327 (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was TraesCS6B02G147900, encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known Tamyb10 gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified TraesCS1D03G0758600 and TraesCS7B03G1296800, involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.
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Affiliation(s)
- Svetlana D. Afonnikova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Antonina A. Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Anna V. Fedyaeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Evgenii G. Komyshev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Vasily S. Koval
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitry A. Afonnikov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena A. Salina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Lu J, Zhang G, Ma C, Li Y, Jiang C, Wang Y, Zhang B, Wang R, Qiu Y, Ma Y, Jia Y, Jiang CZ, Sun X, Ma N, Jiang Y, Gao J. The F-box protein RhSAF destabilizes the gibberellic acid receptor RhGID1 to mediate ethylene-induced petal senescence in rose. THE PLANT CELL 2024; 36:1736-1754. [PMID: 38315889 PMCID: PMC11062431 DOI: 10.1093/plcell/koae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Roses are among the most popular ornamental plants cultivated worldwide for their great economic, symbolic, and cultural importance. Nevertheless, rapid petal senescence markedly reduces rose (Rosa hybrida) flower quality and value. Petal senescence is a developmental process tightly regulated by various phytohormones. Ethylene accelerates petal senescence, while gibberellic acid (GA) delays this process. However, the molecular mechanisms underlying the crosstalk between these phytohormones in the regulation of petal senescence remain largely unclear. Here, we identified SENESCENCE-ASSOCIATED F-BOX (RhSAF), an ethylene-induced F-box protein gene encoding a recognition subunit of the SCF-type E3 ligase. We demonstrated that RhSAF promotes degradation of the GA receptor GIBBERELLIN INSENSITIVE DWARF1 (RhGID1) to accelerate petal senescence. Silencing RhSAF expression delays petal senescence, while suppressing RhGID1 expression accelerates petal senescence. RhSAF physically interacts with RhGID1s and targets them for ubiquitin/26S proteasome-mediated degradation. Accordingly, ethylene-induced RhGID1C degradation and RhDELLA3 accumulation are compromised in RhSAF-RNAi lines. Our results demonstrate that ethylene antagonizes GA activity through RhGID1 degradation mediated by the E3 ligase RhSAF. These findings enhance our understanding of the phytohormone crosstalk regulating petal senescence and provide insights for improving flower longevity.
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Affiliation(s)
- Jingyun Lu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Guifang Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chao Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yao Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chuyan Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yaru Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Bingjie Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Rui Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yuexuan Qiu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yanxing Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yangchao Jia
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA 95616, USA
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Xiaoming Sun
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yunhe Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
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Pubert C, Boniface MC, Legendre A, Chabaud M, Carrère S, Callot C, Cravero C, Dufau I, Patrascoiu M, Baussart A, Belmonte E, Gautier V, Poncet C, Zhao J, Hu L, Zhou W, Langlade N, Vautrin S, Coussy C, Muños S. A cluster of putative resistance genes is associated with a dominant resistance to sunflower broomrape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:103. [PMID: 38613680 DOI: 10.1007/s00122-024-04594-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/05/2024] [Indexed: 04/15/2024]
Abstract
KEY MESSAGE The HaOr5 resistance gene is located in a large genomic insertion containing putative resistance genes and provides resistance to O. cumana, preventing successful connection to the sunflower root vascular system. Orobanche cumana (sunflower broomrape) is a parasitic plant that is part of the Orobanchaceae family and specifically infests sunflower crops. This weed is an obligate parasitic plant that does not carry out photosynthetic activity or develop roots and is fully dependent on its host for its development. It produces thousands of dust-like seeds per plant. It possesses a high spreading ability and has been shown to quickly overcome resistance genes successively introduced by selection in cultivated sunflower varieties. The first part of its life cycle occurs underground. The connection to the sunflower vascular system is essential for parasitic plant survival and development. The HaOr5 gene provides resistance to sunflower broomrape race E by preventing the connection of O. cumana to the root vascular system. We mapped a single position of the HaOr5 gene by quantitative trait locus mapping using two segregating populations. The same location of the HaOr5 gene was identified by genome-wide association. Using a large population of thousands of F2 plants, we restricted the location of the HaOr5 gene to a genomic region of 193 kb. By sequencing the whole genome of the resistant line harboring the major resistance gene HaOr5, we identified a large insertion of a complex genomic region containing a cluster of putative resistance genes.
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Affiliation(s)
- Camille Pubert
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), CNRS, INRAE, Université de Toulouse, Castanet-Tolosan, Toulouse, France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), CNRS, INRAE, Université de Toulouse, Castanet-Tolosan, Toulouse, France
| | - Alexandra Legendre
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), CNRS, INRAE, Université de Toulouse, Castanet-Tolosan, Toulouse, France
| | - Mireille Chabaud
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), CNRS, INRAE, Université de Toulouse, Castanet-Tolosan, Toulouse, France
| | - Sébastien Carrère
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), CNRS, INRAE, Université de Toulouse, Castanet-Tolosan, Toulouse, France
| | - Caroline Callot
- Center National de Ressources Génomiques Végétales (CNRGV), INRAE, Castanet-Tolosan, France
| | - Charlotte Cravero
- Center National de Ressources Génomiques Végétales (CNRGV), INRAE, Castanet-Tolosan, France
| | - Isabelle Dufau
- Center National de Ressources Génomiques Végétales (CNRGV), INRAE, Castanet-Tolosan, France
| | | | | | - Elodie Belmonte
- Plateforme de Génotypage et Séquençage en Auvergne (Gentyane), INRAE, Clermont Ferrand, France
| | - Véronique Gautier
- Plateforme de Génotypage et Séquençage en Auvergne (Gentyane), INRAE, Clermont Ferrand, France
| | - Charles Poncet
- Plateforme de Génotypage et Séquençage en Auvergne (Gentyane), INRAE, Clermont Ferrand, France
| | - Jun Zhao
- Inner Mongolia Agricultural University, Hohhot, China
| | - Luyang Hu
- Postdoctoral Research Station of Mizuda Group, Huzhou, 313000, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Weijun Zhou
- Postdoctoral Research Station of Mizuda Group, Huzhou, 313000, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Nicolas Langlade
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), CNRS, INRAE, Université de Toulouse, Castanet-Tolosan, Toulouse, France
| | - Sonia Vautrin
- Center National de Ressources Génomiques Végétales (CNRGV), INRAE, Castanet-Tolosan, France
| | | | - Stéphane Muños
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), CNRS, INRAE, Université de Toulouse, Castanet-Tolosan, Toulouse, France.
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8
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Mejia S, Santos JLB, Noutsos C. Comprehensive Genome-Wide Natural Variation and Expression Analysis of Tubby-like Proteins Gene Family in Brachypodium distachyon. PLANTS (BASEL, SWITZERLAND) 2024; 13:987. [PMID: 38611516 PMCID: PMC11013449 DOI: 10.3390/plants13070987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3, 4, 7, and 14 are involved in light responses, and BdTLP1 is involved in ABA responses. Furthermore, BdTLP2, 7, 9, and 13 are expressed throughout vegetative and reproductive stages, whereas BdTLP1, 3, 5, and 14 are expressed at germinating grains and early vegetative development, and BdTLP4, 6, 8, and 10 are expressed at the early reproduction stage. The natural variation in the eleven most diverged B. distachyon lines revealed high conservation levels of BdTLP1-6 to high variation in BdTLP7-14 proteins. Based on diversifying selection, we identified amino acids in BdTLP1, 3, 8, and 13, potentially substantially affecting protein functions. This analysis provided valuable information for further functional studies to understand the regulation, pathways involved, and mechanism of BdTLPs.
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Affiliation(s)
- Sendi Mejia
- Biological Sciences Department, Suny Old Westbury, Old Westbury, NY 11568, USA
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN 47907, USA
| | | | - Christos Noutsos
- Biological Sciences Department, Suny Old Westbury, Old Westbury, NY 11568, USA
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9
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Collins E, Shou H, Mao C, Whelan J, Jost R. Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level. Biochem J 2024; 481:363-385. [PMID: 38421035 DOI: 10.1042/bcj20230163] [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: 10/24/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.
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Affiliation(s)
- Emma Collins
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- Hainan Institute, Zhejiang University, Sanya 572025, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
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10
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Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 (BETHESDA, MD.) 2023; 14:jkad247. [PMID: 37875130 PMCID: PMC10755193 DOI: 10.1093/g3journal/jkad247] [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: 05/17/2023] [Revised: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
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Affiliation(s)
- Theodora Lo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Alex Marr
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Inanç Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ashley Thomson
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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11
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Xu W, Yu Y, Jing J, Wu Z, Zhang X, You C, Ma H, Copenhaver GP, He Y, Wang Y. SCF RMF mediates degradation of the meiosis-specific recombinase DMC1. Nat Commun 2023; 14:5044. [PMID: 37598222 PMCID: PMC10439943 DOI: 10.1038/s41467-023-40799-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 08/10/2023] [Indexed: 08/21/2023] Open
Abstract
Meiotic recombination requires the specific RecA homolog DMC1 recombinase to stabilize strand exchange intermediates in most eukaryotes. Normal DMC1 levels are crucial for its function, yet the regulatory mechanisms of DMC1 stability are unknown in any organism. Here, we show that the degradation of Arabidopsis DMC1 by the 26S proteasome depends on F-box proteins RMF1/2-mediated ubiquitination. Furthermore, RMF1/2 interact with the Skp1 ortholog ASK1 to form the ubiquitin ligase complex SCFRMF1/2. Genetic analyses demonstrate that RMF1/2, ASK1 and DMC1 act in the same pathway downstream of SPO11-1 dependent meiotic DNA double strand break formation and that the proper removal of DMC1 is crucial for meiotic crossover formation. Moreover, six DMC1 lysine residues were identified as important for its ubiquitination but not its interaction with RMF1/2. Our results reveal mechanistic insights into how the stability of a key meiotic recombinase that is broadly conserved in eukaryotes is regulated.
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Affiliation(s)
- Wanyue Xu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Yu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Juli Jing
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhen Wu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Chenjiang You
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China.
- College of Life Sciences, Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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12
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Liu G, Liu D, Zhang A, Liu H, Mia MS, Mullan D, Yan G. Identification of KASP markers and candidate genes for drought tolerance in wheat using 90K SNP array genotyping of near-isogenic lines targeting a 4BS quantitative trait locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:190. [PMID: 37584740 PMCID: PMC10432333 DOI: 10.1007/s00122-023-04438-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
KEY MESSAGE This study identified a novel SNP and developed a highly efficient KASP marker for drought tolerance in wheat by genotyping NILs targeting a major QTL for drought tolerance using an SNP array and validation with commercial varieties. Common wheat (Triticum aestivum L.) is an important winter crop worldwide and a typical allopolyploid with a large and complex genome. With global warming, the environmental volatility and incidence of drought in wheat-producing areas will increase. Molecular markers for drought tolerance are urgently needed to enhance drought tolerance breeding. Here, we genotyped four near-isogenic line (NIL) pairs targeting a major QTL qDSI.4B.1 on wheat chromosome arm 4BS for drought tolerance using the 90K SNP Illumina iSelect array and discovered a single nucleotide polymorphism (SNP) (Excalibur_c100336_106) with consistent genotype-phenotype associations among all four NIL pairs and their parents. Then, we converted the SNP into a Kompetitive Allele-Specific PCR (KASP) marker, with an accuracy of 100% for the four NIL pairs and their parents and as high as 81.8% for the 44 tested wheat lines with known phenotypes collected from Australia and China. Two genes near this SNP were suggested as candidate genes for drought tolerance in wheat after checking the Chinese Spring reference genome annotation version 1.1. One gene, TraesCS4B02G085300, encodes an F-box protein reportedly related to the ABA network, a main pathway for drought tolerance, and another gene, TraesCS4B02G085400, encodes a calcineurin-like metallophos-phoesterase transmembrane protein, which participates in Ca2+-dependent phosphorylation regulatory system. Based on this work and previous research on pre-harvest sprouting, we established a quick and efficient general SQV-based approach for KASP marker development, integrating genotyping by SNP arrays (S) using NILs targeting major QTL for a specific trait (Q) and validating them with commercial varieties (V). The identified SNP and developed KASP marker could be applied to marker-assisted selection in drought breeding, and further study of the candidate genes may improve our understanding of drought tolerance in wheat.
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Affiliation(s)
- Guannan Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Aimin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Md Sultan Mia
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Daniel Mullan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
- InterGrain Pty. Ltd., 19 Ambitious Link, Bibra Lake, WA 6163 Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
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13
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Bullones A, Castro AJ, Lima-Cabello E, Fernandez-Pozo N, Bautista R, Alché JDD, Claros MG. Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New Transcription Factors. PLANTS (BASEL, SWITZERLAND) 2023; 12:2894. [PMID: 37631106 PMCID: PMC10459472 DOI: 10.3390/plants12162894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023]
Abstract
The pollen tube is a key innovation of land plants that is essential for successful fertilisation. Its development and growth have been profusely studied in model organisms, but in spite of the economic impact of olive trees, little is known regarding the genome-wide events underlying pollen hydration and growth in this species. To fill this gap, triplicate mRNA samples at 0, 1, 3, and 6 h of in vitro germination of olive cultivar Picual pollen were analysed by RNA-seq. A bioinformatics R workflow called RSeqFlow was developed contemplating the best practices described in the literature, covering from expression data filtering to differential expression and clustering, to finally propose hub genes. The resulting olive pollen transcriptome consisted of 22,418 reliable transcripts, where 5364 were differentially expressed, out of which 173 have no orthologue in plants and up to 3 of them might be pollen-specific transcription factors. Functional enrichment revealed a deep transcriptional reprogramming in mature olive pollen that is also dependent on protein stability and turnover to allow pollen tube emergence, with many hub genes related to heat shock proteins and F-box-containing proteins. Reprogramming extends to the first 3 h of growth, including processes consistent with studies performed in other plant species, such as global down-regulation of biosynthetic processes, vesicle/organelle trafficking and cytoskeleton remodelling. In the last stages, growth should be maintained from persistent transcripts. Mature pollen is equipped with transcripts to successfully cope with adverse environments, even though the in vitro growth seems to induce several stress responses. Finally, pollen-specific transcription factors were proposed as probable drivers of pollen germination in olive trees, which also shows an overall increased number of pollen-specific gene isoforms relative to other plants.
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Affiliation(s)
- Amanda Bullones
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain;
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-UMA-CSIC), 29010 Malaga, Spain;
| | - Antonio Jesús Castro
- Plant Reproductive Biology and Advanced Imaging Laboratory (BReMAP), Estación Experimental del Zaidín (EEZ-CSIC), 18008 Granada, Spain; (A.J.C.); (E.L.-C.); (J.d.D.A.)
| | - Elena Lima-Cabello
- Plant Reproductive Biology and Advanced Imaging Laboratory (BReMAP), Estación Experimental del Zaidín (EEZ-CSIC), 18008 Granada, Spain; (A.J.C.); (E.L.-C.); (J.d.D.A.)
| | - Noe Fernandez-Pozo
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-UMA-CSIC), 29010 Malaga, Spain;
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática, Supercomputing and Bioinnovation Center (SCBI), Universidad de Málaga, 29590 Malaga, Spain;
| | - Juan de Dios Alché
- Plant Reproductive Biology and Advanced Imaging Laboratory (BReMAP), Estación Experimental del Zaidín (EEZ-CSIC), 18008 Granada, Spain; (A.J.C.); (E.L.-C.); (J.d.D.A.)
- University Institute of Research on Olive Grove and Olive Oils (INUO), Universidad de Jaén, 23071 Jaen, Spain
| | - Manuel Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain;
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-UMA-CSIC), 29010 Malaga, Spain;
- CIBER de Enfermedades Raras (CIBERER) U741, 29071 Malaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010 Malaga, Spain
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14
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Ma N, Li N, Yu Z, Chen C, Zhou DX, Zhao Y. The F-box protein SHORT PRIMARY ROOT modulates primary root meristem activity by targeting SEUSS-LIKE protein for degradation in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1937-1949. [PMID: 37013933 DOI: 10.1111/jipb.13492] [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: 01/07/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Root meristem activity is essential for root morphogenesis and adaptation, but the molecular mechanism regulating root meristem activity is not fully understood. Here, we identify an F-box family E3 ubiquitin ligase named SHORT PRIMARY ROOT (SHPR) that regulates primary root (PR) meristem activity and cell proliferation in rice. SHPR loss-of-function mutations impair PR elongation in rice. SHPR is involved in the formation of an SCF complex with the Oryza sativa SKP1-like protein OSK1/20. We show that SHPR interacts with Oryza sativa SEUSS-LIKE (OsSLK) in the nucleus and is required for OsSLK polyubiquitination and degradation by the ubiquitin 26S-proteasome system (UPS). Transgenic plants overexpressing OsSLK display a shorter PR phenotype, which is similar to the SHPR loss-of-function mutants. Genetic analysis suggests that SHPR promotes PR elongation in an OsSLK-dependent manner. Collectively, our study establishes SHPR as an E3 ubiquitin ligase that targets OsSLK for degradation, and uncovers a protein ubiquitination pathway as a mechanism for modulating root meristem activity in rice.
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Affiliation(s)
- Nini Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongmao Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunli Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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15
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Saxena H, Negi H, Sharma B. Role of F-box E3-ubiquitin ligases in plant development and stress responses. PLANT CELL REPORTS 2023:10.1007/s00299-023-03023-8. [PMID: 37195503 DOI: 10.1007/s00299-023-03023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/27/2023] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.
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Affiliation(s)
- Harshita Saxena
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia Griffin Campus, 1109 Experiment Street, Griffin, GA, 30223, USA
| | - Harshita Negi
- Department of Biological Sciences, University of South Carolina, 715 Sumter Street, Columbia, SC, 29208, USA
| | - Bhaskar Sharma
- School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Geelong, VIC, 3216, Australia.
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA, 92521, USA.
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16
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Wei J, Xu L, Shi Y, Cheng T, Tan W, Zhao Y, Li C, Yang X, Ouyang L, Wei M, Wang J, Lu G. Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107750. [PMID: 37210860 DOI: 10.1016/j.plaphy.2023.107750] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/14/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
Indian mustard (Brassica juncea L. Czern and Coss) is an important oil and vegetable crop frequently affected by seasonal drought stress during seed germination, which retards plant growth and causes yield loss considerably. However, the gene networks regulating responses to drought stress in leafy Indian mustard remain elusive. Here, we elucidated the underlying gene networks and pathways of drought response in leafy Indian mustard using next-generation transcriptomic techniques. Phenotypic analysis showed that the drought-tolerant leafy Indian mustard cv. 'WeiLiang' (WL) had a higher germination rate, antioxidant capacity, and better growth performance than the drought-sensitive cv. 'ShuiDong' (SD). Transcriptome analysis identified differentially expressed genes (DEGs) in both cultivars under drought stress during four germination time points (i.e., 0, 12, 24, and 36 h); most of which were classified as drought-responsive, seed germination, and dormancy-related genes. In the Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three main pathways (i.e., starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction) were unveiled involved in response to drought stress during seed germination. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified several hub genes (novel.12726, novel.1856, BjuB027900, BjuA003402, BjuA021578, BjuA005565, BjuB006596, novel.12977, and BjuA033308) associated with seed germination and drought stress in leafy Indian mustard. Taken together, these findings deepen our understanding of the gene networks for drought responses during seed germination in leafy Indian mustard and provide potential target genes for the genetic improvement of drought tolerance in this crop.
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Affiliation(s)
- Jinxing Wei
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Linghui Xu
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Shi
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Tianfang Cheng
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenlan Tan
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yongguo Zhao
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Chunsheng Li
- Hubei Engineering University, Xiaogan, 432000, China
| | - Xinyu Yang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Lejun Ouyang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Mingken Wei
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Junxia Wang
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China.
| | - Guangyuan Lu
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China.
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17
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Li L, Wang K, Zhou Y, Liu X. Review: A silent concert in developing plants: Dynamic assembly of cullin-RING ubiquitin ligases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111662. [PMID: 36822503 PMCID: PMC10065934 DOI: 10.1016/j.plantsci.2023.111662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Plants appear quiet: quietly, they break the ground, expand leaves, search for resources, alert each other to invaders, and heal their own wounds. In contrast to the stationary appearance, the inside world of a plant is full of movements: cells divide to increase the body mass and form new organs; signaling molecules migrate among cells and tissues to drive transcriptional cascades and developmental programs; macromolecules, such as RNAs and proteins, collaborate with different partners to maintain optimal organismal function under changing cellular and environmental conditions. All these activities require a dynamic yet appropriately controlled molecular network in plant cells. In this short review, we used the regulation of cullin-RING ubiquitin ligases (CRLs) as an example to discuss how dynamic biochemical processes contribute to plant development. CRLs comprise a large family of modular multi-unit enzymes that determine the activity and stability of diverse regulatory proteins playing crucial roles in plant growth and development. The mechanism governing the dynamic assembly of CRLs is essential for CRL activity and biological function, and it may provide insights and implications for the regulation of other dynamic multi-unit complexes involved in fundamental processes such as transcription, translation, and protein sorting in plants.
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Affiliation(s)
- Lihong Li
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Kankan Wang
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States.
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18
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Gidhi A, Mohapatra A, Fatima M, Jha SK, Kumar M, Mukhopadhyay K. Insights of auxin signaling F-box genes in wheat (Triticum aestivum L.) and their dynamic expression during the leaf rust infection. PROTOPLASMA 2023; 260:723-739. [PMID: 36100728 DOI: 10.1007/s00709-022-01808-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
The TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) protein serves as auxin receptor and links with Aux/IAA repressor protein leading to its degradation via SKP-Cullin-F box (SCFTIR1/AFB) complex in the auxin signaling pathway. Present study revealed 11 TIR1/AFB genes in wheat by genome-wide search using AFB HMM profile. Phylogenetic analysis clustered these genes in two classes. Several phytohormone, abiotic, and biotic stress responsive cis-elements were detected in promoter regions of TIR1/AFB genes. These genes were localized on homoeologous chromosome groups 2, 3, and 5 showing orthologous relation with other monocot plants. Most genes were interrupted by introns and the gene products were localized in cytoplasm, nucleus, and cell organelles. TaAFB3, TaAFB5, and TaAFB8 had nuclear localization signals. The evolutionary constraint suggested paralogous sister pairs and orthologous genes went through strong purifying selection process and are slowly evolving at protein level. Functional annotation revealed all TaAFB genes participated in auxin activated signaling pathway and SCF-mediated ubiquitination process. Furthermore, in silico expression study revealed their diverse expression profiles during various developmental stages in different tissues and organs as well as during biotic and abiotic stress. QRT-PCR based studies suggested distinct expression pattern of TIR1-1, TIR1-3, TaAFB1, TaAFB2, TaAFB3, TaAFB4, TaAFB5, TaAFB7, and TaAFB8 displaying maximum expression at 24 and 48 h post inoculation in both susceptible and resistant near isogenic wheat lines infected with leaf rust pathogen. Importantly, this also reflects coordinated responses in expression patterns of wheat TIR1/AFB genes during progression stages of leaf rust infection.
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Affiliation(s)
- Anupama Gidhi
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India
| | - Archit Mohapatra
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India
| | - Mehar Fatima
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manish Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India
| | - Kunal Mukhopadhyay
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.
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Genome-Wide Analysis of the FBA Subfamily of the Poplar F-Box Gene Family and Its Role under Drought Stress. Int J Mol Sci 2023; 24:ijms24054823. [PMID: 36902250 PMCID: PMC10002531 DOI: 10.3390/ijms24054823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
F-box proteins are important components of eukaryotic SCF E3 ubiquitin ligase complexes, which specifically determine protein substrate proteasomal degradation during plant growth and development, as well as biotic and abiotic stress. It has been found that the FBA (F-box associated) protein family is one of the largest subgroups of the widely prevalent F-box family and plays significant roles in plant development and stress response. However, the FBA gene family in poplar has not been systematically studied to date. In this study, a total of 337 F-box candidate genes were discovered based on the fourth-generation genome resequencing of P. trichocarpa. The domain analysis and classification of candidate genes revealed that 74 of these candidate genes belong to the FBA protein family. The poplar F-box genes have undergone multiple gene replication events, particularly in the FBA subfamily, and their evolution can be attributed to genome-wide duplication (WGD) and tandem duplication (TD). In addition, we investigated the P. trichocarpa FBA subfamily using the PlantGenIE database and quantitative real-time PCR (qRT-PCR); the results showed that they are expressed in the cambium, phloem and mature tissues, but rarely expressed in young leaves and flowers. Moreover, they are also widely involved in the drought stress response. At last, we selected and cloned PtrFBA60 for physiological function analysis and found that it played an important role in coping with drought stress. Taken together, the family analysis of FBA genes in P. trichocarpa provides a new opportunity for the identification of P. trichocarpa candidate FBA genes and elucidation of their functions in growth, development and stress response, thus demonstrating their utility in the improvement of P. trichocarpa.
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20
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Wang Y, Zhao J, Chen Q, Zheng K, Deng X, Gao W, Pei W, Geng S, Deng Y, Li C, Chen Q, Qu Y. Quantitative trait locus mapping and identification of candidate genes for resistance to Verticillium wilt in four recombinant inbred line populations of Gossypium hirsutum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111562. [PMID: 36509244 DOI: 10.1016/j.plantsci.2022.111562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 05/16/2023]
Abstract
Improving resistance to Verticillium wilt is of great significance for achieving high and stable yields of Upland cotton (Gossypium hirsutum). To deeply understand the genetic basis of cotton resistance to Verticillium wilt, Verticillium wilt-resistant Upland Lumianyan 28 and four Verticillium wilt-susceptible Acala cotton cultivars were used to create four recombinant inbred line (RIL) populations of 469 families through nested hybridization. Phenotypic data collected in five stressful environments were used to select resistant and sensitive lines and create a mixed pool of extreme phenotypes for BSA-seq. A total of 8 QTLs associated with Verticillium wilt resistance were identified on 4 chromosomes, of which qVW-A12-5 was detected simultaneously in the RIL populations and in one of the RIL populations and was identified for the first time. According to the sequence comparison and transcriptome analysis of candidate genes in the QTL interval between parents and pools, 4 genes were identified in the qVW-A12-5 interval. qRT-PCR of parental and phenotypically extreme lines revealed that Gh_CPR30 was induced by and may be a candidate gene for resistance to Verticillium wilt in G. hirsutum. Furthermore, VIGS technology revealed that the disease severity index (DSI) of the Gh_CPR30-silenced plants was significantly higher than that of the control. These results indicate that the Gh_CPR30 gene plays an important role in the resistance of G. hirsutum to Verticillium wilt, and the study provides a molecular basis for analyzing the molecular mechanism underlying G. hirsutum resistance to Verticillium wilt.
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Affiliation(s)
- Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Qin Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Kai Zheng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Xiaojuan Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Wenju Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shiwei Geng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yahui Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Chunping Li
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830052, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China.
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21
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Yan X, Chen S, Pan Z, Zhao W, Rui Y, Zhao L. AgNPs-Triggered Seed Metabolic and Transcriptional Reprogramming Enhanced Rice Salt Tolerance and Blast Resistance. ACS NANO 2023; 17:492-504. [PMID: 36525364 DOI: 10.1021/acsnano.2c09181] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Seeds are facing harsher environments due to the changing climate. Improving seeds' stress resilience is critical to reduce yield loss. Here, we propose that using ROS-generating nanoparticles (NPs) to prestimulate seeds would enhance the stress resilience of seeds and seedlings through triggering stress/immune responses. We examined this hypothesis by exposing AgNPs-primed rice (Oryza sativa L.) seeds under salt conditions (NaCl). The results showed that primed seeds exhibit accelerated germination speed, increased seedling vigor (from 22.5 to 47.6), biomass (11%), and root length (83%) compared to seeds with hydropriming treatment. Multiomics (metabolomics and transcriptomics) analyses reveal that AgNPs-priming triggered metabolic and transcriptional reprogramming in rice seeds. Signaling metabolites, such as salicylic acid, niacinamide, and glycerol-3-phosphate, dramatically increased upon AgNPs-priming. KEGG pathway analysis reveals that AgNPs-priming activated stress signaling and defense related pathways, such as plant hormone signal transduction, glutathione metabolism, flavone and flavonol biosynthesis, MAPK signaling pathway, and plant-pathogen interaction. These metabolic and transcriptional changes indicate that AgNPs-priming triggered stress/immune responses. More importantly, this "stress memory" can last weeks, providing protection to rice seedlings against salt stress and rice blast fungus (Magnaporthe oryzae). Overall, we show that prestimulated seeds with ROS-generating AgNPs not only enable faster and better germination under stress conditions, but also increase seedling resistance to biotic and abiotic stresses. This simple nanobiostimulant-based strategy may contribute to sustainable agriculture by maintaining agricultural production and reducing the use of pesticides.
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Affiliation(s)
- Xin Yan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing210023, China
| | - Si Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing210023, China
| | - Zhengyan Pan
- Liaoning Rice Research Institute, Shenyang110101, China
| | - Weichen Zhao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing100193, China
| | - Yukui Rui
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing100193, China
| | - Lijuan Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing210023, China
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22
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Flower-like meristem conditions and spatial constraints shape architecture of floral pseudanthia in Apioideae. EvoDevo 2022; 13:19. [PMID: 36536450 PMCID: PMC9764545 DOI: 10.1186/s13227-022-00204-6] [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: 03/16/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Pseudanthia are multiflowered units that resemble single flowers, frequently by association with pseudocorollas formed by enlarged peripheral florets (ray flowers). Such resemblance is not only superficial, because numerous pseudanthia originate from peculiar reproductive meristems with flower-like characteristics, i.e. floral unit meristems (FUMs). Complex FUM-derived pseudanthia with ray flowers are especially common in Apiaceae, but our knowledge about their patterning is limited. In this paper, we aimed to investigate both the genetic and morphological basis of their development. RESULTS We analysed umbel morphogenesis with SEM in six species representing four clades of Apiaceae subfamily Apioideae with independently acquired floral pseudanthia. Additionally, using in situ hybridization, we investigated expression patterns of LEAFY (LFY), UNUSUAL FLORAL ORGANS (UFO), and CYCLOIDEA (CYC) during umbel development in carrot (Daucus carota subsp. carota). Here, we show that initial differences in size and shape of umbel meristems influence the position of ray flower formation, whereas an interplay between peripheral promotion and spatial constraints in umbellet meristems take part in the establishment of specific patterns of zygomorphy in ray flowers of Apiaceae. This space-dependent patterning results from flower-like morphogenetic traits of the umbel which are also visible at the molecular level. Transcripts of DcLFY are uniformly distributed in the incipient umbel, umbellet and flower meristems, while DcCYC shows divergent expression in central and peripheral florets. CONCLUSIONS Our results indicate that umbels develop from determinate reproductive meristems with flower-like characteristics, which supports their recognition as floral units. The great architectural diversity and complexity of pseudanthia in Apiaceae can be explained by the unique conditions of FUMs-an interplay between expression of regulatory genes, specific spatio-temporal ontogenetic constraints and morphogenetic gradients arising during expansion and repetitive fractionation. Alongside Asteraceae, umbellifers constitute an interesting model for investigation of patterning in complex pseudanthia.
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23
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Ma D, Cai J, Ma Q, Wang W, Zhao L, Li J, Su L. Comparative time-course transcriptome analysis of two contrasting alfalfa ( Medicago sativa L.) genotypes reveals tolerance mechanisms to salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1070846. [PMID: 36570949 PMCID: PMC9773191 DOI: 10.3389/fpls.2022.1070846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Salt stress is a major abiotic stress affecting plant growth and crop yield. For the successful cultivation of alfalfa (Medicago sativa L.), a key legume forage, in saline-affected areas, it's essential to explore genetic modifications to improve salt-tolerance.Transcriptome assay of two comparative alfalfa genotypes, Adina and Zhaodong, following a 4 h and 8 h's 300 mM NaCl treatment was conducted in this study in order to investigate the molecular mechanism in alfalfa under salt stress conditions. Results showed that we obtained 875,023,571 transcripts and 662,765,594 unigenes were abtained from the sequenced libraries, and 520,091 assembled unigenes were annotated in at least one database. Among them, we identified 1,636 differentially expression genes (DEGs) in Adina, of which 1,426 were up-regulated and 210 down-regulated, and 1,295 DEGs in Zhaodong, of which 565 were up-regulated and 730 down-regulated. GO annotations and KEGG pathway enrichments of the DEGs based on RNA-seq data indicated that DEGs were involved in (1) ion and membrane homeostasis, including ABC transporter, CLC, NCX, and NHX; (2) Ca2+ sensing and transduction, including BK channel, EF-hand domain, and calmodulin binding protein; (3) phytohormone signaling and regulation, including TPR, FBP, LRR, and PP2C; (4) transcription factors, including zinc finger proteins, YABBY, and SBP-box; (5) antioxidation process, including GST, PYROX, and ALDH; (6) post-translational modification, including UCH, ubiquitin family, GT, MT and SOT. The functional roles of DEGs could explain the variations in salt tolerance performance observed between the two alfalfa genotypes Adina and Zhaodong. Our study widens the understanding of the sophisticated molecular response and tolerance mechanism to salt stress, providing novel insights on candidate genes and pathways for genetic modification involved in salt stress adaptation in alfalfa.
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Affiliation(s)
- Dongmei Ma
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jinjun Cai
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Qiaoli Ma
- Agricultural College, Ningxia University, Yinchuan, China
| | - Wenjing Wang
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Lijuan Zhao
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jiawen Li
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Lina Su
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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Pan J, Zhou X, Ahmad N, Zhang K, Tang R, Zhao H, Jiang J, Tian M, Li C, Li A, Zhang X, He L, Ma J, Li X, Tian R, Ma C, Pandey MK, Varshney RK, Wang X, Zhao C. BSA‑seq and genetic mapping identified candidate genes for branching habit in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4457-4468. [PMID: 36181525 DOI: 10.1007/s00122-022-04231-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The candidate gene AhLBA1 controlling lateral branch angel of peanut was fine-mapped to a 136.65-kb physical region on chromosome 15 using the BSA-seq and QTL mapping. Lateral branch angel (LBA) is an important plant architecture trait of peanut, which plays key role in lodging, peg soil penetration and pod yield. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for LBA in peanut. In this project, a mapping population was constructed using a spreading variety Tifrunner and the erect variety Fuhuasheng. Through bulked segregant analysis sequencing (BSA-seq), a major gene related to LBA, named as AhLBA1, was preliminarily mapped at the region of Chr.15: 150-160 Mb. Then, using traditional QTL approach, AhLBA1 was narrowed to a 1.12 cM region, corresponding to a 136.65-kb physical interval of the reference genome. Of the nine genes housed in this region, three of them were involved in hormone metabolism and regulation, including one "F-box protein" and two "2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase (2OG oxygenase)" encoding genes. In addition, we found that the level of some classes of cytokinin (CK), auxin and ethylene showed significant differences between spreading and erect peanuts at the junction of main stem and lateral branch. These findings will aid further elucidation of the genetic mechanism of LBA in peanut and facilitating marker-assisted selection (MAS) in the future breeding program.
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Affiliation(s)
- Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Ximeng Zhou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Naveed Ahmad
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Kun Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, 250100, People's Republic of China
| | - Ronghua Tang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Huiling Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Jing Jiang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Mengdi Tian
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, People's Republic of China
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Aiqin Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Xianying Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Liangqiong He
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jing Ma
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaojie Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
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Liang N, Cheng D, Zhao L, Lu H, Xu L, Bi Y. Identification of the Genes Encoding B3 Domain-Containing Proteins Related to Vernalization of Beta vulgaris. Genes (Basel) 2022; 13:genes13122217. [PMID: 36553484 PMCID: PMC9778101 DOI: 10.3390/genes13122217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Vernalization is the process of exposure to low temperatures, which is crucial for the transition from vegetative to reproductive growth of plants. In this study, the global landscape vernalization-related mRNAs and long noncoding RNAs (lncRNAs) were identified in Beta vulgaris. A total of 22,159 differentially expressed mRNAs and 4418 differentially expressed lncRNAs were uncovered between the vernalized and nonvernalized samples. Various regulatory proteins, such as zinc finger CCCH domain-containing proteins, F-box proteins, flowering-time-related proteins FY and FPA, PHD finger protein EHD3 and B3 domain proteins were identified. Intriguingly, a novel vernalization-related lncRNA-mRNA target-gene co-expression regulatory network and the candidate vernalization genes, VRN1, VRN1-like, VAL1 and VAL2, encoding B3 domain-containing proteins were also unveiled. The results of this study pave the way for further illumination of the molecular mechanisms underlying the vernalization of B. vulgaris.
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Affiliation(s)
- Naiguo Liang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
- Correspondence:
| | - Dayou Cheng
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Li Zhao
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Hedong Lu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Lei Xu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Yanhong Bi
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
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Wan S, Yang M, Ni F, Chen W, Wang Y, Chu P, Guan R. A small chromosomal inversion mediated by MITE transposons confers cleistogamy in Brassica napus. PLANT PHYSIOLOGY 2022; 190:1841-1853. [PMID: 36005931 PMCID: PMC9614453 DOI: 10.1093/plphys/kiac395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Cleistogamy, self-pollination within closed flowers, can help maintain seed purity, accelerate breeding speed, and aid in the development of ornamental flowers. However, the mechanism underlying petal closing/opening behavior remains elusive. Here, we found that a Brassica napus petal closing/opening behavior was inherited in a Mendelian manner. Fine mapping and positional cloning experiments revealed that the Mendelian factor originated from a short (29.8 kb) inversion mediated by BnDTH9 miniature inverted-repeat transposable elements (MITEs) on chromosome C03. This inversion led to tissue-specific gene promoter exchange between BnaC03.FBA (BnaC03G0156800ZS encoding an F-Box-associated domain-containing protein) and BnaC03.EFO1 (BnaC03G0157400ZS encoding an EARLY FLOWERING BY OVEREXPRESSION 1 protein) positioned near the respective inversion breakpoints. Our genetic transformation work demonstrated that the cleistogamy originated from high tissue-specific expression of the BnaC03.FBA gene caused by promoter changes due to the MITE-mediated inversion. BnaC03.FBA is involved in the formation of an SCF (Skp1-Cullin-F-box) complex, which participates in ubiquitin-mediated protein targeting for degradation through the ubiquitin 26S-proteasome system. Our results shed light on a molecular model of petal-closing behavior.
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Affiliation(s)
- Shubei Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mao Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Ni
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Pu Chu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongzhan Guan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Varshney V, Majee M. Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits. PLANT CELL REPORTS 2022; 41:1805-1826. [PMID: 35678849 DOI: 10.1007/s00299-022-02884-9] [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: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.
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Affiliation(s)
- Vishal Varshney
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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28
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Liu G, Mullan D, Zhang A, Liu H, Liu D, Yan G. Identification of KASP markers and putative genes for pre-harvest sprouting resistance in common wheat (Triticum aestivum L.). THE CROP JOURNAL 2022. [DOI: 10.1016/j.cj.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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29
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Comparative Transcriptome Profiling Reveals Potential Candidate Genes, Transcription Factors, and Biosynthetic Pathways for Phosphite Response in Potato (Solanum tuberosum L.). Genes (Basel) 2022; 13:genes13081379. [PMID: 36011289 PMCID: PMC9407107 DOI: 10.3390/genes13081379] [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: 07/09/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
The study was conducted with C31 and C80 genotypes of the potato (Solanum tuberosum L.), which are tolerant and susceptible to phosphite (Phi, H2PO3), respectively. To decipher the molecular mechanisms underlying tolerance and susceptibility to Phi in the potato, RNA sequencing was used to study the global transcriptional patterns of the two genotypes. Media were prepared with 0.25 and 0.50 mM Phi, No-phosphorus (P), and 1.25 mM (phosphate, Pi as control). The values of fragments per kilobase of exon per million mapped fragments of the samples were also subjected to a principal component analysis, grouping the biological replicates of each sample. Using stringent criteria, a minimum of 819 differential (DEGs) were detected in both C80-Phi-0.25_vs_C80-Phi-0.50 (comprising 517 upregulated and 302 downregulated) and C80-Phi-0.50_vs_C80-Phi-0.25 (comprising 302 upregulated and 517 downregulated) and a maximum of 5214 DEGs in both C31-Con_vs_C31-Phi-0.25 (comprising 1947 upregulated and 3267 downregulated) and C31-Phi-0.25_vs_C31-Con (comprising 3267 upregulated and 1947 downregulated). DEGs related to the ribosome, plant hormone signal transduction, photosynthesis, and plant–pathogen interaction performed important functions under Phi stress, as shown by the Kyoto Encyclopedia of Genes and Genomes annotation. The expressions of transcription factors increased significantly in C31 compared with C80. For example, the expressions of Soltu.DM.01G047240, Soltu.DM.08G015900, Soltu.DM.06G012130, and Soltu.DM.08G012710 increased under P deficiency conditions (Phi-0.25, Phi-0.50, and No-P) relative to the control (P sufficiency) in C31. This study adds to the growing body of transcriptome data on Phi stress and provides important clues to the Phi tolerance response of the C31 genotype.
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Gao L, Jia S, Cao L, Ma Y, Wang J, Lan D, Guo G, Chai J, Bi C. An F-box protein from wheat, TaFBA-2A, negatively regulates JA biosynthesis and confers improved salt tolerance and increased JA responsiveness to transgenic rice plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 182:227-239. [PMID: 35526420 DOI: 10.1016/j.plaphy.2022.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/26/2022] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
Soil salinity is a serious problem encountered by agriculture worldwide, which will lead to many harmful effects on plant growth, development, and even crop yield. F-box protein is the core subunit of the Skp1-Cullin-F-box (SCF) complex E3 ligase and plays crucial roles in regulating the growth, development, biotic & abiotic stresses, as well as hormone signaling pathway in plants. In this study, an FBA type F-box gene TaFBA-2A was isolated from wheat (Triticum aestivum L.). This study showed that TaFBA-2A could interact with TaSKP1, and TaOPR2, the crucial enzyme involving in jasmonic acid (JA) biosynthesis. TaFBA-2A negatively regulates JA biosynthesis, probably by mediating the degradation of TaOPR2 via the ubiquitin-26S proteasome pathway. Ectopic expression of TaFBA-2A improved the salt tolerance and increased the JA responsiveness of the transgenic rice lines. In addition, some agronomic traits closely related to crop yield were significantly enhanced in the rice lines ectopic expressing TaFBA-2A. The data obtained in this study shed light on the function and mechanisms of TaFBA-2A in JA biosynthesis and the responses to salt stress and JA treatment; this study also suggested that TaFBA-2A has the potential in improving the salt tolerance and crop yield of transgenic rice plants.
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Affiliation(s)
- Liting Gao
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Shuzhen Jia
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Lu Cao
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Yingjuan Ma
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Junling Wang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Di Lan
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Guangyan Guo
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Jianfang Chai
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050051, China.
| | - Caili Bi
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
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Guo J, Xie Z, Jiang H, Xu H, Liu B, Meng Q, Peng Q, Tang Y, Duan Y. The Molecular Mechanism of Yellow Mushroom (Floccularia luteovirens) Response to Strong Ultraviolet Radiation on the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:918491. [PMID: 35794915 PMCID: PMC9251379 DOI: 10.3389/fmicb.2022.918491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) is the highest plateau in the world, and its ultraviolet (UV) radiation is much greater than that of other regions in the world. Yellow mushroom (Floccularia luteovirens) is a unique and widely distributed edible fungus on the QTP. However, the molecular mechanism of F. luteovirens’s response to strong UV radiation remains unclear. Herein, we reported the 205 environmental adaptation and information processing genes from genome of F. luteovirens. In addition, we assembled the RNA sequence of UV-affected F. luteovirens at different growth stages. The results showed that in response to strong UV radiation, a total of 11,871 significantly different genes were identified, of which 4,444 genes in the vegetative mycelium (VM) stage were significantly different from the young fruiting bodies (YFB) stage, and only 2,431 genes in the YFB stage were significantly different from fruiting bodies (FB) stage. A total of 225 differentially expressed genes (DEGs) were found to be involved in environmental signal transduction, biochemical reaction preparation and stress response pathway, pigment metabolism pathway, and growth cycle regulation, so as to sense UV radiation, promote repair damage, regulate intracellular homeostasis, and reduce oxidative damage of UV radiation. On the basis of these results, a molecular regulation model was proposed for the response of F. luteovirens to strong UV radiation. These results revealed the molecular mechanism of adaptation of F. luteovirens adapting to strong UV radiation, and provided novel insights into mechanisms of fungi adapting to extreme environmental conditions on the QTP; the production the riboflavin pigment of the endemic fungi (Yellow mushroom) in the QTP was one of the response to extreme environment of the strong UV radiation.
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Affiliation(s)
- Jing Guo
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | - Zhanling Xie
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
- *Correspondence: Zhanling Xie,
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
| | - Hongyan Xu
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Baolong Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qing Meng
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | - Qingqing Peng
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | | | - Yingzhu Duan
- Test Station for Grassland Improvement, Xining, China
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32
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Reim S, Winkelmann T, Cestaro A, Rohr AD, Flachowsky H. Identification of Candidate Genes Associated With Tolerance to Apple Replant Disease by Genome-Wide Transcriptome Analysis. Front Microbiol 2022; 13:888908. [PMID: 35615498 PMCID: PMC9125221 DOI: 10.3389/fmicb.2022.888908] [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: 03/03/2022] [Accepted: 03/29/2022] [Indexed: 12/03/2022] Open
Abstract
Apple replant disease (ARD) is a worldwide economic risk in apple cultivation for fruit tree nurseries and fruit growers. Several studies on the reaction of apple plants to ARD are documented but less is known about the genetic mechanisms behind this symptomatology. RNA-seq analysis is a powerful tool for revealing candidate genes that are involved in the molecular responses to biotic stresses in plants. The aim of our work was to find differentially expressed genes in response to ARD in Malus. For this, we compared transcriptome data of the rootstock ‘M9’ (susceptible) and the wild apple genotype M. ×robusta 5 (Mr5, tolerant) after cultivation in ARD soil and disinfected ARD soil, respectively. When comparing apple plantlets grown in ARD soil to those grown in disinfected ARD soil, 1,206 differentially expressed genes (DEGs) were identified based on a log2 fold change, (LFC) ≥ 1 for up– and ≤ −1 for downregulation (p < 0.05). Subsequent validation revealed a highly significant positive correlation (r = 0.91; p < 0.0001) between RNA-seq and RT-qPCR results indicating a high reliability of the RNA-seq data. PageMan analysis showed that transcripts of genes involved in gibberellic acid (GA) biosynthesis were significantly enriched in the DEG dataset. Most of these GA biosynthesis genes were associated with functions in cell wall stabilization. Further genes were related to detoxification processes. Genes of both groups were expressed significantly higher in Mr5, suggesting that the lower susceptibility to ARD in Mr5 is not due to a single mechanism. These findings contribute to a better insight into ARD response in susceptible and tolerant apple genotypes. However, future research is needed to identify the defense mechanisms, which are most effective for the plant to overcome ARD.
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Affiliation(s)
- Stefanie Reim
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
- *Correspondence: Stefanie Reim,
| | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz University Hannover, Hanover, Germany
| | - Alessandro Cestaro
- Computational Biology Unit, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Annmarie-Deetja Rohr
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz University Hannover, Hanover, Germany
| | - Henryk Flachowsky
- Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
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Tang R, Dong H, He L, Li P, Shi Y, Yang Q, Jia X, Li XQ. Genome-wide identification, evolutionary and functional analyses of KFB family members in potato. BMC PLANT BIOLOGY 2022; 22:226. [PMID: 35501691 PMCID: PMC9063267 DOI: 10.1186/s12870-022-03611-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but the family members and functions have not been systematically identified and analyzed in potato. RESULTS Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the StKFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes of potato. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of the StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses, respectively. Multiple StKFB genes were differentially expressed in yellow- (cultivar 'Jin-16'), red- (cultivar 'Red rose-2') and purple-fleshed (cultivar 'Xisen-8') potato tubers, suggesting that they may play important roles in the regulation of anthocyanin biosynthesis in potato. CONCLUSIONS This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings pave the way for further investigation of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.
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Affiliation(s)
- Ruimin Tang
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Haitao Dong
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Liheng He
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Peng Li
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Yuanrui Shi
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Qing Yang
- College of life sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Xiaoyun Jia
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick E3B 4Z7 Canada
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Wu B, Yun P, Zhou H, Xia D, Gu Y, Li P, Yao J, Zhou Z, Chen J, Liu R, Cheng S, Zhang H, Zheng Y, Lou G, Chen P, Wan S, Zhou M, Li Y, Gao G, Zhang Q, Li X, Lian X, He Y. Natural variation in WHITE-CORE RATE 1 regulates redox homeostasis in rice endosperm to affect grain quality. THE PLANT CELL 2022; 34:1912-1932. [PMID: 35171272 PMCID: PMC9048946 DOI: 10.1093/plcell/koac057] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/09/2022] [Indexed: 05/11/2023]
Abstract
Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.
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Affiliation(s)
- Bian Wu
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Peng Yun
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuan Gu
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jialing Yao
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhuqing Zhou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianxian Chen
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shiyuan Cheng
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hao Zhang
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuanyuan Zheng
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Pingli Chen
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shanshan Wan
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingsong Zhou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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Al-Saharin R, Hellmann H, Mooney S. Plant E3 Ligases and Their Role in Abiotic Stress Response. Cells 2022; 11:cells11050890. [PMID: 35269512 PMCID: PMC8909703 DOI: 10.3390/cells11050890] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
Plants, as sessile organisms, have limited means to cope with environmental changes. Consequently, they have developed complex regulatory systems to ameliorate abiotic stresses im-posed by environmental changes. One such system is the ubiquitin proteasome pathway, which utilizes E3 ligases to target proteins for proteolytic degradation via the 26S proteasome. Plants ex-press a plethora of E3 ligases that are categorized into four major groups depending on their structure. They are involved in many biological and developmental processes in plants, such as DNA repair, photomorphogenesis, phytohormones signaling, and biotic stress. Moreover, many E3 ligase targets are proteins involved in abiotic stress responses, such as salt, drought, heat, and cold. In this review, we will provide a comprehensive overview of E3 ligases and their substrates that have been connected with abiotic stress in order to illustrate the diversity and complexity of how this pathway enables plant survival under stress conditions.
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Affiliation(s)
- Raed Al-Saharin
- Department of Applied Biology, Tafila Technical University, At-Tafilah 66110, Jordan
- Correspondence:
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA; (H.H.); (S.M.)
| | - Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA; (H.H.); (S.M.)
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(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants. Life (Basel) 2022; 12:life12020324. [PMID: 35207610 PMCID: PMC8874572 DOI: 10.3390/life12020324] [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: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.
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Li BW, Gao S, Yang ZM, Song JB. The F-box E3 ubiquitin ligase AtSDR is involved in salt and drought stress responses in Arabidopsis. Gene 2022; 809:146011. [PMID: 34655724 DOI: 10.1016/j.gene.2021.146011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 11/04/2022]
Abstract
F-box protein genes have been shown to play vital roles in plant development and stress respones. In Arabidopsis, there are more than 600 F-box proteins, and most of their functions are unclear. The present study shows that the F-box (SKP1-Cullin/CDC53-F-box) gene At5g15710 (Salt and Drought Responsiveness, SDR) is involved in abiotic stress responses in Arabidopsis. SDR is expressed in all tissues of Arabidopsis and is upregulated by salt and heat stresses and ABA treatment but downregulated by drought stress. Subcellular localization analysis shows that the SDR protein colocalizes with the nucleus. 35S:AntiSDR plants are hypersensitive to salt stress, but 35S:SDR plants display a salt-tolerant phenotype. Furthermore, 35S:SDR plants are hypersensitive to drought stress, while 35S:AntiSDR plants are significantly more drought tolerant. Overall, our results suggest that SDR is involved in salt and drought stress responses in Arabidopsis.
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Affiliation(s)
- Bo Wen Li
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China; Department of Neurosurgery, The First People's Hospital of Changzhou, Changzhou 213003 , PR China
| | - Shuai Gao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, PR China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jian Bo Song
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China.
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Liu HL, Harris AJ, Wang ZF, Chen HF, Li ZA, Wei X. The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. DNA Res 2022; 29:6523039. [PMID: 35137004 PMCID: PMC8825261 DOI: 10.1093/dnares/dsac003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.
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Affiliation(s)
- Hai-Lin Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangzhou, 510640, China
| | - A J Harris
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hong-Feng Chen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhi-An Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xiao Wei
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, 541006, China
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Liu M, Sun T, Liu C, Zhang H, Wang W, Wang Y, Xiang L, Chan Z. Integrated physiological and transcriptomic analyses of two warm- and cool-season turfgrass species in response to heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:275-286. [PMID: 34929431 DOI: 10.1016/j.plaphy.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Warm- and cool-season turfgrasses were originated from different locations with contrasting heat tolerance. The molecular mechanisms of heat tolerance have not been extensively studied in turfgrass species. In this study, transcriptomic analysis showed that bermudagrass was more tolerant to heat stress as evidenced by lower contents of H2O2, proline and glutathione than those in tall fescue after heat treatment. RNA sequencing analysis revealed that 32.7% and 17.7% more genes were changed in tall fescue than in bermudagrass after 2 and 12h heat treatment, respectively. GO terms of redox were enriched in bermudagrass whereas metabolite transportation ones were over-represented in tall fescue after 2h treatment. Ubiquitin dependent degradation pathways were commonly regulated in both grass species. CdF-box and FaF-box transgenic Arabidopsis exhibited improved tolerance to heat stress. Regulatory elements analysis revealed that four ABA-responsive elements present in CdF-box promoter, indicating CdF-box could be potentially regulated by ABRE binding factors (ABFs). All these findings provide evidences for understanding heat stress response in warm- and cool-season grass species.
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Affiliation(s)
- Mengyao Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Tianxiao Sun
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chunling Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hui Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Weiliang Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yanping Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lin Xiang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhulong Chan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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40
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Li Y, Xue S, He Q, Wang J, Zhu L, Zou J, Zhang J, Zuo C, Fan Z, Yue J, Zhang C, Yang K, Le J. Arabidopsis F-BOX STRESS INDUCED 4 is required to repress excessive divisions in stomatal development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:56-72. [PMID: 34817930 DOI: 10.1111/jipb.13193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
During the terminal stage of stomatal development, the R2R3-MYB transcription factors FOUR LIPS (FLP/MYB124) and MYB88 limit guard mother cell division by repressing the transcript levels of multiple cell-cycle genes. In Arabidopsis thaliana possessing the weak allele flp-1, an extra guard mother cell division results in two stomata having direct contact. Here, we identified an ethylmethane sulfonate-mutagenized mutant, flp-1 xs01c, which exhibited more severe defects than flp-1 alone, producing giant tumor-like cell clusters. XS01C, encoding F-BOX STRESS-INDUCED 4 (FBS4), is preferentially expressed in epidermal stomatal precursor cells. Overexpressing FBS4 rescued the defective stomatal phenotypes of flp-1 xs01c and flp-1 mutants. The deletion or substitution of a conserved residue (Proline166) within the F-box domain of FBS4 abolished or reduced, respectively, its interaction with Arabidopsis Skp1-Like1 (ASK1), the core subunit of the Skp1/Cullin/F-box E3 ubiquitin ligase complex. Furthermore, the FBS4 protein physically interacted with CYCA2;3 and induced its degradation through the ubiquitin-26S proteasome pathway. Thus, in addition to the known transcriptional pathway, the terminal symmetric division in stomatal development is ensured at the post-translational level, such as through the ubiquitination of target proteins recognized by the stomatal lineage F-box protein FBS4.
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Affiliation(s)
- Yi Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan Xue
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- The Institute of Scientific and Technical Information of China, Beijing, 100038, China
| | - Qixiumei He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junxue Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Wenbo School, Jinan, 250100, China
| | - Lingling Zhu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjie Zou
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoran Zuo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Fan
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junling Yue
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxia Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Kezhen Yang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Paul S, Bravo Vázquez LA, Márquez Nafarrate M, Gutiérrez Reséndiz AI, Srivastava A, Sharma A. The regulatory activities of microRNAs in non-vascular plants: a mini review. PLANTA 2021; 254:57. [PMID: 34424349 DOI: 10.1007/s00425-021-03707-z] [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: 06/10/2021] [Accepted: 08/14/2021] [Indexed: 05/21/2023]
Abstract
MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
| | - Luis Alberto Bravo Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Marilyn Márquez Nafarrate
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Av. Eugenio Garza Sada, No. 2501 Tecnologico, CP 64849, Monterrey, Mexico
| | - Ana Isabel Gutiérrez Reséndiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
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Li S, Wang Z, Wang F, Lv H, Cao M, Zhang N, Li F, Wang H, Li X, Yuan X, Zhao B, Guo YD. A tubby-like protein CsTLP8 acts in the ABA signaling pathway and negatively regulates osmotic stresses tolerance during seed germination. BMC PLANT BIOLOGY 2021; 21:340. [PMID: 34273968 PMCID: PMC8286588 DOI: 10.1186/s12870-021-03126-y] [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: 03/29/2021] [Accepted: 07/06/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND TLPs (Tubby-like proteins) are widespread in eukaryotes and highly conserved in plants and animals. TLP is involved in many biological processes, such as growth, development, biotic and abiotic stress responses, while the underlying molecular mechanism remains largely unknown. In this paper we characterized the biological function of cucumber (Cucumis sativus L.) Tubby-like protein 8 (CsTLP8) in Arabidopsis. RESULTS In cucumber, the expression of the tubby-like protein CsTLP8 was induced by NaCl treatment, but reduced by PEG (Polyethylene Glycol) and ABA (Abscisic Acid) treatment. Subcellular localization and transcriptional activation activity analysis revealed that CsTLP8 possessed two characteristics of classical transcription factors: nuclear localization and trans-activation activity. Yeast two-hybrid assay revealed interactions of CsTLP8 with CsSKP1a and CsSKP1c, suggesting that CsTLP8 might function as a subunit of E3 ubiquitin ligase. The growth activity of yeast with ectopically expressed CsTLP8 was lower than the control under NaCl and mannitol treatments. Under osmotic and salt stresses, overexpression of CsTLP8 inhibited seed germination and the growth of Arabidopsis seedlings, increased the content of MDA (Malondialdehyde), and decreased the activities of SOD (Superoxide Dismutase), POD (Peroxidase) and CAT (Catalase) in Arabidopsis seedlings. Overexpression of CsTLP8 also increased the sensitivity to ABA during seed germination and ABA-mediated stomatal closure. CONCLUSION Under osmotic stress, CsTLP8 might inhibit seed germination and seedling growth by affecting antioxidant enzymes activities. CsTLP8 acts as a negative regulator in osmotic stress and its effects may be related to ABA.
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Affiliation(s)
- Shuangtao Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Zhirong Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Fei Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Hongmei Lv
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Meng Cao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Na Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Fengju Li
- Tianjin Academy of Agricultural Sciences, 300192, Tianjin, China
| | - Hao Wang
- Tianjin Academy of Agricultural Sciences, 300192, Tianjin, China
| | - Xingsheng Li
- Shandong Provincial Key Laboratory of Cucurbitaceae Vegetable Biological Breeding, Shandong Huasheng Agriculture Co. Ltd, Qingzhou, 262500, Shandong, China
| | - Xiaowei Yuan
- Shandong Provincial Key Laboratory of Cucurbitaceae Vegetable Biological Breeding, Shandong Huasheng Agriculture Co. Ltd, Qingzhou, 262500, Shandong, China
| | - Bing Zhao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Yang-Dong Guo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Song J, Shang L, Chen S, Lu Y, Zhang Y, Ouyang B, Ye Z, Zhang J. Interactions between ShPP2-1, an F-box family gene, and ACR11A regulate cold tolerance of tomato. HORTICULTURE RESEARCH 2021; 8:148. [PMID: 34193825 PMCID: PMC8245493 DOI: 10.1038/s41438-021-00582-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/12/2021] [Accepted: 03/26/2021] [Indexed: 05/24/2023]
Abstract
There is a critical need to identify germplasm resources and genes that promote cold tolerance of tomato because global tomato production is threatened by cold stress. We found that the expression of an F-box gene family member named ShPP2-1 from Solanum habrochaites is cold inducible and studied its contribution to cold tolerance. Overexpression of ShPP2-1 in cultivated tomato (AC) reduced cold tolerance by intensifying damage to cell membranes. To explore the underlying molecular mechanism, we conducted a yeast two-hybrid library screen and found that a protein containing ACT domain repeats named ACR11A interacts with PP2-1. Overexpression of SlACR11A in AC enhanced the cold tolerance of seedlings and germinating seeds. Cold tolerance decreased in tomato plants that overexpressed both of these genes. Additionally, we performed seed germination experiments in the cold with 177 tomato accessions and identified two alleles of SlACR11A that differ in one single-nucleotide polymorphism. We found that one of these alleles, SlACR11AG, is significantly enriched in cold-tolerant tomato plants. Taken together, our findings indicate that the combination of low expression levels of PP2-1 and high expression levels of ACR11A can promote cold tolerance. These genes may therefore serve as direct targets for both genetic engineering and improvement projects that aim to enhance the cold tolerance of tomato.
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Affiliation(s)
- Jianwen Song
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lele Shang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shiwei Chen
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China.
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China.
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Lombardo F, Gramazio P, Ezura H. Increase in Phloem Area in the Tomato hawaiian skirt Mutant Is Associated with Enhanced Sugar Transport. Genes (Basel) 2021; 12:genes12060932. [PMID: 34207298 PMCID: PMC8234570 DOI: 10.3390/genes12060932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022] Open
Abstract
The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of changes in the microRNA metabolism. In the rice mutant, improvement in panicle architecture is associated with an increase in grain yield. Knowing that hws tomato fruits show a higher Brix level, it was suspected that vascular bundles might also be altered in this species, in a similar fashion to the rice phenotype. The pedicel structure of the hws-1 line was therefore examined under the microscope and sugar concentrations from phloem exudate were determined in an enzymatic assay. A distinct increase in the phloem area was observed as well as a higher sugar content in mutant phloem exudates, which is hypothesized to contribute to the high Brix level in the mutant fruits. Furthermore, the described phenotype in this study bridges the gap between Arabidopsis and rice phenotypes, suggesting that the modulation of the microRNA metabolism by HWS influences traits of agricultural interest across several species.
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Affiliation(s)
- Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Correspondence:
| | - Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan;
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Xu R, Guo Y, Peng S, Liu J, Li P, Jia W, Zhao J. Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis. Biomolecules 2021; 11:biom11050688. [PMID: 34063698 PMCID: PMC8147800 DOI: 10.3390/biom11050688] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Cyclic AMP (cAMP) is a pivotal signaling molecule existing in almost all living organisms. However, the mechanism of cAMP signaling in plants remains very poorly understood. Here, we employ the engineered activity of soluble adenylate cyclase to induce cellular cAMP elevation in Arabidopsis thaliana plants and identify 427 cAMP-responsive genes (CRGs) through RNA-seq analysis. Induction of cellular cAMP elevation inhibits seed germination, disturbs phytohormone contents, promotes leaf senescence, impairs ethylene response, and compromises salt stress tolerance and pathogen resistance. A set of 62 transcription factors are among the CRGs, supporting a prominent role of cAMP in transcriptional regulation. The CRGs are significantly overrepresented in the pathways of plant hormone signal transduction, MAPK signaling, and diterpenoid biosynthesis, but they are also implicated in lipid, sugar, K+, nitrate signaling, and beyond. Our results provide a basic framework of cAMP signaling for the community to explore. The regulatory roles of cAMP signaling in plant plasticity are discussed.
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Affiliation(s)
- Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: ; Tel.: +86-0371-6778-5095
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Junheng Zhao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
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Pagano L, Rossi R, Paesano L, Marmiroli N, Marmiroli M. miRNA regulation and stress adaptation in plants. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2021. [PMID: 0 DOI: 10.1016/j.envexpbot.2020.104369] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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Malik A, Gul A, Amir R, Munir F, Babar MM, Bakhtiar SM, Hayat MQ, Paracha RZ, Khalid Z, Alipour H. Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113. Front Genet 2020; 11:609668. [PMID: 33381153 PMCID: PMC7767997 DOI: 10.3389/fgene.2020.609668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
In plants, F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins. Most F-box proteins are shown to be an integral part of SCF complexes, which carry out the degradation of proteins and regulate diverse important biological processes. Anthers and pollen development have a huge importance in crop breeding. Despite the vast diversity of FBPs in Arabidopsis male reproductive organs, their role in anther and pollen development is not much explored. Moreover, a standard nomenclature for naming FBPs is also lacking. Here, we propose a standard nomenclature for naming the FBPs of Arabidopsis thaliana uniformly and carry out a systematic analysis of sperm cell-specific FBP gene, i.e., 3p.AtFBP113 due to its reported high and preferential expression, for detailed functional annotation. The results revealed that 3p.AtFBP113 is located on the small arm of chromosome and encodes 397 amino acid long soluble, stable, and hydrophilic protein with the possibility of localization in various cellular compartments. The presence of the C-terminal F-box associated domain (FBA) with immunoglobulin-like fold anticipated its role in protein binding. Gene ontology based functional annotation and tissue-specific gene co-expression analysis further strengthened its role in protein binding and ubiquitination. Moreover, various potential post/co-translational modifications were anticipated and the predicted tertiary structure also showed the presence of characteristic domains and fold. Thus, the outcomes of the study will be useful in developing a better understating of the function of 3p.AtFBP113 during the process of pollen development, which will be helpful for targeting the gene for manipulation of male fertility that has immense importance in hybrid breeding.
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Affiliation(s)
- Afsheen Malik
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mustafeez Mujtaba Babar
- Department of Biosciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Qasim Hayat
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Zoya Khalid
- Computational Biology Research Lab, Department of Computer Science, National University of Computer and Emerging Sciences-FAST, Islamabad, Pakistan
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
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