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Liu L, Liu X, Bai Z, Tanveer M, Zhang Y, Chen W, Shabala S, Huang L. Small but powerful: RALF peptides in plant adaptive and developmental responses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112085. [PMID: 38588983 DOI: 10.1016/j.plantsci.2024.112085] [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: 01/25/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024]
Abstract
Plants live in a highly dynamic environment and require to rapidly respond to a plethora of environmental stimuli, so that to maintain their optimal growth and development. A small plant peptide, rapid alkalization factor (RALF), can rapidly increase the pH value of the extracellular matrix in plant cells. RALFs always function with its corresponding receptors. Mechanistically, effective amount of RALF is induced and released at the critical period of plant growth and development or under different external environmental factors. Recent studies also highlighted the role of RALF peptides as important regulators in plant intercellular communications, as well as their operation in signal perception and as ligands for different receptor kinases on the surface of the plasma membrane, to integrate various environmental cues. In this context, understanding the fine-print of above processes may be essential to solve the problems of crop adaptation to various harsh environments under current climate trends scenarios, by genetic means. This paper summarizes the current knowledge about the structure and diversity of RALF peptides and their roles in plant development and response to stresses, highlighting unanswered questions and problems to be solved.
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Affiliation(s)
- Lining Liu
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Xing Liu
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhenkun Bai
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Mohsin Tanveer
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Yujing Zhang
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Wenjie Chen
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Sergey Shabala
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China; School of Biological Science, University of Western Australia, Crawley, Perth, Australia.
| | - Liping Huang
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, China.
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Jing XQ, Shi PT, Zhang R, Zhou MR, Shalmani A, Wang GF, Liu WT, Li WQ, Chen KM. Rice kinase OsMRLK63 contributes to drought tolerance by regulating reactive oxygen species production. PLANT PHYSIOLOGY 2024; 194:2679-2696. [PMID: 38146904 DOI: 10.1093/plphys/kiad684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 10/16/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023]
Abstract
Drought is a major adverse environmental factor that plants face in nature but the molecular mechanism by which plants transduce stress signals and further endow themselves with tolerance remains unclear. Malectin/malectin-like domains containing receptor-like kinases (MRLKs) have been proposed to act as receptors in multiple biological signaling pathways, but limited studies show their roles in drought-stress signaling and tolerance. In this study, we demonstrate OsMRLK63 in rice (Oryza sativa L.) functions in drought tolerance by acting as the receptor of 2 rapid alkalization factors, OsRALF45 and OsRALF46. We show OsMRLK63 is a typical receptor-like kinase that positively regulates drought tolerance and reactive oxygen species (ROS) production. OsMRLK63 interacts with and phosphorylates several nicotinamide adenine dinucleotide phosphate (NADPH) oxidases with the primarily phosphorylated site at Ser26 in the N-terminal of RESPIRATORY BURST OXIDASE HOMOLOGUE A (OsRbohA). The application of the 2 small signal peptides (OsRALF45/46) on rice can greatly alleviate the dehydration of plants induced by mimic drought. This function depends on the existence of OsMRLK63 and the NADPH oxidase-dependent ROS production. The 2 RALFs interact with OsMRLK63 by binding to its extracellular domain, suggesting they may act as drought/dehydration signal sensors for the OsMRLK63-mediated process. Our study reveals a OsRALF45/46-OsMRLK63-OsRbohs module which contributes to drought-stress signaling and tolerance in rice.
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Affiliation(s)
- Xiu-Qing Jing
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, Shanxi 030619, China
| | - Peng-Tao Shi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meng-Ru Zhou
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Abdullah Shalmani
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gang-Feng Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Ting Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Qiang Li
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun-Ming Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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Xi R, Liu H, Chen Y, Zhuang H, Han H, Wang H, Wang Q, Li N. Genome-Wide Characterization of Tomato FAD Gene Family and Expression Analysis under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:3818. [PMID: 38005715 PMCID: PMC10675527 DOI: 10.3390/plants12223818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023]
Abstract
The fatty acid desaturase (FAD) gene family plays a crucial regulatory role in the resistance process of plant biomembranes. To understand the role of FADs in tomato growth and development, this study identified and analyzed the tomato FAD gene family based on bioinformatics analysis methods. In this study, 26 SlFADs were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the SlFAD gene family was divided into six branches, and the exon-intron composition and conserved motifs of SlFADs clustered in the same branch were quite conservative. Several hormone and stress response elements in the SlFAD promoter suggest that the expression of SlFAD members is subject to complex regulation; the construction of a tomato FAD protein interaction network found that SlFAD proteins have apparent synergistic effects with SPA and GPAT proteins. qRT-PCR verification results show that SlFAD participates in the expression of tomato root, stem, and leaf tissues; SlFAD8 is mainly highly expressed in leaves; SlFAD9 plays a vital role in response to salt stress; and SlFAB5 regulates all stages of fruit development under the action of exogenous hormones. In summary, this study provides a basis for a systematic understanding of the SlFAD gene family. It provides a theoretical basis for in-depth research on the functional characteristics of tomato SlFAD genes.
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Affiliation(s)
- Rui Xi
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Huifang Liu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Yijia Chen
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hongmei Zhuang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Hongwei Han
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Hao Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Qiang Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
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Li X, Zhu T, Wang X, Zhu M. Genome-wide identification of glutamate receptor-like gene family in soybean. Heliyon 2023; 9:e21655. [PMID: 38027661 PMCID: PMC10651524 DOI: 10.1016/j.heliyon.2023.e21655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/02/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Glutamate receptor-like genes (GLRs) are essential in the growth and development of plants and many physiological and biochemical processes; however, related information in soybean is lacking. In this study, 105 GLRs, including 67 Glycine soja and 38 Glycine max GLRs, were identified and divided into two clades (Clades II and III) according to their phylogenetic relationships. GLR members in the same branch had a relatively conservative motif composition and genetic structure. Furthermore, the soybean GLR family mainly experienced purification selection during evolution. Cis-acting element analysis, gene ontology, and Kyoto Encyclopedia of Genes and Genomic annotations indicated the complexity of the gene regulation and functional diversity of the soybean GLR. Moreover, transcriptome data analysis showed that these GLRs had different expression profiles in different tissues, and Clade III members had higher and more common expression patterns. Additionally, the expression profiles under jasmonic acid treatment and salt stress indicate that the GLR participated in the jasmonic acid signaling pathway and plays a role in salt treatment. This study provides information for a comprehensive understanding of the soybean GLR family and a reference for further functional research and genetic improvement.
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Affiliation(s)
- Xinran Li
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
| | - Tianhao Zhu
- College of Mathematical Sciences, Harbin Engineering University, Harbin, China
| | - Xuying Wang
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
| | - Miao Zhu
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
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Cen Y, Geng S, Gao L, Wang X, Yan X, Hou Y, Wang P. Genome-Wide Identification and Expression Analysis of RLCK-VII Subfamily Genes Reveal Their Roles in Stress Responses of Upland Cotton. PLANTS (BASEL, SWITZERLAND) 2023; 12:3170. [PMID: 37687414 PMCID: PMC10490013 DOI: 10.3390/plants12173170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
Receptor-like cytoplasmic kinase VII (RLCK-VII) subfamily members are vital players in plant innate immunity and are also involved in plant development and abiotic stress tolerance. As a widely cultivated textile crop, upland cotton (Gossypium hirsutum) attaches great importance to the cotton industry worldwide. To obtain details of the composition, phylogeny, and putative function of RLCK-VII genes in upland cotton, genome-wide identification, evolutionary event analysis, and expression pattern examination of RLCK-VII subfamily genes in G. hirsutum were performed. There are 129 RLCK-VII members in upland cotton (GhRLCKs) and they were divided into nine groups based on their phylogenetic relationships. The gene structure and sequence features are relatively conserved within each group, which were divided based on their phylogenetic relationships, and consistent with those in Arabidopsis. The phylogenetic analysis results showed that RLCK-VII subfamily genes evolved in plants before the speciation of Arabidopsis and cotton, and segmental duplication was the major factor that caused the expansion of GhRLCKs. The diverse expression patterns of GhRLCKs in response to abiotic stresses (temperature, salt, and drought) and V. dahliae infection were observed. The candidates that may be involved in cotton's response to these stresses are highlighted. GhRLCK7 (GhRLCK7A and D), which is notably induced by V. dahliae infection, was demonstrated to positively regulate cotton defense against V. dahliae by the loss-of-function assay in cotton. These findings shed light on the details of the RLCK-VII subfamily in cotton and provide a scaffold for the further function elucidation and application of GhRLCKs for the germplasm innovation of cotton.
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Affiliation(s)
- Yuhan Cen
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Shiyi Geng
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Linying Gao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
| | - Xinyue Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Xin Yan
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
| | - Yuxia Hou
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
| | - Ping Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China (S.G.)
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
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Zhang R, Shi PT, Zhou M, Liu HZ, Xu XJ, Liu WT, Chen KM. Rapid alkalinization factor: function, regulation, and potential applications in agriculture. STRESS BIOLOGY 2023; 3:16. [PMID: 37676530 PMCID: PMC10442051 DOI: 10.1007/s44154-023-00093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/10/2023] [Indexed: 09/08/2023]
Abstract
Rapid alkalinization factor (RALF) is widespread throughout the plant kingdom and controls many aspects of plant life. Current studies on the regulatory mechanism underlying RALF function mainly focus on Arabidopsis, but little is known about the role of RALF in crop plants. Here, we systematically and comprehensively analyzed the relation between RALF family genes from five important crops and those in the model plant Arabidopsis thaliana. Simultaneously, we summarized the functions of RALFs in controlling growth and developmental behavior using conservative motifs as cues and predicted the regulatory role of RALFs in cereal crops. In conclusion, RALF has considerable application potential in improving crop yields and increasing economic benefits. Using gene editing technology or taking advantage of RALF as a hormone additive are effective way to amplify the role of RALF in crop plants.
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Affiliation(s)
- Ran Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peng-Tao Shi
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Min Zhou
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huai-Zeng Liu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiao-Jing Xu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Jia Y, Li Y. Genome-Wide Identification and Comparative Analysis of RALF Gene Family in Legume and Non-Legume Species. Int J Mol Sci 2023; 24:ijms24108842. [PMID: 37240187 DOI: 10.3390/ijms24108842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Rapid alkalinization factor (RALF) are small secreted peptide hormones that can induce rapid alkalinization in a medium. They act as signaling molecules in plants, playing a critical role in plant development and growth, especially in plant immunity. Although the function of RALF peptides has been comprehensively analyzed, the evolutionary mechanism of RALFs in symbiosis has not been studied. In this study, 41, 24, 17 and 12 RALFs were identified in Arabidopsis, soybean, Lotus and Medicago, respectively. A comparative analysis including the molecular characteristics and conserved motifs suggested that the RALF pre-peptides in soybean represented a higher value of isoelectric point and more conservative motifs/residues composition than other species. All 94 RALFs were divided into two clades according to the phylogenetic analysis. Chromosome distribution and synteny analysis suggested that the expansion of the RALF gene family in Arabidopsis mainly depended on tandem duplication, while segment duplication played a dominant role in legume species. The expression levels of most RALFs in soybean were significantly affected by the treatment of rhizobia. Seven GmRALFs are potentially involved in the release of rhizobia in the cortex cells. Overall, our research provides novel insights into the understanding of the role of the RALF gene family in nodule symbiosis.
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Affiliation(s)
- Yancui Jia
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China
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Shaheen N, Khan UM, Farooq A, Zafar UB, Khan SH, Ahmad S, Azhar MT, Atif RM, Rana IA, Seo H. Comparative transcriptomic and evolutionary analysis of FAD-like genes of Brassica species revealed their role in fatty acid biosynthesis and stress tolerance. BMC PLANT BIOLOGY 2023; 23:250. [PMID: 37173631 PMCID: PMC10176799 DOI: 10.1186/s12870-023-04232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Fatty acid desaturases (FADs) are involved in regulating plant fatty acid composition by adding double bonds to growing hydrocarbon chain. Apart from regulating fatty acid composition FADs are of great importance, and are involved in stress responsiveness, plant development, and defense mechanisms. FADs have been extensively studied in crop plants, and are broadly classed into soluble and non-soluble fatty acids. However, FADs have not yet been characterized in Brassica carinata and its progenitors. RESULTS Here we have performed comparative genome-wide identification of FADs and have identified 131 soluble and 28 non-soluble FADs in allotetraploid B. carinata and its diploid parents. Most soluble FAD proteins are predicted to be resided in endomembrane system, whereas FAB proteins were found to be localized in chloroplast. Phylogenetic analysis classed the soluble and non-soluble FAD proteins into seven and four clusters, respectively. Positive type of selection seemed to be dominant in both FADs suggesting the impact of evolution on these gene families. Upstream regions of both FADs were enriched in stress related cis-regulatory elements and among them ABRE type of elements were in abundance. Comparative transcriptomic data analysis output highlighted that FADs expression reduced gradually in mature seed and embryonic tissues. Moreover, under heat stress during seed and embryo development seven genes remained up-regulated regardless of external stress. Three FADs were only induced under elevated temperature whereas five genes were upregulated under Xanthomonas campestris stress suggesting their involvement in abiotic and biotic stress response. CONCLUSIONS The current study provides insights into the evolution of FADs and their role in B. carinata under stress conditions. Moreover, the functional characterization of stress-related genes would exploit their utilization in future breeding programs of B. carinata and its progenitors.
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Affiliation(s)
- Nabeel Shaheen
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Uzair Muhammad Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ayesha Farooq
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ummul Buneen Zafar
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Sultan Habibullah Khan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- School of Agriculture Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Precision Agriculture and Analytics Lab, National Center in Big Data and Cloud Computing (NCBC), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Iqrar Ahmad Rana
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan.
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan.
| | - Hyojin Seo
- Korea Soybean Research Institute, Jinju, 52840, Korea.
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He H, Crabbe MJC, Ren Z. Genome-wide identification and characterization of the chemosensory relative protein genes in Rhus gall aphid Schlechtendalia chinensis. BMC Genomics 2023; 24:222. [PMID: 37118660 PMCID: PMC10142413 DOI: 10.1186/s12864-023-09322-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND The Rhus gall aphid Schlechtendalia chinensis specially uses the only species Rhus chinensis and certain moss species (Mniaceae) as its primary host plant and secondary host plants, respectively. Rhus galls are formed on the primary host by the sucking of aphids, and used in traditional medicine as well as other various areas due to their high tannin contents. Chemoreception is critical for insect behaviors such as host searching, location and identification of mates and reproductive behavior. The process of chemoreception is mediated by a series of protein gene families, including odorant-binding proteins (OBPs), chemosensory proteins (CSPs), olfactory receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), and sensory neuron membrane proteins (SNMPs). However, there have been no reports on the analysis of molecular components related to the chemoreception system of S. chinensis at the genome level. RESULTS We examined the genes of eight OBPs, nine CSPs, 24 ORs, 16 GRs, 22 IRs, and five SNMPs in the S. chinensis genome using homological searches, and these chemosensory genes appeared mostly on chromosome 1. Phylogenetic and gene number analysis revealed that the gene families, e.g., ORs, GRs, CSPs and SNMPs in S. chinensis, have experienced major contractions by comparing to Myzus persicae, while the two gene families OBPs and IRs had slight expansion. The current results might be related to the broader host range of M. persicae versus the specialization of S. chinensis on only a host plant. There were 28 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the chemoreceptor gene families by collinear comparison. Ka/Ks ratios (< 1) indicated that the genes of S. chinensis were mainly affected by purification selection during evolution. We also found the lower number and expression level of chemoreception genes in S. chinensis than in other 11 aphid species, such as ORs, GRs and IRs, which play an important role in host search. CONCLUSION Our study firstly identified the genes of the different chemosensory protein gene families in the S. chinensis genome, and analyzed their general features and expression profile, demonstrating the importance of chemoreception in the aphid and providing new information for further functional research.
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Affiliation(s)
- Hongli He
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China
- Wolfson College, Oxford University, Oxford, OX2 6UD, UK
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton, LU1 3JU, UK
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China.
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Solís-Miranda J, Juárez-Verdayes MA, Nava N, Rosas P, Leija-Salas A, Cárdenas L, Quinto C. The Phaseolus vulgaris Receptor-Like Kinase PvFER1 and the Small Peptides PvRALF1 and PvRALF6 Regulate Nodule Number as a Function of Nitrate Availability. Int J Mol Sci 2023; 24:ijms24065230. [PMID: 36982308 PMCID: PMC10049175 DOI: 10.3390/ijms24065230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
Legumes associate with Gram-negative soil bacteria called rhizobia, resulting in the formation of a nitrogen-fixing organ, the nodule. Nodules are an important sink for photosynthates for legumes, so these plants have developed a systemic regulation mechanism that controls their optimal number of nodules, the so-called autoregulation of nodulation (AON) pathway, to balance energy costs with the benefits of nitrogen fixation. In addition, soil nitrate inhibits nodulation in a dose-dependent manner, through systemic and local mechanisms. The CLE family of peptides and their receptors are key to tightly controlling these inhibitory responses. In the present study, a functional analysis revealed that PvFER1, PvRALF1, and PvRALF6 act as positive regulators of the nodule number in growth medium containing 0 mM of nitrate but as negative regulators in medium with 2 and 5 mM of nitrate. Furthermore, the effect on nodule number was found to be consistent with changes in the expression levels of genes associated with the AON pathway and with the nitrate-mediated regulation of nodulation (NRN). Collectively, these data suggest that PvFER1, PvRALF1, and PvRALF6 regulate the optimal number of nodules as a function of nitrate availability.
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Affiliation(s)
- Jorge Solís-Miranda
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Marco A. Juárez-Verdayes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
- Departamento de Docencia, Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila 25315, Mexico
| | - Noreide Nava
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Paul Rosas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Alfonso Leija-Salas
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
- Correspondence:
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11
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İncili ÇY, Arslan B, Çelik ENY, Ulu F, Horuz E, Baloglu MC, Çağlıyan E, Burcu G, Bayarslan AU, Altunoglu YC. Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon. PROTOPLASMA 2023; 260:509-527. [PMID: 35804193 DOI: 10.1007/s00709-022-01793-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Watermelon and melon are members of the Cucurbitaceae family including economically significant crops in the world. The expansin protein family, which is one of the members of the cell wall, breaks down the non-covalent bonds between cell wall polysaccharides, causing pressure-dependent cell expansion. Comparative bioinformatics and molecular characterization analysis of the expansin protein family were carried out in the watermelon (Citrullus lanatus) and melon (Cucumis melo) plants in the study. Gene expression levels of expansin family members were analyzed in leaf and root tissues of watermelon and melon under ABA, drought, heat, cold, and salt stress conditions by quantitative real-time PCR analysis. After comprehensive searches, 40 expansin proteins (22 ClaEXPA, 14 ClaEXPLA, and 4 ClaEXPB) in watermelon and 43 expansin proteins (19 CmEXPA, 15 CmEXPLA, 3 CmEXPB, and 6 CmEXPLB) in melon were identified. The greatest orthologous genes were identified with soybean expansin genes for watermelon and melon. However, the latest divergence time between orthologous genes was determined with poplar expansin genes for watermelon and melon expansin genes. ClaEXPA-04, ClaEXPA-09, ClaEXPB-01, ClaEXPB-03, and ClaEXPLA-13 genes in watermelon and CmEXPA-12, CmEXPA-10, and CmEXPLA-01 genes in melon can be involved in tissue development and abiotic stress response of the plant. The current study combining bioinformatics and experimental analysis can provide a detailed characterization of the expansin superfamily which has roles in growth and reaction to the stress of the plant. The study ensures detailed data for future studies examining gene functions including the roles in plant growth and stress conditions.
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Affiliation(s)
- Çınar Yiğit İncili
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Büşra Arslan
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Esra Nurten Yer Çelik
- Department of Silviculture, Faculty of Forestry, Kastamonu University, Kastamonu, Turkey
| | - Ferhat Ulu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Erdoğan Horuz
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Mehmet Cengiz Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Ebrar Çağlıyan
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Gamze Burcu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Aslı Ugurlu Bayarslan
- Department of Biology, Faculty of Science and Arts, Kastamonu University, Kastamonu, Turkey
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey.
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Jiang Y, Zhang S, Xu H, Tian H, Zhang M, Zhu S, Wang C, Hou J, Chen G, Tang X, Wang W, Wu J, Huang X, Zhang J, Yuan L. Identification of the BcLEA Gene Family and Functional Analysis of the BcLEA73 Gene in Wucai ( Brassica campestris L.). Genes (Basel) 2023; 14:415. [PMID: 36833342 PMCID: PMC9957401 DOI: 10.3390/genes14020415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Late embryogenesis abundant (LEA) proteins are important developmental proteins in the response of plants to abiotic stress. In our previous study, BcLEA73 was differentially expressed under low-temperature stress. Herein, we combined bioinformatics analysis, subcellular localization, expression assays, and stress experiments (including salt, drought, and osmotic stress) to identify and analyze the BcLEA gene family. Gene cloning and functional analysis of BcLEA73 were performed in tobacco and Arabidopsis. Based on the sequence homology and the available conservative motif, 82 BrLEA gene family members were identified and were divided into eight subfamilies in the genome-wide database of Chinese cabbage. The analysis showed that the BrLEA73 gene was located on chromosome A09 and belonged to the LEA_6 subfamily. Quantitative real-time PCR analysis indicated that the BcLEA genes were differentially expressed to varying degrees in the roots, stems, leaves, and petioles of Wucai. The overexpressed BcLEA73 transgenic plants exhibited no significant differences in root length and seed germination rates compared to the wild-type (WT) plants under control conditions. Under salt and osmotic stress treatment, the root length and seed germination rates of the BcLEA73-OE strain were significantly greater than those of WT plants. Under salt stress, the total antioxidant capacity (T-AOC) of the BcLEA73-OE lines increased significantly, and the relative conductivity, (REL), hydrogen peroxide (H2O2) content, and superoxide anion (O2-) production rate decreased significantly. Under drought treatment, the survival rate of the BcLEA73-OE lines was significantly higher than that of WT plants. These results showed that the BcLEA73 gene of Wucai functions in enhancing the tolerance of plants to salt, drought, and osmotic stress. This study provides a theoretical basis to explore the relevant functions of the BcLEA gene family members of Wucai.
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Affiliation(s)
- Yueyue Jiang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Shengnan Zhang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Hongcheng Xu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Hong Tian
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Mengyun Zhang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Shidong Zhu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Xiaoyan Tang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Wenjie Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Jianqiang Wu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Xingxue Huang
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinlong Zhang
- Vegetable Industry Office, Agricultural and Rural Bureau of He County, Maanshan 238201, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
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Lv X, Huang S, Wang J, Han D, Li J, Guo D, Zhu H. Genome-wide identification of Mg 2+ transporters and functional characteristics of DlMGT1 in Dimocarpus longan. FRONTIERS IN PLANT SCIENCE 2023; 14:1110005. [PMID: 36818860 PMCID: PMC9932547 DOI: 10.3389/fpls.2023.1110005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Longan (Dimocarpus Longan) is one of the most important fruit crops in Southern China. Lack of available Mg in acidic soil conditions is a limitation to further increasing longan yield. Magnesium transporter (MGT/MRS2) mediates the uptake, transport, and redistribution of Mg2+ in higher plants. To understand the role of MGTs family members in longan Mg deficiency. We identified and analyzed the protein characteristics, phylogeny, expression changes, subcellular localization, and transcriptional regulation of DlMGTs members. The results showed that, twelve DlMGTs are localized in the cell membrane, chloroplast, and nucleus. The evolutionary differences in MGTs between herbaceous and woody species in different plants. The DlMGTs promoters contained many cis-acting elements and transcription factor binding sites related to the hormone, environmental, and stress response. Subcellular localization assays showed that DlMGT1 localizes in the cell membrane of Arabidopsis protoplasts. The candidate transcription factor DlGATA16, which may regulate the expression of DlMGT1, was localized in the nucleus of tobacco leaves. Dual luciferase analysis demonstrated that DlGATA16 is a potential factor regulating the transcriptional activity of DlMGT1. In this study, we identified and analyzed DlMGTs on a genome-wide scale and the subcellular localization and interaction of DlMGT1 and DlGATA16, which has important implications for further functional analysis studies of MGTs and the use of MGT for longan genetic improvement.
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Affiliation(s)
- Xinmin Lv
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Shilian Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Jing Wang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Dongmei Han
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Jianguang Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Dongliang Guo
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Haifeng Zhu
- Key Laboratory of Crop Harvesting Equipment Technology of Zhejiang Province, Jinhua Polytechnic, Jinhua, China
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Mamaeva A, Lyapina I, Knyazev A, Golub N, Mollaev T, Chudinova E, Elansky S, Babenko VV, Veselovsky VA, Klimina KM, Gribova T, Kharlampieva D, Lazarev V, Fesenko I. RALF peptides modulate immune response in the moss Physcomitrium patens. FRONTIERS IN PLANT SCIENCE 2023; 14:1077301. [PMID: 36818838 PMCID: PMC9933782 DOI: 10.3389/fpls.2023.1077301] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND RAPID ALKALINIZATION FACTOR (RALFs) are cysteine-rich peptides that regulate multiple physiological processes in plants. This peptide family has considerably expanded during land plant evolution, but the role of ancient RALFs in modulating stress responses is unknown.Results: Here, we used the moss Physcomitrium patens as a model to gain insight into the role of RALF peptides in the coordination of plant growth and stress response in non-vascular plants. The quantitative proteomic analysis revealed concerted downregulation of M6 metalloprotease and some membrane proteins, including those involved in stress response, in PpRALF1, 2 and 3 knockout (KO) lines. The subsequent analysis revealed the role of PpRALF3 in growth regulation under abiotic and biotic stress conditions, implying the importance of RALFs in responding to various adverse conditions in bryophytes. We found that knockout of the PpRALF2 and PpRALF3 genes resulted in increased resistance to bacterial and fungal phytopathogens, Pectobacterium carotovorum and Fusarium solani, suggesting the role of these peptides in negative regulation of the immune response in P. patens. Comparing the transcriptomes of PpRALF3 KO and wild-type plants infected by F. solani showed that the regulation of genes in the phenylpropanoid pathway and those involved in cell wall modification and biogenesis was different in these two genotypes. CONCLUSION Thus, our study sheds light on the function of the previously uncharacterized PpRALF3 peptide and gives a clue to the ancestral functions of RALF peptides in plant stress response.
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Affiliation(s)
- Anna Mamaeva
- Laboratory of System Analysis of Proteins and Peptides, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina Lyapina
- Laboratory of System Analysis of Proteins and Peptides, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Knyazev
- Laboratory of System Analysis of Proteins and Peptides, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nina Golub
- Laboratory of System Analysis of Proteins and Peptides, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Timur Mollaev
- Agrarian and Technological Institute, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Elena Chudinova
- Agrarian and Technological Institute, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Sergey Elansky
- Agrarian and Technological Institute, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladislav V. Babenko
- Laboratory of Genetic Engineering, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vladimir A. Veselovsky
- Laboratory of Genetic Engineering, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ksenia M. Klimina
- Laboratory of Genetic Engineering, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana Gribova
- Laboratory of Genetic Engineering, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria Kharlampieva
- Laboratory of Genetic Engineering, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vassili Lazarev
- Laboratory of Genetic Engineering, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow, Russia
| | - Igor Fesenko
- Laboratory of System Analysis of Proteins and Peptides, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Sui J, Xiao X, Yang J, Fan Y, Zhu S, Zhu J, Zhou B, Yu F, Tang C. The rubber tree RALF peptide hormone and its receptor protein kinase FER implicates in rubber production. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111510. [PMID: 36341879 DOI: 10.1016/j.plantsci.2022.111510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
RAPID ALKALINIZATION FACTORs (RALFs), which are secreted peptides serving as extracellular signals transduced to the inside of the cell, interact with the receptor-like kinase FERONIA (FER) and participates in various biological pathways. Here, we identified 23 RALF and 2 FER genes in Hevea brasiliensis (para rubber tree), and characterized their expression patterns in different tissues, across the process of leaf development, and in response to the rubber yield-stimulating treatments of tapping and ethylene. Four Hevea latex (the cytoplasm of rubber-producing laticifers)-abundant RALF isoforms, HbRALF19, HbRALF3, HbRALF22, and HbRALF16 were listed with descending expression levels. Of the four HbRALFs, expressions of HbRALF3 were markedly regulated in an opposite way by the treatments of tapping (depression) and ethylene (stimulation). All of the four latex-abundant RALFs specifically interacted with the extracellular domain of HbFER1. Transgenic Arabidopsis plants overexpressing these HbRALFs displayed phenotypes similar to those reported for AtRALFs, such as shorter roots, smaller plant architecture, and delayed flowering. The application of HbRALF3 and HbRALF19 recombinant proteins significantly reduced the pH of Hevea latex, an important factor regulating latex metabolism. An in vitro rubber biosynthesis assay in a mixture of latex cytosol (C-serum) revealed a positive role of HbFER1 in rubber biosynthesis. Taken together, these data provide evidence for the participation of the HbRALF-FER module in rubber production.
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Affiliation(s)
- Jinlei Sui
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Hainan University, Haikou 570228, China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Scientific Research Centre, Key Laboratory of Emergency and Trauma, Ministry of Education, Hainan Medical University, Haikou 571199, China
| | - Xiaohu Xiao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianghua Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yujie Fan
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Hainan University, Haikou 570228, China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Sirui Zhu
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Jinheng Zhu
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Hainan University, Haikou 570228, China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Binhui Zhou
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Hainan University, Haikou 570228, China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Feng Yu
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China.
| | - Chaorong Tang
- Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC, Hainan University, Haikou 570228, China.
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Wei H, Movahedi A, Xu S, Zhang Y, Liu G, Aghaei-Dargiri S, Ghaderi Zefrehei M, Zhu S, Yu C, Chen Y, Zhong F, Zhang J. Genome-Wide Characterization and Expression Analysis of Fatty acid Desaturase Gene Family in Poplar. Int J Mol Sci 2022; 23:ijms231911109. [PMID: 36232411 PMCID: PMC9570219 DOI: 10.3390/ijms231911109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Fatty acid desaturases (FADs) modulate carbon–carbon single bonds to form carbon–carbon double bonds in acyl chains, leading to unsaturated fatty acids (UFAs) that have vital roles in plant growth and development and their response to environmental stresses. In this study, a total of 23 Populus trichocarpaFAD (PtFAD) candidates were identified from the poplar genome and clustered into seven clades, including FAB2, FAD2, FAD3/7/8, FAD5, FAD6, DSD, and SLD. The exon–intron compositions and conserved motifs of the PtFADs, clustered into the same clade, were considerably conserved. It was found that segmental duplication events are predominantly attributable to the PtFAD gene family expansion. Several hormone- and stress-responsive elements in the PtFAD promoters implied that the expression of the PtFAD members was complicatedly regulated. A gene expression pattern analysis revealed that some PtFAD mRNA levels were significantly induced by abiotic stress. An interaction proteins and gene ontology (GO) analysis indicated that the PtFADs are closely associated with the UFAs biosynthesis. In addition, the UFA contents in poplars were significantly changed under drought and salt stresses, especially the ratio of linoleic and linolenic acids. The integration of the PtFAD expression patterns and UFA contents showed that the abiotic stress-induced PtFAD3/7/8 members mediating the conversion of linoleic and linolenic acids play vital roles in response to osmotic stress. This study highlights the profiles and functions of the PtFADs and identifies some valuable genes for forest improvements.
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Affiliation(s)
- Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226001, China
| | - Ali Movahedi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- College of Arts and Sciences, Arlington International University, Wilmington, DE 19804, USA
- Correspondence: (A.M.); (J.Z.)
| | - Songzhi Xu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226001, China
| | - Yanyan Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Guoyuan Liu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226001, China
| | - Soheila Aghaei-Dargiri
- Department of Horticulture, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Mostafa Ghaderi Zefrehei
- Department of Animal Science, Faculty of Agriculture, Yasouj University, Yasouj 7591874831, Iran
| | - Sheng Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Chunmei Yu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226001, China
| | - Yanhong Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226001, China
| | - Fei Zhong
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226001, China
| | - Jian Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226001, China
- Correspondence: (A.M.); (J.Z.)
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Detoxification Gene Families at the Genome-Wide Level of Rhus Gall Aphid Schlechtendalia chinensis. Genes (Basel) 2022; 13:genes13091627. [PMID: 36140795 PMCID: PMC9498883 DOI: 10.3390/genes13091627] [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: 07/30/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
The Rhus gall aphid Schlechtendalia chinensis uses the species Rhus chinensis as its primary host plant, on which galls are produced. The galls have medicinal properties and can be used in various situations due to their high tannin content. Detoxification enzymes play significant roles in the insect lifecycle. In this study, we focused on five detoxification gene families, i.e., glutathione-S-transferase (GST), ABC transporter (ABC), Carboxylesterase (CCE), cyto-chrome P450 (CYP), and UDP-glycosyltransferase (UDP), and manually annotated 144 detoxification genes of S. chinensis using genome-wide techniques. The detoxification genes appeared mostly on chromosome 1, where a total of two pair genes were identified to show tandem duplications. There were 38 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the detoxification gene families by collinear comparison. Ka/Ks ratios showed that detoxification genes of S. chinensis were mainly affected by purification selection during evolution. The gene expression numbers of P450s and ABCs by transcriptome sequencing data were greater, while gene expression of CCEs was the highest, suggesting they might be important in the detoxification process. Our study has firstly identified the genes of the different detoxification gene families in the S. chinensis genome, and then analyzed their general features and expression, demonstrating the importance of the detoxification genes in the aphid and providing new information for further research.
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Abstract
Peptide signaling is an emerging paradigm in molecular plant-microbe interactions with vast implications for our understanding of plant-nematode interactions and beyond. Plant-like peptide hormones, first discovered in cyst nematodes, are now recognized as an important class of peptide effectors mediating several different types of pathogenic and symbiotic interactions. Here, we summarize what has been learned about nematode-secreted CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) peptide effectors since the last comprehensive review on this topic a decade ago. We also highlight new discoveries of a diverse array of peptide effectors that go beyond the CLE peptide effector family in not only phytonematodes but in organisms beyond the phylum Nematoda.
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Affiliation(s)
- Melissa G Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, USA; ,
| | - Xunliang Liu
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, USA; ,
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RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2121058119. [PMID: 35878023 PMCID: PMC9351349 DOI: 10.1073/pnas.2121058119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379-402 (2020); Blackburn et al., Plant Physiol. 182, 1657-1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term.
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Jiang W, Li C, Li L, Li Y, Wang Z, Yu F, Yi F, Zhang J, Zhu JK, Zhang H, Li Y, Zhao C. Genome-Wide Analysis of CqCrRLK1L and CqRALF Gene Families in Chenopodium quinoa and Their Roles in Salt Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:918594. [PMID: 35873972 PMCID: PMC9302450 DOI: 10.3389/fpls.2022.918594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Chenopodium quinoa is a halophyte with exceptional nutritional qualities, and therefore it is potentially an ideal crop to grow in saline soils, not only addressing the problem of land salinization, but also providing nutrient food for the health of humans. Currently, the molecular mechanisms underlying salt tolerance in quinoa are still largely unknown. In Arabidopsis thaliana, Catharanthus roseus receptor-like kinase (CrRLK1Ls) FERONIA (FER) and its ligands rapid alkalinization factors (RALFs) have been reported that participate in the regulation of salt tolerance. Here, we performed a genome-wide analysis and identified 26 CqCrRLK1L and 18 CqRALF family genes in quinoa genome. Transcriptomic profiling of the leaf, root, stamen, and pistil tissues of quinoa reveals that different CqCrRLK1L and CqRALF genes exhibit tissue-specific expression patterns, which is consistent with that observed in other plant species. RNA-seq data show that three CqCrRLK1L genes are highly up-regulated after salt treatment, suggesting that some CqCrRLK1L family genes are transcriptionally responsive to salt stress in quinoa. Biochemical study indicates that CqRALF15, a paralog of Arabidopsis RALF22, is physically associated with CrRLK1L proteins CqFER and AtFER. CqRALF15 and AtRALF22 are functionally conserved in inducing the internalization of AtFER and in triggering root growth inhibition in both quinoa and Arabidopsis. Moreover, overexpression of CqRALF15 in Arabidopsis results in enhanced leaf bleaching under salt stress, indicating that CqRALF15 is involved in salt stress response. Together, our study characterizes CqCrRLK1L and CqRALF family genes in quinoa at genomic, transcriptional, and protein levels, and provides evidence to support their roles in salt stress response.
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Affiliation(s)
- Wei Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chao Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Leiting Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yali Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhihao Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Feiyu Yu
- The Bright Seed Industry Company, Shanghai, China
| | - Feng Yi
- Agricultural Technology Center of Bright Rice (Group) Co., Ltd., Shanghai, China
| | - Jianhan Zhang
- Agricultural Technology Center of Bright Rice (Group) Co., Ltd., Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Heng Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
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21
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Cheng C, Liu F, Sun X, Wang B, Liu J, Ni X, Hu C, Deng G, Tong Z, Zhang Y, Lü P. Genome-wide identification of FAD gene family and their contributions to the temperature stresses and mutualistic and parasitic fungi colonization responses in banana. Int J Biol Macromol 2022; 204:661-676. [PMID: 35181326 DOI: 10.1016/j.ijbiomac.2022.02.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/29/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022]
Abstract
Fatty acid desaturase (FAD) plays important roles in plant growth and development and plant defense processes. In this study, we identified 27 MaFAD genes from the banana genome. According to the amino acid sequence similarities, their encoded proteins could be classified into five subfamilies. This classification is consistently supported by their gene and protein structures, conserved motifs and subcellular localizations. Segmental duplication events were found to play predominant roles in the MaFAD gene family expansion. Thirty miRNAs targeting MaFADs were identified and many hormone- and stress-responsive cis-acting elements and transcription factor binding sites (TFBSs) were identified in their promoters, indicating that the MaFADs expression regulation was very complicated. Gene expression analysis showed that some MaFADs showed significant differential expression in response to high and low temperature. FocTR4 influenced greatly the expression of several MaFADs and greatly induced the fatty acid (FA) accumulations in roots. Although S. indica showed no significant influence on the expression of most MaFADs, it could greatly alleviate the influence of FocTR4 on several MaFADs and FA biosynthesis. Our study revealed that MaFADs contributed greatly to the responses of high and low temperature stresses and mutualistic and parasitic fungi colonization in banana.
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Affiliation(s)
- Chunzhen Cheng
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Fan Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xueli Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Bin Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiapeng Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueting Ni
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zheng Tong
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yongyan Zhang
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Peitao Lü
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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22
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Fang Y, Jiang J, Hou X, Guo J, Li X, Zhao D, Xie X. Plant protein-coding gene families: Their origin and evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:995746. [PMID: 36160967 PMCID: PMC9490259 DOI: 10.3389/fpls.2022.995746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/15/2022] [Indexed: 05/13/2023]
Abstract
Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Degang Zhao
- Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Ministry of Education, College of Life Sciences, Institute of Agricultural Bioengineering, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- *Correspondence: Degang Zhao,
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- Xin Xie,
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23
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Zhu S, Fu Q, Xu F, Zheng H, Yu F. New paradigms in cell adaptation: decades of discoveries on the CrRLK1L receptor kinase signalling network. THE NEW PHYTOLOGIST 2021; 232:1168-1183. [PMID: 34424552 DOI: 10.1111/nph.17683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/15/2021] [Indexed: 05/15/2023]
Abstract
Receptor-like kinases (RLKs), which constitute the largest receptor family in plants, are essential for perceiving and relaying information about various environmental stimuli. Tremendous progress has been made in the past few decades towards elucidating the mechanisms of action of several RLKs, with emerging paradigms pointing to their roles in cell adaptations. Among these paradigms, Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) proteins and their rapid alkalinization factor (RALF) peptide ligands have attracted much interest. In particular, FERONIA (FER) is a CrRLK1L protein that participates in a wide array of physiological processes associated with RALF signalling, including cell growth and monitoring cell wall integrity, RNA and energy metabolism, and phytohormone and stress responses. Here, we analyse FER in the context of CrRLK1L members and their ligands in multiple species. The FER working model raises many questions about the role of CrRLK1L signalling networks during cell adaptation. For example, how do CrRLK1Ls recognize various RALF peptides from different organisms to initiate specific phosphorylation signal cascades? How do RALF-FER complexes achieve their specific, sometimes opposite, functions in different cell types? Here, we summarize recent major findings and highlight future perspectives in the field of CrRLK1L signalling networks.
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Affiliation(s)
- Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Qiong Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Heping Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Centre, Changsha, 410125, China
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24
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In Silico Analysis of Fatty Acid Desaturases Structures in Camelina sativa, and Functional Evaluation of Csafad7 and Csafad8 on Seed Oil Formation and Seed Morphology. Int J Mol Sci 2021; 22:ijms221910857. [PMID: 34639198 PMCID: PMC8532002 DOI: 10.3390/ijms221910857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/19/2022] Open
Abstract
Fatty acid desaturases add a second bond into a single bond of carbon atoms in fatty acid chains, resulting in an unsaturated bond between the two carbons. They are classified into soluble and membrane-bound desaturases, according to their structure, subcellular location, and function. The orthologous genes in Camelina sativa were identified and analyzed, and a total of 62 desaturase genes were identified. It was revealed that they had the common fatty acid desaturase domain, which has evolved separately, and the proteins of the same family also originated from the same ancestry. A mix of conserved, gained, or lost intron structure was obvious. Besides, conserved histidine motifs were found in each family, and transmembrane domains were exclusively revealed in the membrane-bound desaturases. The expression profile analysis of C. sativa desaturases revealed an increase in young leaves, seeds, and flowers. C. sativa ω3-fatty acid desaturases CsaFAD7 and CsaDAF8 were cloned and the subcellular localization analysis showed their location in the chloroplast. They were transferred into Arabidopsis thaliana to obtain transgenic lines. It was revealed that the ω3-fatty acid desaturase could increase the C18:3 level at the expense of C18:2, but decreases in oil content and seed weight, and wrinkled phenotypes were observed in transgenic CsaFAD7 lines, while no significant change was observed in transgenic CsaFAD8 lines in comparison to the wild-type. These findings gave insights into the characteristics of desaturase genes, which could provide an excellent basis for further investigation for C. sativa improvement, and overexpression of ω3-fatty acid desaturases in seeds could be useful in genetic engineering strategies, which are aimed at modifying the fatty acid composition of seed oil.
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25
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Abarca A, Franck CM, Zipfel C. Family-wide evaluation of RAPID ALKALINIZATION FACTOR peptides. PLANT PHYSIOLOGY 2021; 187:996-1010. [PMID: 34608971 PMCID: PMC8491022 DOI: 10.1093/plphys/kiab308] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/14/2021] [Indexed: 05/04/2023]
Abstract
Plant peptide hormones are important players that control various aspects of the lives of plants. RAPID ALKALINIZATION FACTOR (RALF) peptides have recently emerged as important players in multiple physiological processes. Numerous studies have increased our understanding of the evolutionary processes that shaped the RALF family of peptides. Nevertheless, to date, there is no comprehensive, family-wide functional study on RALF peptides. Here, we analyzed the phylogeny of the proposed multigenic RALF peptide family in the model plant Arabidopsis (Arabidopsis thaliana), ecotype Col-0, and tested a variety of physiological responses triggered by RALFs. Our phylogenetic analysis reveals that two of the previously proposed RALF peptides are not genuine RALF peptides, which leads us to propose a revision to the consensus AtRALF peptide family annotation. We show that the majority of AtRALF peptides, when applied exogenously as synthetic peptides, induce seedling or root growth inhibition and modulate reactive oxygen species (ROS) production in Arabidopsis. Moreover, our findings suggest that alkalinization and growth inhibition are, generally, coupled characteristics of RALF peptides. Additionally, we show that for the majority of the peptides, these responses are genetically dependent on FERONIA, suggesting a pivotal role for this receptor kinase in the perception of multiple RALF peptides.
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Affiliation(s)
- Alicia Abarca
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Christina M. Franck
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
- Author for communication:
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26
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Tanaka K, Heil M. Damage-Associated Molecular Patterns (DAMPs) in Plant Innate Immunity: Applying the Danger Model and Evolutionary Perspectives. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:53-75. [PMID: 33900789 DOI: 10.1146/annurev-phyto-082718-100146] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Danger signals trigger immune responses upon perception by a complex surveillance system. Such signals can originate from the infectious nonself or the damaged self, the latter termed damage-associated molecular patterns (DAMPs). Here, we apply Matzinger's danger model to plant innate immunity to discuss the adaptive advantages of DAMPs and their integration into preexisting signaling pathways. Constitutive DAMPs (cDAMPs), e.g., extracellular ATP, histones, and self-DNA, fulfill primary, conserved functions and adopt a signaling role only when cellular damage causes their fragmentation or localization to aberrant compartments. By contrast, immunomodulatory peptides (also known as phytocytokines) exclusively function as signals and, upon damage, are activated as inducible DAMPs (iDAMPs). Dynamic coevolutionary processes between the signals and their emerging receptors and shared co-receptors have likely linked danger recognition to preexisting, conserved downstream pathways.
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Affiliation(s)
- Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, Washington 99163, USA;
| | - Martin Heil
- Departamento de Ingeniería Genética, CINVESTAV, 36821 Irapuato, Guanajuato, México
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27
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The Roles of Peptide Hormones and Their Receptors during Plant Root Development. Genes (Basel) 2020; 12:genes12010022. [PMID: 33375648 PMCID: PMC7823343 DOI: 10.3390/genes12010022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 02/03/2023] Open
Abstract
Peptide hormones play pivotal roles in many physiological processes through coordinating developmental and environmental cues among different cells. Peptide hormones are recognized by their receptors that convey signals to downstream targets and interact with multiple pathways to fine-tune plant growth. Extensive research has illustrated the mechanisms of peptides in shoots but functional studies of peptides in roots are scarce. Reactive oxygen species (ROS) are known to be involved in stress-related events. However, recent studies have shown that they are also associated with many processes that regulate plant development. Here, we focus on recent advances in understanding the relationships between peptide hormones and their receptors during root growth including outlines of how ROS are integrated with these networks.
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28
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Hajiahmadi Z, Abedi A, Wei H, Sun W, Ruan H, Zhuge Q, Movahedi A. Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.). BMC Genomics 2020; 21:778. [PMID: 33167859 PMCID: PMC7653692 DOI: 10.1186/s12864-020-07199-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/27/2020] [Indexed: 12/28/2022] Open
Abstract
Backgrounds Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs). Results 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07199-1.
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Affiliation(s)
- Zahra Hajiahmadi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, 4199613776, Iran
| | - Amin Abedi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, 4199613776, Iran
| | - Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.
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Zhang X, Peng H, Zhu S, Xing J, Li X, Zhu Z, Zheng J, Wang L, Wang B, Chen J, Ming Z, Yao K, Jian J, Luan S, Coleman-Derr D, Liao H, Peng Y, Peng D, Yu F. Nematode-Encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase. MOLECULAR PLANT 2020; 13:1434-1454. [PMID: 32896643 DOI: 10.1016/j.molp.2020.08.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 05/22/2023]
Abstract
The molecular mechanism by which plants defend against plant root-knot nematodes (RKNs) is largely unknown. The plant receptor kinase FERONIA and its peptide ligands, rapid alkalinization factors (RALFs), regulate plant immune responses and cell expansion, which are two important factors for successful RKN parasitism. In this study, we found that mutation of FERONIA in Arabidopsis thaliana resulted in plants showing low susceptibility to the RKN Meloidogyne incognita. To identify the underlying mechanisms associated with this phenomenon, we identified 18 novel RALF-likes from multiple species of RKNs and showed that two RALF-likes (i.e., MiRALF1 and MiRALF3) from M. incognita were expressed in the esophageal gland with high expression during the parasitic stages of nematode development. These nematode RALF-likes also possess the typical activities of plant RALFs and can directly bind to the extracellular domain of FERONIA to modulate specific steps of nematode parasitism-related immune responses and cell expansion. Genetically, both MiRALF1/3 and FERONIA are required for RKN parasitism in Arabidopsis and rice. Collectively, our study suggests that nematode-encoded RALFs facilitate parasitism via plant-encoded FERONIA and provides a novel paradigm for studying host-pathogen interactions.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Huan Peng
- State Key Laboratory of Plant Disease and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, P.R. China
| | - Xin Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Zhaozhong Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Jingyuan Zheng
- Institute of Vegetable Research, Hunan Academy of Agricultural Sciences, Changsha 410125, P.R. China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Bingqian Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Jia Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, P.R. China
| | - Ke Yao
- State Key Laboratory of Plant Disease and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Jinzhuo Jian
- State Key Laboratory of Plant Disease and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Hongdong Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China.
| | - Yousong Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China.
| | - Deliang Peng
- State Key Laboratory of Plant Disease and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, P.R. China.
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Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis. Genes (Basel) 2020; 11:genes11070793. [PMID: 32674446 PMCID: PMC7397338 DOI: 10.3390/genes11070793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in symbiotic nodulation. We performed a phylogenetic analysis of CrRLK1L subfamily receptors of 57 different plant species and identified 1050 CrRLK1L proteins, clustered into 11 clades. This analysis revealed that the CrRLK1L subfamily probably arose in plants during the transition from chlorophytes to embryophytes and has undergone several duplication events during its evolution. Among the CrRLK1Ls of legumes and A. thaliana, protein structure, gene structure, and expression patterns were highly conserved. Some legume CrRLK1L genes were active in nodules. A detailed analysis of eight nodule-expressed genes in Phaseolus vulgaris L. showed that these genes were differentially expressed in roots at different stages of the symbiotic process. These data suggest that CrRLK1Ls are both conserved and underwent diversification in a wide group of plants, and shed light on the roles of these genes in legume–rhizobia symbiosis.
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31
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Li Q, Wang C, Mou Z. Perception of Damaged Self in Plants. PLANT PHYSIOLOGY 2020; 182:1545-1565. [PMID: 31907298 PMCID: PMC7140957 DOI: 10.1104/pp.19.01242] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/16/2019] [Indexed: 05/04/2023]
Abstract
Plants use specific receptor proteins on the cell surface to detect host-derived danger signals released in response to attacks by pathogens or herbivores and activate immune responses against them.
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Affiliation(s)
- Qi Li
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Chenggang Wang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Zhonglin Mou
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
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32
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Blackburn MR, Haruta M, Moura DS. Twenty Years of Progress in Physiological and Biochemical Investigation of RALF Peptides. PLANT PHYSIOLOGY 2020; 182:1657-1666. [PMID: 32071151 PMCID: PMC7140910 DOI: 10.1104/pp.19.01310] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/16/2020] [Indexed: 05/20/2023]
Abstract
RALF isoforms play many biological roles, and their specific functions are defined by combinatorial interactions with dynamic receptor complexes that vary more than initially thought.
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Affiliation(s)
- Matthew R Blackburn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Miyoshi Haruta
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Daniel S Moura
- Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ/USP), Piracicaba, SP 13418-900, Brazil
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33
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The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae). Genes (Basel) 2020; 11:genes11020174. [PMID: 32041308 PMCID: PMC7073784 DOI: 10.3390/genes11020174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/31/2020] [Accepted: 02/01/2020] [Indexed: 11/21/2022] Open
Abstract
The rapid alkalinization factor (RALF) gene family is essential for the plant growth and development. However, there is little known about these genes among Rosaceae species. Here, we identify 124 RALF-like genes from seven Rosaceae species, and 39 genes from Arabidopsis, totally 163 genes, divided into four clades according to the phylogenetic analysis, which includes 45 mature RALF genes from Rosaceae species. The YISY motif and RRXL cleavage site are typical features of true RALF genes, but some variants were detected in our study, such as YISP, YIST, NISY, YINY, YIGY, YVGY, FIGY, YIAY, and RRVM. Motif1 is widely distributed among all the clades. According to screening of cis-regulatory elements, GO annotation, expression sequence tags (EST), RNA-seq, and RT-qPCR, we reported that 24 RALF genes coding mature proteins related to tissue development, fungal infection, and hormone response. Purifying selection may play an important role in the evolutionary process of RALF-like genes among Rosaceae species according to the result from ka/ks. The tandem duplication event just occurs in four gene pairs (Fv-RALF9 and Fv-RALF10, Md-RALF7 and Md-RALF8, Pm-RALF2 and Pm-RALF8, and Pp-RALF11 and Pp-RALF14) from four Rosaceae species. Our research provides a wide overview of RALF-like genes in seven Rosaceae species involved in identification, classification, structure, expression, and evolution analysis.
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34
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Wang P, Yao S, Kosami K, Guo T, Li J, Zhang Y, Fukao Y, Kaneko‐Kawano T, Zhang H, She Y, Wang P, Xing W, Hanada K, Liu R, Kawano Y. Identification of endogenous small peptides involved in rice immunity through transcriptomics- and proteomics-based screening. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:415-428. [PMID: 31301098 PMCID: PMC6953209 DOI: 10.1111/pbi.13208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/30/2019] [Accepted: 07/10/2019] [Indexed: 05/10/2023]
Abstract
Small signalling peptides, generated from larger protein precursors, are important components to orchestrate various plant processes such as development and immune responses. However, small signalling peptides involved in plant immunity remain largely unknown. Here, we developed a pipeline using transcriptomics- and proteomics-based screening to identify putative precursors of small signalling peptides: small secreted proteins (SSPs) in rice, induced by rice blast fungus Magnaporthe oryzae and its elicitor, chitin. We identified 236 SSPs including members of two known small signalling peptide families, namely rapid alkalinization factors and phytosulfokines, as well as many other protein families that are known to be involved in immunity, such as proteinase inhibitors and pathogenesis-related protein families. We also isolated 52 unannotated SSPs and among them, we found one gene which we named immune response peptide (IRP) that appeared to encode the precursor of a small signalling peptide regulating rice immunity. In rice suspension cells, the expression of IRP was induced by bacterial peptidoglycan and fungal chitin. Overexpression of IRP enhanced the expression of a defence gene, PAL1 and induced the activation of the MAPKs in rice suspension cells. Moreover, the IRP protein level increased in suspension cell medium after chitin treatment. Collectively, we established a simple and efficient pipeline to discover SSP candidates that probably play important roles in rice immunity and identified 52 unannotated SSPs that may be useful for further elucidation of rice immunity. Our method can be applied to identify SSPs that are involved not only in immunity but also in other plant functions.
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Affiliation(s)
- Pingyu Wang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaolun Yao
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ken‐ichi Kosami
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Ting Guo
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jing Li
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuanyuan Zhang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yoichiro Fukao
- Department of BioinformaticsRitsumeikan UniversityShigaJapan
| | | | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Yi‐Min She
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- Present address:
Centre for Biologics EvaluationBiologics and Genetic Therapies Directorate, Health CanadaOttawaOntarioCanada
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Weiman Xing
- Biomolecular Structure and DesignShanghai Center for Plant Stress BiologyShanghaiChina
| | - Kousuke Hanada
- Department of Bioscience and BioinformaticsKyushu Institute of TechnologyFukuokaJapan
| | - Renyi Liu
- Center for Agroforestry Mega Data Science and FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yoji Kawano
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- Kihara Institute for Biological ResearchYokohama City UniversityKanagawaJapan
- Institute of Plant Science and ResourcesOkayama UniversityOkayamaJapan
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35
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Wu C, Ding X, Ding Z, Tie W, Yan Y, Wang Y, Yang H, Hu W. The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression. Int J Mol Sci 2019; 20:ijms20112730. [PMID: 31163686 PMCID: PMC6600411 DOI: 10.3390/ijms20112730] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/27/2023] Open
Abstract
The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops.
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Affiliation(s)
- Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xupo Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yu Wang
- Beijing Commerce and Trade School, Beijing 100162, China.
| | - Hai Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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Loss of function mutation of the Rapid Alkalinization Factor (RALF1)-like peptide in the dandelion Taraxacum koksaghyz entails a high-biomass taproot phenotype. PLoS One 2019; 14:e0217454. [PMID: 31125376 PMCID: PMC6534333 DOI: 10.1371/journal.pone.0217454] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 05/13/2019] [Indexed: 12/16/2022] Open
Abstract
The Russian dandelion (Taraxacum koksaghyz) is a promising source of inulin and natural rubber because large amounts of both feedstocks can be extracted from its roots. However, the domestication of T. koksaghyz requires the development of stable agronomic traits such as higher yields of inulin and natural rubber, a higher root biomass, and an agronomically preferable root morphology which is more suitable for cultivation and harvesting. Arabidopsis thaliana Rapid Alkalinisation Factor 1 (RALF1) has been shown to suppress root growth. We identified the T. koksaghyz orthologue TkRALF-like 1 and knocked out the corresponding gene (TkRALFL1) using the CRISPR/Cas9 system to determine its impact on root morphology, biomass, and inulin and natural rubber yields. The TkRALFL1 knockout lines more frequently developed a taproot phenotype which is easier to cultivate and harvest, as well as a higher root biomass and greater yields of both inulin and natural rubber. The TkRALFL1 gene could therefore be suitable as a genetic marker to support the breeding of profitable new dandelion varieties with improved agronomic traits. To our knowledge, this is the first study addressing the root system of T. koksaghyz to enhance the agronomic performance.
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Olsson V, Joos L, Zhu S, Gevaert K, Butenko MA, De Smet I. Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:153-186. [PMID: 30525926 DOI: 10.1146/annurev-arplant-042817-040413] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
During the past decade, a flurry of research focusing on the role of peptides as short- and long-distance signaling molecules in plant cell communication has been undertaken. Here, we focus on peptides derived from nonfunctional precursors, and we address several key questions regarding peptide signaling. We provide an overview of the regulatory steps involved in producing a biologically active peptide ligand that can bind its corresponding receptor(s) and discuss how this binding and subsequent activation lead to specific cellular outputs. We discuss different experimental approaches that can be used to match peptide ligands with their receptors. Lastly, we explore how peptides evolved from basic signaling units regulating essential processes in plants to more complex signaling systems as new adaptive traits developed and how nonplant organisms exploit this signaling machinery by producing peptide mimics.
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Affiliation(s)
- Vilde Olsson
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
| | - Lisa Joos
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Shanshuo Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Melinka A Butenko
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB-UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
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38
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Mittal S, Banduni P, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize. Front Chem 2018; 6:177. [PMID: 29876347 PMCID: PMC5974147 DOI: 10.3389/fchem.2018.00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/03/2018] [Indexed: 01/22/2023] Open
Abstract
Drought is one of the major threats to the maize yield especially in subtropical production systems. Understanding the genes and regulatory mechanisms of drought tolerance is important to sustain the yield. Transcription factors (TFs) play a major role in gene regulation under drought stress. In the present study, a set of 15 major TF families comprising 1,436 genes was structurally and functionally characterized. The functional annotation indicated that the genes were involved in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed for individual TF and combined TF families. Phylogenetic analysis clustered the genes into specific and mixed groups. Gene structure analysis revealed that more number of genes were intron-rich as compared to intron-less. Drought-responsive cis-regulatory elements such as ABREA, ABREB, DRE1, and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. Protein-protein interaction network of 269 drought-responsive genes belonging to different TFs has been provided. The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pooja Banduni
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prashant A Jain
- Department of Computational Biology & Bioinformatics, J.I.B.B., Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India
| | - Prasanta K Dash
- National Research Centre on Plant Biotechnology, New Delhi, India
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Celik Altunoglu Y, Unel NM, Baloglu MC, Ulu F, Can TH, Cetinkaya R. Comparative identification and evolutionary relationship of fatty acid desaturase (FAD) genes in some oil crops: the sunflower model for evaluation of gene expression pattern under drought stress. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1480421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Necdet Mehmet Unel
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Mehmet Cengiz Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Ferhat Ulu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Tevfik Hasan Can
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Rahmi Cetinkaya
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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40
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Campos WF, Dressano K, Ceciliato PHO, Guerrero-Abad JC, Silva AL, Fiori CS, Morato do Canto A, Bergonci T, Claus LAN, Silva-Filho MC, Moura DS. Arabidopsis thaliana rapid alkalinization factor 1-mediated root growth inhibition is dependent on calmodulin-like protein 38. J Biol Chem 2018; 293:2159-2171. [PMID: 29282286 PMCID: PMC5808775 DOI: 10.1074/jbc.m117.808881] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/09/2017] [Indexed: 11/06/2022] Open
Abstract
Arabidopsis thaliana rapid alkalinization factor 1 (AtRALF1) is a small secreted peptide hormone that inhibits root growth by repressing cell expansion. Although it is known that AtRALF1 binds the plasma membrane receptor FERONIA and conveys its signals via phosphorylation, the AtRALF1 signaling pathway is largely unknown. Here, using a yeast two-hybrid system to search for AtRALF1-interacting proteins in Arabidopsis, we identified calmodulin-like protein 38 (CML38) as an AtRALF1-interacting partner. We also found that CML38 and AtRALF1 are both secreted proteins that physically interact in a Ca2+- and pH-dependent manner. CML38-knockout mutants generated via T-DNA insertion were insensitive to AtRALF1, and simultaneous treatment with both AtRALF1 and CML38 proteins restored sensitivity in these mutants. Hybrid plants lacking CML38 and having high accumulation of the AtRALF1 peptide did not exhibit the characteristic short-root phenotype caused by AtRALF1 overexpression. Although CML38 was essential for AtRALF1-mediated root inhibition, it appeared not to have an effect on the AtRALF1-induced alkalinization response. Moreover, acridinium-labeling of AtRALF1 indicated that the binding of AtRALF1 to intact roots is CML38-dependent. In summary, we describe a new component of the AtRALF1 response pathway. The new component is a calmodulin-like protein that binds AtRALF1, is essential for root growth inhibition, and has no role in AtRALF1 alkalinization.
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Affiliation(s)
- Wellington F Campos
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Keini Dressano
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Paulo H O Ceciliato
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Juan Carlos Guerrero-Abad
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Aparecida Leonir Silva
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Celso S Fiori
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Amanda Morato do Canto
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Tábata Bergonci
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Lucas A N Claus
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
| | - Marcio C Silva-Filho
- the Laboratório de Biologia Molecular de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900, Brazil
| | - Daniel S Moura
- From the Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, USP, Piracicaba, SP, 13418-900 and
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Celik Altunoglu Y, Baloglu MC, Baloglu P, Yer EN, Kara S. Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:5-21. [PMID: 28250580 PMCID: PMC5313409 DOI: 10.1007/s12298-016-0405-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/29/2016] [Indexed: 05/20/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are large and diverse group of polypeptides which were first identified during seed dehydration and then in vegetative plant tissues during different stress responses. Now, gene family members of LEA proteins have been detected in various organisms. However, there is no report for this protein family in watermelon and melon until this study. A total of 73 LEA genes from watermelon (ClLEA) and 61 LEA genes from melon (CmLEA) were identified in this comprehensive study. They were classified into four and three distinct clusters in watermelon and melon, respectively. There was a correlation between gene structure and motif composition among each LEA groups. Segmental duplication played an important role for LEA gene expansion in watermelon. Maximum gene ontology of LEA genes was observed with poplar LEA genes. For evaluation of tissue specific expression patterns of ClLEA and CmLEA genes, publicly available RNA-seq data were analyzed. The expression analysis of selected LEA genes in root and leaf tissues of drought-stressed watermelon and melon were examined using qRT-PCR. Among them, ClLEA-12-17-46 genes were quickly induced after drought application. Therefore, they might be considered as early response genes for water limitation conditions in watermelon. In addition, CmLEA-42-43 genes were found to be up-regulated in both tissues of melon under drought stress. Our results can open up new frontiers about understanding of functions of these important family members under normal developmental stages and stress conditions by bioinformatics and transcriptomic approaches.
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Affiliation(s)
- Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, 37150 Kastamonu, Turkey
| | - Mehmet Cengiz Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, 37150 Kastamonu, Turkey
| | - Pinar Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, 37150 Kastamonu, Turkey
- Research and Application Center, Kastamonu University, Kastamonu, Turkey
| | - Esra Nurten Yer
- Department of Forest Engineering, Faculty of Forestry, Kastamonu University, Kastamonu, Turkey
| | - Sibel Kara
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, 37150 Kastamonu, Turkey
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Campbell L, Turner SR. A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups. FRONTIERS IN PLANT SCIENCE 2017; 8:37. [PMID: 28174582 PMCID: PMC5258720 DOI: 10.3389/fpls.2017.00037] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/09/2017] [Indexed: 05/20/2023]
Abstract
Rapid Alkalinization Factors (RALFs) are small, cysteine-rich peptides known to be involved in various aspects of plant development and growth. Although RALF peptides have been identified within many species, a single wide-ranging phylogenetic analysis of the family across the plant kingdom has not yet been undertaken. Here, we identified RALF proteins from 51 plant species that represent a variety of land plant lineages. The inferred evolutionary history of the 795 identified RALFs suggests that the family has diverged into four major clades. We found that much of the variation across the family exists within the mature peptide region, suggesting clade-specific functional diversification. Clades I, II, and III contain the features that have been identified as important for RALF activity, including the RRXL cleavage site and the YISY motif required for receptor binding. In contrast, members of clades IV that represent a third of the total dataset, is highly diverged and lacks these features that are typical of RALFs. Members of clade IV also exhibit distinct expression patterns and physico-chemical properties. These differences suggest a functional divergence of clades and consequently, we propose that the peptides within clade IV are not true RALFs, but are more accurately described as RALF-related peptides. Expansion of this RALF-related clade in the Brassicaceae is responsible for the large number of RALF genes that have been previously described in Arabidopsis thaliana. Future experimental work will help to establish the nature of the relationship between the true RALFs and the RALF-related peptides, and whether they function in a similar manner.
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Sharma A, Hussain A, Mun BG, Imran QM, Falak N, Lee SU, Kim JY, Hong JK, Loake GJ, Ali A, Yun BW. Comprehensive analysis of plant rapid alkalization factor (RALF) genes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 106:82-90. [PMID: 27155375 DOI: 10.1016/j.plaphy.2016.03.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/14/2016] [Accepted: 03/27/2016] [Indexed: 05/04/2023]
Abstract
Receptor mediated signal carriers play a critical role in the regulation of plant defense and development. Rapid alkalization factor (RALF) proteins potentially comprise important signaling components which may have a key role in plant biology. The RALF gene family contains large number of genes in several plant species, however, only a few RALF genes have been characterized to date. In this study, an extensive database search identified 39, 43, 34 and 18 RALF genes in Arabidopsis, rice, maize and soybean, respectively. These RALF genes were found to be highly conserved across the 4 plant species. A comprehensive analysis including the chromosomal location, gene structure, subcellular location, conserved motifs, protein structure, protein-ligand interaction and promoter analysis was performed. RALF genes from four plant species were divided into 7 groups based on phylogenetic analysis. In silico expression analysis of these genes, using microarray and EST data, revealed that these genes exhibit a variety of expression patterns. Furthermore, RALF genes showed distinct expression patterns of transcript accumulation in vivo following nitrosative and oxidative stresses in Arabidopsis. Predicted interaction between RALF and heme ligand also showed that RALF proteins may contribute towards transporting or scavenging oxygen moieties. This suggests a possible role for RALF genes during changes in cellular redox status. Collectively, our data provides a valuable resource to prime future research in the role of RALF genes in plant growth and development.
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Affiliation(s)
- Arti Sharma
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
| | - Adil Hussain
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea; Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan.
| | - Bong-Gyu Mun
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
| | - Qari Muhammad Imran
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
| | - Noreen Falak
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
| | - Sang-Uk Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
| | - Jae Young Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
| | - Jeum Kyu Hong
- Department of Horticultural Science, Gyeongnam National University of Science and Technology (GNTech), Jinju, Republic of Korea.
| | - Gary John Loake
- Institute of Molecular Plant Sciences, The University of Edinburgh, United Kingdom.
| | - Asad Ali
- Department of Plant Pathology, The University of Agriculture, Peshawar, Pakistan.
| | - Byung-Wook Yun
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
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Galindo-Trigo S, Gray JE, Smith LM. Conserved Roles of CrRLK1L Receptor-Like Kinases in Cell Expansion and Reproduction from Algae to Angiosperms. FRONTIERS IN PLANT SCIENCE 2016; 7:1269. [PMID: 27621737 PMCID: PMC5002434 DOI: 10.3389/fpls.2016.01269] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/10/2016] [Indexed: 05/20/2023]
Abstract
Receptor-like kinases (RLKs) are regulators of plant development through allowing cells to sense their extracellular environment. They facilitate detection of local endogenous signals, in addition to external biotic and abiotic stimuli. The Catharanthus roseus RLK1-like (CrRLK1L) protein kinase subfamily, which contains FERONIA, plays a central role in regulating fertilization and in cell expansion mechanisms such as cell elongation and tip growth, as well as having indirect links to plant-pathogen interactions. Several components of CrRLK1L signaling pathways have been identified, including an extracellular ligand, coreceptors, and downstream signaling elements. The presence and abundance of the CrRLK1L proteins in the plant kingdom suggest an origin within the Streptophyta lineage, with a notable increase in prevalence in the seeded land plants. Given the function of the sole CrRLK1L protein in a charophycean alga, the possibility of a conserved role in detection and/or regulation of cell wall integrity throughout the Strephtophytes is discussed. Orthologs of signaling pathway components are also present in extant representatives of non-vascular land plants and early vascular land plants including the liverwort Marchantia polymorpha, the moss Physcomitrella patens and the lycophyte Selaginella moellendorffii. Deciphering the roles in development of the CrRLK1L protein kinases in early diverging land plants will provide insights into their ancestral function, furthering our understanding of this diversified subfamily of receptors in higher plants.
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Affiliation(s)
| | - Julie E. Gray
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
| | - Lisa M. Smith
- Department of Animal and Plant Sciences, University of SheffieldSheffield, UK
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45
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Cao J. Analysis of the Prefoldin Gene Family in 14 Plant Species. FRONTIERS IN PLANT SCIENCE 2016; 7:317. [PMID: 27014333 PMCID: PMC4792155 DOI: 10.3389/fpls.2016.00317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/29/2016] [Indexed: 05/03/2023]
Abstract
Prefoldin is a hexameric molecular chaperone complex present in all eukaryotes and archaea. The evolution of this gene family in plants is unknown. Here, I identified 140 prefoldin genes in 14 plant species. These prefoldin proteins were divided into nine groups through phylogenetic analysis. Highly conserved gene organization and motif distribution exist in each prefoldin group, implying their functional conservation. I also observed the segmental duplication of maize prefoldin gene family. Moreover, a few functional divergence sites were identified within each group pairs. Functional network analyses identified 78 co-expressed genes, and most of them were involved in carrying, binding and kinase activity. Divergent expression profiles of the maize prefoldin genes were further investigated in different tissues and development periods and under auxin and some abiotic stresses. I also found a few cis-elements responding to abiotic stress and phytohormone in the upstream sequences of the maize prefoldin genes. The results provided a foundation for exploring the characterization of the prefoldin genes in plants and will offer insights for additional functional studies.
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Tavormina P, De Coninck B, Nikonorova N, De Smet I, Cammue BPA. The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions. THE PLANT CELL 2015; 27:2095-118. [PMID: 26276833 PMCID: PMC4568509 DOI: 10.1105/tpc.15.00440] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/08/2015] [Accepted: 07/25/2015] [Indexed: 05/18/2023]
Abstract
Peptides fulfill a plethora of functions in plant growth, development, and stress responses. They act as key components of cell-to-cell communication, interfere with signaling and response pathways, or display antimicrobial activity. Strikingly, both the diversity and amount of plant peptides have been largely underestimated. Most characterized plant peptides to date acting as small signaling peptides or antimicrobial peptides are derived from nonfunctional precursor proteins. However, evidence is emerging on peptides derived from a functional protein, directly translated from small open reading frames (without the involvement of a precursor) or even encoded by primary transcripts of microRNAs. These novel types of peptides further add to the complexity of the plant peptidome, even though their number is still limited and functional characterization as well as translational evidence are often controversial. Here, we provide a comprehensive overview of the reported types of plant peptides, including their described functional and structural properties. We propose a novel, unifying peptide classification system to emphasize the enormous diversity in peptide synthesis and consequent complexity of the still expanding knowledge on the plant peptidome.
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Affiliation(s)
- Patrizia Tavormina
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Natalia Nikonorova
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, United Kingdom Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
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47
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Cao J, Li X. Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato (Solanum lycopersicum). PLANTA 2015; 241:757-72. [PMID: 25491641 DOI: 10.1007/s00425-014-2215-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/25/2014] [Indexed: 05/19/2023]
Abstract
This study provided a comparative genomic analysis of the LEA gene family, and these may provide valuable information for their functional investigations in the future. Late embryogenesis abundant (LEA) proteins are a group of proteins that accumulate in response to cellular dehydration in many organisms. Here, we identified 27 LEA genes in tomato. A strong correlation between phylogeny, gene structure, and motif composition was found. The predicted SlLEA genes were non-randomly distributed within their chromosomes, and segmental and tandem duplications were probably important for their expansion. Many cis-elements potentially mediating transcription in response to abiotic stress were also found in the 1,000 bp upstream sequence of the promoter region. An additional intragenic recombination played an important role in the evolution of SlLEA genes. Selection analysis also identified some significant site-specific constraints that acted on the evolution of most LEA paralogs. Expression analysis using both microarray data and quantitative real-time PCR indicated that SlLEA genes were widely expressed in various tissues, and that a few members responded to some abiotic stresses. Our study provides useful information on the LEA genes in tomato and will facilitate their further characterization to better understand their functions.
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Affiliation(s)
- Jun Cao
- Institute of Life Science, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China,
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Cao J, Li X, Lv Y, Ding L. Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. FRONTIERS IN PLANT SCIENCE 2015; 6:515. [PMID: 26217366 PMCID: PMC4499708 DOI: 10.3389/fpls.2015.00515] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/26/2015] [Indexed: 05/18/2023]
Abstract
Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.
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Affiliation(s)
- Jun Cao
- *Correspondence: Jun Cao, Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Jiangsu, Zhenjiang 212013, China,
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Busch A, Horn S, Zachgo S. Differential transcriptome analysis reveals insight into monosymmetric corolla development of the crucifer Iberis amara. BMC PLANT BIOLOGY 2014; 14:285. [PMID: 25407089 PMCID: PMC4245847 DOI: 10.1186/s12870-014-0285-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/14/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND In the co-evolution between insects and plants, the establishment of floral monosymmetry was an important step in angiosperm development as it facilitated the interaction with insect pollinators and, by that, likely enhanced angiosperm diversification. In Antirrhinum majus, the TCP transcription factor CYCLOIDEA is the molecular key regulator driving the formation of floral monosymmetry. Although most Brassicaceae form a polysymmetric corolla, six genera develop monosymmetric flowers with two petal pairs of unequal size. In the monosymmetric crucifer Iberis amara, formation of the different petal pairs coincides with a stronger expression of the CYC-homolog IaTCP1 in the small, adaxial petals. RESULTS In this study, RNA-Seq was employed to reconstruct the petal transcriptome of the non-model species Iberis amara. About 9 Gb of sequence data was generated, processed and re-assembled into 18,139 likely Iberis unigenes, from which 15,983 showed high sequence homology to Arabidopsis proteins. The transcriptome gives detailed insight into the molecular mechanisms governing late petal development. In addition, it was used as a scaffold to detect genes differentially expressed between the small, adaxial and the large, abaxial petals in order to understand the molecular mechanisms driving unequal petal growth. Far more genes are expressed in adaxial compared to abaxial petals implying that IaTCP1 activates more genes than it represses. Amongst all genes upregulated in adaxial petals, a significantly enhanced proportion is associated with cell wall modification and cell-cell signalling processes. Furthermore, microarrays were used to detect and compare quantitative differences in TCP target genes in transgenic Arabidopsis plants ectopically expressing different TCP transcription factors. CONCLUSIONS The increased occurrences of genes implicated in cell wall modification and signalling implies that unequal petal growth is achieved through an earlier stop of the cell proliferation phase in the small, adaxial petals, followed by the onset of cell expansion. This process, which forms the monosymmetric corolla of Iberis amara, is likely driven by the enhanced activity of IaTCP1 in adaxial petals.
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Affiliation(s)
- Andrea Busch
- Department of Botany, Osnabrück University, Barbarastrasse, 11, Osnabrück, 49076 Germany
| | - Stefanie Horn
- Department of Botany, Osnabrück University, Barbarastrasse, 11, Osnabrück, 49076 Germany
| | - Sabine Zachgo
- Department of Botany, Osnabrück University, Barbarastrasse, 11, Osnabrück, 49076 Germany
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50
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Murphy E, De Smet I. Understanding the RALF family: a tale of many species. TRENDS IN PLANT SCIENCE 2014; 19:664-71. [PMID: 24999241 DOI: 10.1016/j.tplants.2014.06.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 05/02/2023]
Abstract
Small secreted peptides are gaining importance as signalling molecules in plants. Among the 1000 open reading frames (ORFs) in the Arabidopsis (Arabidopsis thaliana) genome potentially encoding small secreted peptides, the members of the RAPID ALKALINIZATION FACTOR (RALF) family of peptides have been linked to several physiological and developmental processes. Here, we provide a comprehensive overview of current knowledge on the RALF family. Discovered in tobacco (Nicotiana tabacum), the role of RALF peptides has been investigated in numerous plant species. Together, these observations suggest that RALF peptides impact on acidification and cell expansion during growth and development. Although few components of the signalling pathway have been revealed, the recent identification of FERONIA (FER) as a RALF receptor and plasma membrane H(+)-ATPase 2 as a downstream target provide a major step forward.
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Affiliation(s)
- Evan Murphy
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK; Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.
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