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Zhang Y, Ma Y, Zhao D, Tang Z, Zhang T, Zhang K, Dong J, Zhang H. Genetic regulation of lateral root development. PLANT SIGNALING & BEHAVIOR 2023; 18:2081397. [PMID: 35642513 PMCID: PMC10761116 DOI: 10.1080/15592324.2022.2081397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Lateral roots (LRs) are an important part of plant root systems. In dicots, for example, after plants adapted from aquatic to terrestrial environments, filamentous pseudorhizae evolved to allow nutrient absorption. A typical plant root system comprises a primary root, LRs, root hairs, and a root cap. Classical plant roots exhibit geotropism (the tendency to grow downward into the ground) and can synthesize plant hormones and other essential substances. Root vascular bundles and complex spatial structures enable plants to absorb water and nutrients to meet their nutrient quotas and grow. The primary root carries out most functions during early growth stages but is later overtaken by LRs, underscoring the importance of LR development water and mineral uptake and the soil fixation capacity of the root. LR development is modulated by endogenous plant hormones and external environmental factors, and its underlying mechanisms have been dissected in great detail in Arabidopsis, thanks to its simple root anatomy and the ease of obtaining mutants. This review comprehensively and systematically summarizes past research (largely in Arabidopsis) on LR basic structure, development stages, and molecular mechanisms regulated by different factors, as well as future prospects in LR research, to provide broad background knowledge for root researchers.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- Pear Engineering and Technology Research Center of Hebei, College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Yuru Ma
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Ziyan Tang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Tengteng Zhang
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Hao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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Mahmoud A, Qi R, Chi X, Liao N, Malangisha GK, Ali A, Moustafa-Farag M, Yang J, Zhang M, Hu Z. Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon. Int J Mol Sci 2023; 25:65. [PMID: 38203237 PMCID: PMC10779233 DOI: 10.3390/ijms25010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.
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Affiliation(s)
- Ahmed Mahmoud
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Rui Qi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Xiaolu Chi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Guy Kateta Malangisha
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Abid Ali
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Mohamed Moustafa-Farag
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Jinghua Yang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Zhongyuan Hu
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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Hummel NFC, Markel K, Stefani J, Staller MV, Shih PM. Systematic identification of transcriptional activator domains from non-transcription factor proteins in plants and yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557247. [PMID: 37745555 PMCID: PMC10515812 DOI: 10.1101/2023.09.12.557247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Transcription factors promote gene expression via trans-regulatory activation domains. Although whole genome scale screens in model organisms (e.g. human, yeast, fly) have helped identify activation domains from transcription factors, such screens have been less extensively used to explore the occurrence of activation domains in non-transcription factor proteins, such as transcriptional coactivators, chromatin regulators and some cytosolic proteins, leaving a blind spot on what role activation domains in these proteins could play in regulating transcription. We utilized the activation domain predictor PADDLE to mine the entire proteomes of two model eukaryotes, Arabidopsis thaliana and Saccharomyces cerevisiae ( 1 ). We characterized 18,000 fragments covering predicted activation domains from >800 non-transcription factor genes in both species, and experimentally validated that 89% of proteins contained fragments capable of activating transcription in yeast. Peptides with similar sequence composition show a broad range of activities, which is explained by the arrangement of key amino acids. We also annotated hundreds of nuclear proteins with activation domains as putative coactivators; many of which have never been ascribed any function in plants. Furthermore, our library contains >250 non-nuclear proteins containing peptides with activation domain function across both eukaryotic lineages, suggesting that there are unknown biological roles of these peptides beyond transcription. Finally, we identify and validate short, 'universal' eukaryotic activation domains that activate transcription in both yeast and plants with comparable or stronger performance to state-of-the-art activation domains. Overall, our dual host screen provides a blueprint on how to systematically discover novel genetic parts for synthetic biology that function across a wide diversity of eukaryotes. Significance Statement Activation domains promote transcription and play a critical role in regulating gene expression. Although the mapping of activation domains from transcription factors has been carried out in previous genome-wide screens, their occurrence in non-transcription factors has been less explored. We utilize an activation domain predictor to mine the entire proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae for new activation domains on non-transcription factor proteins. We validate peptides derived from >750 non-transcription factor proteins capable of activating transcription, discovering many potentially new coactivators in plants. Importantly, we identify novel genetic parts that can function across both species, representing unique synthetic biology tools.
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Wang L, Wang L, Tan M, Wang L, Zhao W, You J, Wang L, Yan X, Wang W. The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed (Linum usitatissimum L.) response to repeated drought stresses. Biol Res 2023; 56:12. [PMID: 36922868 PMCID: PMC10018860 DOI: 10.1186/s40659-023-00424-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Drought stress has significantly hampered agricultural productivity worldwide and can also result in modifications to DNA methylation levels. However, the dynamics of DNA methylation and its association with the changes in gene transcription and alternative splicing (AS) under drought stress are unknown in linseed, which is frequently cultivated in arid and semiarid regions. RESULTS We analysed AS events and DNA methylation patterns in drought-tolerant (Z141) and drought-sensitive (NY-17) linseed under drought stress (DS) and repeated drought stress (RD) treatments. We found that the number of intron-retention (IR) and alternative 3' splice site (Alt3'SS) events were significantly higher in Z141 and NY-17 under drought stress. We found that the linseed response to the DS treatment was mainly regulated by transcription, while the response to the RD treatment was coregulated by transcription and AS. Whole genome-wide DNA methylation analysis revealed that drought stress caused an increase in the overall methylation level of linseed. Although we did not observe any correlation between differentially methylated genes (DMGs) and differentially spliced genes (DSGs) in this study, we found that the DSGs whose gene body region was hypermethylated in Z141 and hypomethylated in NY-17 were enriched in abiotic stress response Gene Ontology (GO) terms. This finding implies that gene body methylation plays an important role in AS regulation in some specific genes. CONCLUSION Our study is the first comprehensive genome-wide analysis of the relationship between linseed methylation changes and AS under drought and repeated drought stress. Our study revealed different interaction patterns between differentially expressed genes (DEGs) and DSGs under DS and RD treatments and differences between methylation and AS regulation in drought-tolerant and drought-sensitive linseed varieties. The findings will probably be of interest in the future. Our results provide interesting insights into the association between gene expression, AS, and DNA methylation in linseed under drought stress. Differences in these associations may account for the differences in linseed drought tolerance.
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Affiliation(s)
- Ling Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Meilian Tan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Wei Zhao
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | | | - Xingchu Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, 430062, China.
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Patel A, Sahu KP, Mehta S, Javed M, Balamurugan A, Ashajyothi M, Sheoran N, Ganesan P, Kundu A, Gopalakrishnan S, Gogoi R, Kumar A. New Insights on Endophytic Microbacterium-Assisted Blast Disease Suppression and Growth Promotion in Rice: Revelation by Polyphasic Functional Characterization and Transcriptomics. Microorganisms 2023; 11:microorganisms11020362. [PMID: 36838327 PMCID: PMC9963279 DOI: 10.3390/microorganisms11020362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/24/2022] [Accepted: 01/01/2023] [Indexed: 02/05/2023] Open
Abstract
Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we report agriculturally beneficial traits of rice-leaf-adapted endophytic Microbacterium testaceum. Our polyphasic taxonomic investigations revealed its identity as M. testaceum. The bacterium displayed typical endophytism in rice leaves, indicated by the green fluorescence of GFP-tagged M. testaceum in confocal laser scanning microscopy. Furthermore, the bacterium showed mineral solubilization and production of IAA, ammonia, and hydrolytic enzymes. Tobacco leaf infiltration assay confirmed its non-pathogenic nature on plants. The bacterium showed antifungal activity on Magnaporthe oryzae, as exemplified by secreted and volatile organic metabolome-mediated mycelial growth inhibition. GC-MS analysis of the volatilome of M. testaceum indicated the abundance of antimicrobial compounds. Bacterization of rice seedlings showed phenotypic traits of MAMP-triggered immunity (MTI), over-expression of OsNPR1 and OsCERK, and the consequent blast suppressive activity. Strikingly, M. testaceum induced the transcriptional tradeoff between physiological growth and host defense pathways as indicated by up- and downregulated DEGs. Coupled with its plant probiotic features and the defense elicitation activity, the present study paves the way for developing Microbacterium testaceum-mediated bioformulation for sustainably managing rice blast disease.
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Varshney V, Majee M. Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits. PLANT CELL REPORTS 2022; 41:1805-1826. [PMID: 35678849 DOI: 10.1007/s00299-022-02884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.
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Affiliation(s)
- Vishal Varshney
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Panibe JP, Wang L, Lee YC, Wang CS, Li WH. Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution. BOTANICAL STUDIES 2022; 63:9. [PMID: 35347474 PMCID: PMC8960516 DOI: 10.1186/s40529-022-00336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. RESULTS Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. CONCLUSIONS We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1's blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.
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Affiliation(s)
- Jerome P. Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023 China
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung, 40227 Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
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Francisco FR, Aono AH, da Silva CC, Gonçalves PS, Scaloppi Junior EJ, Le Guen V, Fritsche-Neto R, Souza LM, de Souza AP. Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches. FRONTIERS IN PLANT SCIENCE 2021; 12:768589. [PMID: 34992619 PMCID: PMC8724537 DOI: 10.3389/fpls.2021.768589] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.
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Affiliation(s)
- Felipe Roberto Francisco
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Cristina da Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Paulo S. Gonçalves
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute (IAC), Votuporanga, Brazil
| | | | - Vincent Le Guen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Roberto Fritsche-Neto
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Livia Moura Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- São Francisco University (USF), Itatiba, Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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Abstract
Development encapsulates the morphogenesis of an organism from a single fertilized cell to a functional adult. A critical part of development is the specification of organ forms. Beyond the molecular control of morphogenesis, shape in essence entails structural constraints and thus mechanics. Revisiting recent results in biophysics and development, and comparing animal and plant model systems, we derive key overarching principles behind the formation of organs across kingdoms. In particular, we highlight how growing organs are active rather than passive systems and how such behavior plays a role in shaping the organ. We discuss the importance of considering different scales in understanding how organs form. Such an integrative view of organ development generates new questions while calling for more cross-fertilization between scientific fields and model system communities.
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Affiliation(s)
- O Hamant
- Laboratoire de Reproduction et Développement des Plantes, École normale supérieure (ENS) de Lyon, Université Claude Bernard Lyon (UCBL), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), CNRS, Université de Lyon, 69364 Lyon, France;
| | - T E Saunders
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore 117411; .,Institute of Molecular and Cell Biology, A*Star, Proteos, Singapore 138673
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Abd-Hamid NA, Ahmad-Fauzi MI, Zainal Z, Ismail I. Diverse and dynamic roles of F-box proteins in plant biology. PLANTA 2020; 251:68. [PMID: 32072251 DOI: 10.1007/s00425-020-03356-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Muhammad-Izzat Ahmad-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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11
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Sertse D, You FM, Ravichandran S, Cloutier S. The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:1483. [PMID: 31798617 PMCID: PMC6878218 DOI: 10.3389/fpls.2019.01483] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/25/2019] [Indexed: 05/05/2023]
Abstract
Roots are fundamental organs for water and nutrient uptake as well as for signal transduction in response to biotic and abiotic stresses. Flax has a shallow tap root system that relies mostly on top soil nutrient and moisture resources. The crop can easily be outcompeted by weeds or other crops in intercropping systems, especially in moisture deficit conditions. However, there is a wide range of variation among genotypes in terms of performance under scarce resources such as moisture limitation. Here we phenotyped 15 root, two shoot traits and shoot to root dry weight ratio on 115 flax accessions grown in a hydroponic pouch system and performed a genome-wide association study (GWAS) based on seven different models to identify quantitative trait loci underlying these traits. Significant variation among genotypes was observed for the two shoot and 12 of the 14 root traits. Shoot dry weight was correlated with root network volume, length, surface area, and root dry weight (r > 0.5, P < 0.001) but not significantly correlated with root depth (r = 0.033, P > 0.05). The seven GWAS models detected a total of 228 quantitative trait nucleotides (QTNs) for 16 traits. Most loci, defined by an interval of 100 kb up and downstream of the QTNs, harbored genes known to play role(s) in root and shoot development, suggesting them as candidates. Examples of candidate genes linked to root network QTNs included genes encoding GRAS transcription factors, mitogen-activated protein kinases, and auxin related lateral organ boundary proteins while QTN loci for shoot dry weight harbored genes involved in photomorphogenesis and plant immunity. These results provide insights into the genetic bases of early shoot and root development traits in flax that could be capitalized upon to improve its root architecture, particularly in view of better withstanding water limiting conditions during the cropping season.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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12
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Comparative proteomic analysis provides new insights into the specialization of shoots and stolons in bermudagrass (Cynodon dactylon L.). BMC Genomics 2019; 20:708. [PMID: 31510936 PMCID: PMC6740039 DOI: 10.1186/s12864-019-6077-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/04/2019] [Indexed: 12/26/2022] Open
Abstract
Background Bermudagrass (Cynodon dactylon L.) is an important turfgrass species with two types of stems, shoots and stolons. Despite their importance in determining the morphological variance and plasticity of bermudagrass, the intrinsic differences between stolons and shoots are poorly understood. Results In this study, we compared the proteomes of internode sections of shoots and stolons in the bermudagrass cultivar Yangjiang. The results indicated that 376 protein species were differentially accumulated in the two types of stems. Pathway enrichment analysis revealed that five and nine biochemical pathways were significantly enriched in stolons and shoots, respectively. Specifically, enzymes participating in starch synthesis all preferentially accumulated in stolons, whereas proteins involved in glycolysis and diverse transport processes showed relatively higher abundance in shoots. ADP-glucose pyrophosphorylase (AGPase) and pyruvate kinase (PK), which catalyze rate-limiting steps of starch synthesis and glycolysis, showed high expression levels and enzyme activity in stolons and shoots, respectively, in accordance with the different starch and soluble sugar contents of the two types of stems. Conclusions Our study revealed the differences between the shoots and stolons of bermudagrass at the proteome level. The results not only expand our understanding of the specialization of stolons and shoots but also provide clues for the breeding of bermudagrass and other turfgrasses with different plant architectures. Supplementary material Supplementary information accompanies this paper at 10.1186/s12864-019-6077-3.
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Podia V, Milioni D, Katsareli E, Valassakis C, Roussis A, Haralampidis K. Molecular and functional characterization of Arabidopsis thaliana VPNB1 gene involved in plant vascular development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:11-19. [PMID: 30466575 DOI: 10.1016/j.plantsci.2018.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 06/09/2023]
Abstract
Armadillo (ARM) repeat containing proteins constitute a large family in plants and are involved in diverse cellular functions, like signal transduction, proliferation and differentiation. In animals, ARM repeat proteins have been implicated in cancer development. In this study, we aimed in characterizing the VPNB1 gene from Arabidopsis thaliana and its role in plant development, by implementing a number of genetic and molecular approaches. AtVPNB1 encodes for an ARM repeat protein of unknown function, exclusively expressed in the cambium as well as in the differentiating xylem and phloem cells of the vascular system. Subcellular localization experiments showed that VPNB is confined in nucleoplasmic speckle-like structures unrelated to cajal bodies. Transgenic VPNB-impaired plants exhibit a slower growing phenotype and a non-canonical pattern of xylem tissue. On the contrary, VPNB overexpression lines display an inverted phenotype of increased growth, accompanied by an increased deposition of phloem and xylem cell layers. In line with the above data, qPCR analysis revealed a deregulation of several key master genes of secondary wall biosynthesis, underlining the involvement of VPNB1 in the regulation and differentiation of the root and shoot vascular tissue.
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Affiliation(s)
- Varvara Podia
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Dimitra Milioni
- Agricultural University of Athens, Department of Agricultural Biotechnology, Iera Odos 75, 11855 Athens, Greece.
| | - Efthimia Katsareli
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Chryssanthi Valassakis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Andreas Roussis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Kosmas Haralampidis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
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14
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Liu W, Pei M, Zhang A. Studying on the strictly self-compatibility mechanism of 'Liuyefeitao' peach (Prunus persica L.). PLoS One 2018; 13:e0200914. [PMID: 30067848 PMCID: PMC6070229 DOI: 10.1371/journal.pone.0200914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/04/2018] [Indexed: 11/18/2022] Open
Abstract
Peach (Prunus persica L.) generally exhibits self-pollination, however, they can also be pollinated by other varieties of pollen. Here we found two varieties that are different from other peaches: 'Daifei' and 'Liuyefeitao'. 'Daifei' produces less pollen, which needs artificial pollination, honeybee pollination, and the fruit setting depends on other varieties of peach pollen. 'Liuyefeitao' exhibits strictly self-pollination, hence pollen from other species is rejected. To explore the mechanism of this phenomenon, we performed a high-throughput sequencing of the stigma (including style) of 'Daifei' and 'Liuyefeitao' to explain the rejection mechanism of other varieties of pollen of 'Liuyefeitao' peach. In our study, we found one S gene, and lots of non-S-locus factors such as: F-box proteins, Ub/26S, MAPKs, RLK, and transcription factor were differential expressed between 'Daifei' and 'Liuyefeitao'. We supposed that the strictly self-compatible of 'Liuyefeitao' may result from the synthesis of these factors.
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Affiliation(s)
- Wei Liu
- Shandong Institute of Pomology, Taian, Shandong, People’s Republic of China
| | - Maosong Pei
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Anning Zhang
- Shandong Institute of Pomology, Taian, Shandong, People’s Republic of China
- * E-mail:
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15
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Eng RC, Halat LS, Livingston SJ, Sakai T, Motose H, Wasteneys GO. The ARM Domain of ARMADILLO-REPEAT KINESIN 1 is Not Required for Microtubule Catastrophe But Can Negatively Regulate NIMA-RELATED KINASE 6 in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:1350-1363. [PMID: 28505371 DOI: 10.1093/pcp/pcx070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 05/03/2017] [Indexed: 05/07/2023]
Abstract
Microtubules are dynamic filaments, the assembly and disassembly of which are under precise control of various associated proteins, including motor proteins and regulatory enzymes. In Arabidopsis thaliana, two such proteins are the ARMADILLO-REPEAT KINESIN 1 (ARK1), which promotes microtubule disassembly, and the NIMA-RELATED KINASE 6 (NEK6), which has a role in organizing microtubule arrays. Previous yeast two-hybrid and in vitro pull-down assays determined that NEK6 can interact with ARK1 through the latter protein's Armadillo-repeat (ARM) cargo domain. To explore the function of the ARM domain, we generated fluorescent reporter fusion proteins to ARK1 lacking the ARM domain (ARK1ΔARM-GFP) and to the ARM domain alone (ARM-GFP). Both of these constructs strongly associated with the growing plus ends of microtubules, but only ARK1ΔARM-GFP was capable of inducing microtubule catastrophe and rescuing the ark1-1 root hair phenotype. These results indicate that neither the ARM domain nor NEK6's putative interaction with it is required for ARK1 to induce microtubule catastrophe. In further exploration of the ARK1-NEK6 relationship, we demonstrated that, despite evidence that NEK6 can phosphorylate ARK1 in vitro, the in vivo distribution and function of ARK1 were not affected by the loss of NEK6, and vice versa. Moreover, NEK6 and ARK1 were found to have overlapping but non-identical distribution on microtubules, and hormone treatments known to affect NEK6 activity did not stimulate interaction. These findings suggest that ARK1 and NEK6 function independently in microtubule dynamics and cell morphogenesis. Despite the results of this functional analysis, we found that overexpression of the ARM domain led to complete loss of NEK6 transcription, suggesting that the ARM domain might have a regulatory role in NEK6 expression.
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Affiliation(s)
- Ryan C Eng
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Laryssa S Halat
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Samuel J Livingston
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Tatsuya Sakai
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Hiroyasu Motose
- Graduate School of Natural Science & Technology, Okayama University, Okayama 700-8530, Japan
| | - Geoffrey O Wasteneys
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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16
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Quan J, Meng S, Guo E, Zhang S, Zhao Z, Yang X. De novo sequencing and comparative transcriptome analysis of adventitious root development induced by exogenous indole-3-butyric acid in cuttings of tetraploid black locust. BMC Genomics 2017; 18:179. [PMID: 28209181 PMCID: PMC5314683 DOI: 10.1186/s12864-017-3554-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 02/03/2017] [Indexed: 11/15/2022] Open
Abstract
Background Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups. Results The short reads were assembled into 127,038 unitranscripts and 101,209 unigenes, with average lengths of 986 and 852 bp. In total, 10,181 and 14,924 differentially expressed genes (DEGs) were detected in the CK and IBA-treated groups, respectively. Comparison of the four consecutive developmental stages showed that 282 and 260 DEGs were shared between IBA-treated and CK, suggesting that IBA treatment increased the number of DEGs. We observed 1,721 up-regulated and 849 down-regulated genes in CI vs. II, 849 up-regulated and 836 down-regulated genes in CC vs. IC, 881 up-regulated and 631 down-regulated genes in CRP vs. IRP, and 5,626 up-regulated and 4,932 down-regulated genes in CAR vs. IAR, of which 25 up-regulated DEGs were common to four pairs, and these DEGs were significantly up-regulated at AR. These results suggest that substantial changes in gene expression are associated with adventitious rooting. GO functional category analysis indicated that IBA significantly up- or down-regulated processes associated with regulation of transcription, transcription of DNA dependent, integral to membrane and ATP binding during the development process. KEGG pathway enrichment indicated that glycolysis/gluconeogenesis, cysteine and methionine metabolism, photosynthesis, nucleotide sugar metabolism, and lysosome were the pathways most highly regulated by IBA. We identified a number of differentially regulated unigenes, including 12 methionine-related genes and 12 ethylene-related genes, associated with the KEGG pathway cysteine and methionine metabolism. The GO enrichment, pathway mapping, and gene expression profile analyses revealed molecular traits for root induction and initiation. Conclusion Our study presents a global view of the transcriptomic profiles of tetraploid black locust cuttings in response to IBA treatment and provides new insights into the fundamental mechanisms associated with auxin-induced adventitious rooting. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3554-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jine Quan
- The Environment and Ecology Key Laboratory of of Education Ministry in West China, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China.,Department of Forestry, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Seng Meng
- The Environment and Ecology Key Laboratory of of Education Ministry in West China, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China
| | - Erhui Guo
- Department of Forestry, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Sheng Zhang
- The Environment and Ecology Key Laboratory of of Education Ministry in West China, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China
| | - Zhong Zhao
- The Environment and Ecology Key Laboratory of of Education Ministry in West China, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China.
| | - Xitian Yang
- The Environment and Ecology Key Laboratory of of Education Ministry in West China, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China. .,Department of Forestry, Henan Agricultural University, Zhengzhou, Henan Province, China.
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17
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Moody LA, Saidi Y, Gibbs DJ, Choudhary A, Holloway D, Vesty EF, Bansal KK, Bradshaw SJ, Coates JC. An ancient and conserved function for Armadillo-related proteins in the control of spore and seed germination by abscisic acid. THE NEW PHYTOLOGIST 2016; 211:940-51. [PMID: 27040616 PMCID: PMC4982054 DOI: 10.1111/nph.13938] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/15/2016] [Indexed: 05/27/2023]
Abstract
Armadillo-related proteins regulate development throughout eukaryotic kingdoms. In the flowering plant Arabidopsis thaliana, Armadillo-related ARABIDILLO proteins promote multicellular root branching. ARABIDILLO homologues exist throughout land plants, including early-diverging species lacking true roots, suggesting that early-evolving ARABIDILLOs had additional biological roles. Here we investigated, using molecular genetics, the conservation and diversification of ARABIDILLO protein function in plants separated by c. 450 million years of evolution. We demonstrate that ARABIDILLO homologues in the moss Physcomitrella patens regulate a previously undiscovered inhibitory effect of abscisic acid (ABA) on spore germination. Furthermore, we show that A. thaliana ARABIDILLOs function similarly during seed germination. Early-diverging ARABIDILLO homologues from both P. patens and the lycophyte Selaginella moellendorffii can substitute for ARABIDILLO function during A. thaliana root development and seed germination. We conclude that (1) ABA was co-opted early in plant evolution to regulate functionally analogous processes in spore- and seed-producing plants and (2) plant ARABIDILLO germination functions were co-opted early into both gametophyte and sporophyte, with a specific rooting function evolving later in the land plant lineage.
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Affiliation(s)
- Laura A. Moody
- School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Younousse Saidi
- School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Daniel J. Gibbs
- School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | | | - Daniel Holloway
- School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Eleanor F. Vesty
- School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | | | | | - Juliet C. Coates
- School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
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18
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Bonhomme M, Boitard S, San Clemente H, Dumas B, Young N, Jacquet C. Genomic Signature of Selective Sweeps Illuminates Adaptation of Medicago truncatula to Root-Associated Microorganisms. Mol Biol Evol 2015; 32:2097-110. [PMID: 25901015 DOI: 10.1093/molbev/msv092] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Medicago truncatula is a model legume species used to investigate plant-microorganism interactions, notably root symbioses. Massive population genomic and transcriptomic data now available for this species open the way for a comprehensive investigation of genomic variations associated with adaptation of M. truncatula to its environment. Here we performed a fine-scale genome scan of selective sweep signatures in M. truncatula using more than 15 million single nucleotide polymorphisms identified on 283 accessions from two populations (Circum and Far West), and exploited annotation and published transcriptomic data to identify biological processes associated with molecular adaptation. We identified 58 swept genomic regions with a 15 kb average length and comprising 3.3 gene models on average. The unimodal sweep state probability distribution in these regions enabled us to focus on the best single candidate gene per region. We detected two unambiguous species-wide selective sweeps, one of which appears to underlie morphological adaptation. Population genomic analyses of the remaining 56 sweep signatures indicate that sweeps identified in the Far West population are less population-specific and probably more ancient than those identified in the Circum population. Functional annotation revealed a predominance of immunity-related adaptations in the Circum population. Transcriptomic data from accessions of the Far West population allowed inference of four clusters of coregulated genes putatively involved in the adaptive control of symbiotic carbon flow and nodule senescence, as well as in other root adaptations upon infection with soil microorganisms. We demonstrate that molecular adaptations in M. truncatula were primarily triggered by selective pressures from root-associated microorganisms.
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Affiliation(s)
- Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
| | - Simon Boitard
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique & AgroParisTech, Jouy-en-Josas, France Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle & Ecole Pratique des Hautes Etudes & CNRS & Université Pierre et Marie Curie, Paris, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
| | - Nevin Young
- Department of Plant Biology, University of Minnesota Department of Plant Pathology, University of Minnesota
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
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Gupta S, Garg V, Kant C, Bhatia S. Genome-wide survey and expression analysis of F-box genes in chickpea. BMC Genomics 2015; 16:67. [PMID: 25759239 PMCID: PMC4340835 DOI: 10.1186/s12864-015-1293-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea. RESULTS A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR. CONCLUSIONS The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.
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Affiliation(s)
- Shefali Gupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India.
| | - Vanika Garg
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India.
| | - Chandra Kant
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India.
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India.
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20
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Satbhai SB, Ristova D, Busch W. Underground tuning: quantitative regulation of root growth. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1099-112. [PMID: 25628329 DOI: 10.1093/jxb/eru529] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plants display a high degree of phenotypic plasticity that allows them to tune their form and function to changing environments. The plant root system has evolved mechanisms to anchor the plant and to efficiently explore soils to forage for soil resources. Key to this is an enormous capacity for plasticity of multiple traits that shape the distribution of roots in the soil. Such root system architecture-related traits are determined by root growth rates, root growth direction, and root branching. In this review, we describe how the root system is constituted, and which mechanisms, pathways, and genes mainly regulate plasticity of the root system in response to environmental variation.
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Affiliation(s)
- Santosh B Satbhai
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocentre (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Daniela Ristova
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocentre (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocentre (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
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Sharma M, Pandey GK. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1218. [PMID: 26793205 PMCID: PMC4707873 DOI: 10.3389/fpls.2015.01218] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants.
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Moses T, Papadopoulou KK, Osbourn A. Metabolic and functional diversity of saponins, biosynthetic intermediates and semi-synthetic derivatives. Crit Rev Biochem Mol Biol 2014; 49:439-62. [PMID: 25286183 PMCID: PMC4266039 DOI: 10.3109/10409238.2014.953628] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 01/11/2023]
Abstract
Saponins are widely distributed plant natural products with vast structural and functional diversity. They are typically composed of a hydrophobic aglycone, which is extensively decorated with functional groups prior to the addition of hydrophilic sugar moieties, to result in surface-active amphipathic compounds. The saponins are broadly classified as triterpenoids, steroids or steroidal glycoalkaloids, based on the aglycone structure from which they are derived. The saponins and their biosynthetic intermediates display a variety of biological activities of interest to the pharmaceutical, cosmetic and food sectors. Although their relevance in industrial applications has long been recognized, their role in plants is underexplored. Recent research on modulating native pathway flux in saponin biosynthesis has demonstrated the roles of saponins and their biosynthetic intermediates in plant growth and development. Here, we review the literature on the effects of these molecules on plant physiology, which collectively implicate them in plant primary processes. The industrial uses and potential of saponins are discussed with respect to structure and activity, highlighting the undoubted value of these molecules as therapeutics.
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Affiliation(s)
- Tessa Moses
- Department of Metabolic Biology, John Innes CentreColney Lane, NorwichUK
| | | | - Anne Osbourn
- Department of Metabolic Biology, John Innes CentreColney Lane, NorwichUK
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Gibbs DJ, Voß U, Harding SA, Fannon J, Moody LA, Yamada E, Swarup K, Nibau C, Bassel GW, Choudhary A, Lavenus J, Bradshaw SJ, Stekel DJ, Bennett MJ, Coates JC. AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis. THE NEW PHYTOLOGIST 2014; 203:1194-1207. [PMID: 24902892 PMCID: PMC4286813 DOI: 10.1111/nph.12879] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/07/2014] [Indexed: 05/18/2023]
Abstract
Plant root system plasticity is critical for survival in changing environmental conditions. One important aspect of root architecture is lateral root development, a complex process regulated by hormone, environmental and protein signalling pathways. Here we show, using molecular genetic approaches, that the MYB transcription factor AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis. We identify AtMYB93 as an interaction partner of the lateral-root-promoting ARABIDILLO proteins. Atmyb93 mutants have faster lateral root developmental progression and enhanced lateral root densities, while AtMYB93-overexpressing lines display the opposite phenotype. AtMYB93 is expressed strongly, specifically and transiently in the endodermal cells overlying early lateral root primordia and is additionally induced by auxin in the basal meristem of the primary root. Furthermore, Atmyb93 mutant lateral root development is insensitive to auxin, indicating that AtMYB93 is required for normal auxin responses during lateral root development. We propose that AtMYB93 is part of a novel auxin-induced negative feedback loop stimulated in a select few endodermal cells early during lateral root development, ensuring that lateral roots only develop when absolutely required. Putative AtMYB93 homologues are detected throughout flowering plants and represent promising targets for manipulating root systems in diverse crop species.
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Affiliation(s)
- Daniel J Gibbs
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ute Voß
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Susan A Harding
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jessica Fannon
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Laura A Moody
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Erika Yamada
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kamal Swarup
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Candida Nibau
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - George W Bassel
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Anushree Choudhary
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Julien Lavenus
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Susan J Bradshaw
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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25
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Komatsu S, Hiraga S, Nouri MZ. Analysis of flooding-responsive proteins localized in the nucleus of soybean root tips. Mol Biol Rep 2014; 41:1127-39. [PMID: 24385303 DOI: 10.1007/s11033-013-2959-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 12/21/2013] [Indexed: 12/11/2022]
Abstract
Flooding stress has negative impact on soybean cultivation as it severely impairs plant growth and development. To examine whether nuclear function is affected in soybean under flooding stress, abundance of nuclear proteins and their mRNA expression were analyzed. Two-day-old soybean seedlings were treated with flooding for 2 days, and nuclear proteins were purified from root tips. Gel-free proteomics analysis identified a total of 39 flooding-responsive proteins, of which abundance of 8 and 31 was increased and decreased, respectively, in soybean root tips. Among these differentially regulated proteins, the mRNA expression levels of five nuclear-localized proteins were further analyzed. The mRNA levels of four proteins, which are splicing factor PWI domain-containing protein, epsilon2-COP, beta-catenin, and clathrin heavy chain decreased under flooding stress, were also down-regulated. In addition, mRNA level of a receptor for activated protein kinase C1(RACK1) was down-regulated, though its protein was accumulated in the soybean nucleus in response to flooding stress. These results suggest that several nuclear-related proteins are decreased at both the protein and mRNA level in the root tips of soybean under flooding stress. Furthermore, RACK1 might have an important role with accumulation in the soybean nucleus under flooding-stress conditions.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba, 305-8518, Japan,
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26
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Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, Kapoor S, Tyagi AK, Pandey GK. Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development. DNA Res 2014; 21:267-83. [PMID: 24398598 PMCID: PMC4060948 DOI: 10.1093/dnares/dst056] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genes in the Armadillo (ARM)-repeat superfamily encode proteins with a range of developmental and physiological processes in unicellular and multicellular eukaryotes. These 42 amino acid, long tandem repeat-containing proteins have been abundantly recognized in many plant species. Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis. In this study, we performed a computational analysis in the rice genome (Oryza sativa L. subsp. japonica), and identified 158 genes of Armadillo superfamily. Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them. An in-depth analysis of gene expression through microarray and Q-PCR revealed a number of ARM proteins expressing differentially in abiotic stresses and developmental conditions, suggesting a potential roles of this superfamily in development and stress signalling. Comparative phylogenetic analysis between Arabidopsis and rice Armadillo genes revealed a high degree of evolutionary conservation between the orthologues in two plant species. The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection. This genome-wide identification and expression analysis provides a basis for further functional analysis of Armadillo genes under abiotic stress and reproductive developmental condition in the plant lineage.
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Affiliation(s)
- Manisha Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Amarjeet Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Alka Shankar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Amita Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Vinay Baranwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Akhilesh K Tyagi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi 110067, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
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27
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Vogelmann K, Subert C, Danzberger N, Drechsel G, Bergler J, Kotur T, Burmester T, Hoth S. Plasma membrane-association of SAUL1-type plant U-box armadillo repeat proteins is conserved in land plants. FRONTIERS IN PLANT SCIENCE 2014; 5:37. [PMID: 24600457 PMCID: PMC3928556 DOI: 10.3389/fpls.2014.00037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/27/2014] [Indexed: 05/08/2023]
Abstract
Post-translational protein modification plays a pivotal role in the regulation and specific turnover of proteins. One of these important modifications is the ubiquitination of target proteins, which can occur at distinct cellular compartments. At the plasma membrane, ubiquitination regulates the internalization and thus trafficking of membrane proteins such as receptors and channels. The Arabidopsis plant U-box (PUB) armadillo repeat (PUB-ARM) ubiquitin ligase SAUL1 (SENESCENCE-ASSOCIATED UBIQUITIN LIGASE1) is part of the ubiquitination machinery at the plasma membrane. In contrast to most other PUB-ARM proteins, SAUL1 carries additional C-terminal ARM repeats responsible for plasma membrane-association. Here, we demonstrated that the C-terminal ARM repeat domain is also essential and sufficient to mediate plasma membrane-association of the closest Arabidopis paralog AtPUB43. We investigated targeting of PUB-ARM ubiquitin ligases of different plant species to find out whether plasma membrane-association of SAUL1-type PUB-ARM proteins is conserved. Phylogenetic analysis identified orthologs of SAUL1 in these plant species. Intracellular localization of transiently expressed GFP fusion proteins revealed that indeed plasma membrane-association due to additional C-terminal ARM repeats represents a conserved feature of SAUL1-type proteins. Analyses of transgenic Arabidopsis plants overexpressing N-terminally masked or truncated proteins revealed that interfering with the function of SAUL1-type proteins resulted in severe growth defects. Our results suggest an ancient origin of ubiquitination at the plasma membrane in the evolution of land plants.
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Affiliation(s)
- Katja Vogelmann
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Christa Subert
- Department Biologie, Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Nina Danzberger
- Department Biologie, Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Gabriele Drechsel
- Zentrum für Molekularbiologie der Pflanzen, Allgemeine Genetik, Universität TübingenTübingen, Germany
| | - Johannes Bergler
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Tanja Kotur
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Thorsten Burmester
- Stoffwechselphysiologie, Biozentrum Grindel, Universität HamburgHamburg, Germany
| | - Stefan Hoth
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
- *Correspondence: Stefan Hoth, Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststrasse 18, D-22609 Hamburg, Germany e-mail:
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28
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Plant Cell Wall Polysaccharides: Structure and Biosynthesis. POLYSACCHARIDES 2014. [DOI: 10.1007/978-3-319-03751-6_73-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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29
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Gibbs DJ, Coates JC. AtMYB93 is an endodermis-specific transcriptional regulator of lateral root development in arabidopsis. PLANT SIGNALING & BEHAVIOR 2014; 9:e970406. [PMID: 25482809 PMCID: PMC4622915 DOI: 10.4161/15592316.2014.970406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Plant root systems are critical for survival, acting as the primary interface for nutrient and water acquisition, as well as anchoring the plant to the ground. As plants grow, their root systems become more elaborate, which is largely mediated by the formation of root branches, or lateral roots. Lateral roots initiate deep within the root in the pericycle cell layer, and their development is controlled by a wide range of internal signaling factors and environmental cues, as well as mechanical feedback from the surrounding cells. The endodermal cell layer, which overlies the pericycle, has emerged as an important tissue regulating LR initiation and formation. We recently identified the AtMYB93 transcription factor as a negative regulator of lateral root development in Arabidopsis. Interestingly, AtMYB93 expression is highly restricted to the few endodermal cells overlying developing lateral root primordia, suggesting that this transcriptional regulator might play a key role in mediating the effect of the endodermis on lateral root development. Here we discuss our recent findings in the wider context of root system development - with a particular focus on the role of the endodermis - and propose several potential models to explain AtMYB93 function during lateral root organogenesis.
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Affiliation(s)
- Daniel J Gibbs
- School of Biosciences; University of Birmingham; Edgbaston, UK
| | - Juliet C Coates
- School of Biosciences; University of Birmingham; Edgbaston, UK
- Correspondence to: Juliet C Coates;
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30
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Cuesta C, Wabnik K, Benková E. Systems approaches to study root architecture dynamics. FRONTIERS IN PLANT SCIENCE 2013; 4:537. [PMID: 24421783 PMCID: PMC3872734 DOI: 10.3389/fpls.2013.00537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/11/2013] [Indexed: 05/05/2023]
Abstract
The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.
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Affiliation(s)
- Candela Cuesta
- Institute of Science and Technology AustriaKlosterneuburg, Austria
| | - Krzysztof Wabnik
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent UniversityTechnologiepark, Gent, Belgium
| | - Eva Benková
- Institute of Science and Technology AustriaKlosterneuburg, Austria
- Mendel Centre for Plant Genomics and Proteomics, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Eva Benková, Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria e-mail:
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31
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Parfrey LW, Lahr DJG. Multicellularity arose several times in the evolution of eukaryotes (Response to DOI 10.1002/bies.201100187). Bioessays 2013; 35:339-47. [DOI: 10.1002/bies.201200143] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Di Giacomo E, Serino G, Frugis G. Emerging role of the ubiquitin proteasome system in the control of shoot apical meristem function(f). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:7-20. [PMID: 23164365 DOI: 10.1111/jipb.12010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The shoot apical meristem (SAM) is a population of undifferentiated cells at the tip of the shoot axis that establishes early during plant embryogenesis and gives rise to all shoot organs throughout the plant's life. A plethora of different families of transcription factors (TFs) play a key role in establishing the equilibrium between cell differentiation and stem cell maintenance in the SAM. Fine tuning of these regulatory proteins is crucial for a proper and fast SAM response to environmental and hormonal cues, and for development progression. One effective way to rapidly inactivate TFs involves regulated proteolysis by the ubiquitin/26S proteasome system (UPS). However, a possible role of UPS-dependent protein degradation in the regulation of key SAM TFs has not been thoroughly investigated. Here, we summarize recent evidence supporting a role for the UPS in SAM maintenance and function. We integrate this survey with an in silico analysis of publicly-available microarray databases which identified ubiquitin ligases that are expressed in specific areas within the SAM, suggesting that they may regulate or act downstream of meristem-specific factors.
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Affiliation(s)
- Elisabetta Di Giacomo
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Monterotondo Scalo, Roma 00015, Italy
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Moody LA, Saidi Y, Smiles EJ, Bradshaw SJ, Meddings M, Winn PJ, Coates JC. ARABIDILLO gene homologues in basal land plants: species-specific gene duplication and likely functional redundancy. PLANTA 2012; 236:1927-41. [PMID: 22945313 DOI: 10.1007/s00425-012-1742-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/05/2012] [Indexed: 05/04/2023]
Abstract
ARABIDILLO proteins regulate multicellular root development in Arabidopsis thaliana. Conserved ARABIDILLO homologues are present throughout land plants, even in early-evolving plants that do not possess complex root architecture, suggesting that ARABIDILLO genes have additional functions. Here, we have cloned and characterised ARABIDILLO gene homologues from two early-evolving land plants, the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii. We show that two of the PHYSCODILLO genes (PHYSCODILLO1A and -1B) exist as a tail-to-tail tandem array of two almost identical 12 kb sequences, while a third related gene (PHYSCODILLO2) is located elsewhere in the Physcomitrella genome. Physcomitrella possesses a very low percentage of tandemly arrayed genes compared with the later-evolving plants whose genomes have been sequenced to date. Thus, PHYSCODILLO1A and -1B genes represent a relatively unusual gene arrangement. PHYSCODILLO promoters are active largely in the haploid gametophyte, with additional activity at the foot of the sporophyte. The pattern of promoter activity is uniform in filamentous and leafy tissues, suggesting pleiotropic gene functions and likely functional redundancy: the latter possibility is confirmed by the lack of discernible phenotype in a physcodillo2 deletion mutant. Interestingly, the pattern of PHYSCODILLO promoter activity in female reproductive organs is strikingly similar to that of an Arabidopsis homologue, suggesting co-option of some PHYSCODILLO functions or regulation into both the sporophyte and gametophyte. In conclusion, our work identifies and characterises some of the earliest-evolving land plant ARABIDILLO homologues. We confirm that all land plant ARABIDILLO genes arose from a single common ancestor and suggest that PHYSCODILLO proteins have novel and pleiotropic functions, some of which may be conserved in later-evolving plants.
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Affiliation(s)
- Laura A Moody
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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34
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Ngo QA, Baroux C, Guthörl D, Mozerov P, Collinge MA, Sundaresan V, Grossniklaus U. The Armadillo repeat gene ZAK IXIK promotes Arabidopsis early embryo and endosperm development through a distinctive gametophytic maternal effect. THE PLANT CELL 2012; 24:4026-43. [PMID: 23064319 PMCID: PMC3517234 DOI: 10.1105/tpc.112.102384] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The proper balance of parental genomic contributions to the fertilized embryo and endosperm is essential for their normal growth and development. The characterization of many gametophytic maternal effect (GME) mutants affecting seed development indicates that there are certain classes of genes with a predominant maternal contribution. We present a detailed analysis of the GME mutant zak ixik (zix), which displays delayed and arrested growth at the earliest stages of embryo and endosperm development. ZIX encodes an Armadillo repeat (Arm) protein highly conserved across eukaryotes. Expression studies revealed that ZIX manifests a GME through preferential maternal expression in the early embryo and endosperm. This parent-of-origin-dependent expression is regulated by neither the histone and DNA methylation nor the DNA demethylation pathways known to regulate some other GME mutants. The ZIX protein is localized in the cytoplasm and nucleus of cells in reproductive tissues and actively dividing root zones. The maternal ZIX allele is required for the maternal expression of miniseed3. Collectively, our results reveal a reproductive function of plant Arm proteins in promoting early seed growth, which is achieved through a distinct GME of ZIX that involves mechanisms for maternal allele-specific expression that are independent of the well-established pathways.
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Affiliation(s)
- Quy A. Ngo
- Institute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
- Section of Plant Biology, University of California, Davis, California 95616
- Address correspondence to
| | - Celia Baroux
- Institute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
| | - Daniela Guthörl
- Institute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
| | - Peter Mozerov
- Institute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
| | - Margaret A. Collinge
- Institute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
| | - Venkatesan Sundaresan
- Section of Plant Biology, University of California, Davis, California 95616
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
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35
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Smith S, De Smet I. Root system architecture: insights from Arabidopsis and cereal crops. Philos Trans R Soc Lond B Biol Sci 2012; 367:1441-52. [PMID: 22527386 DOI: 10.1098/rstb.2011.0234] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Understanding the development and architecture of roots holds potential for the exploitation and manipulation of root characteristics to both increase food plant yield and optimize agricultural land use. This theme issue highlights the importance of investigating specific aspects of root architecture in both the model plant Arabidopsis thaliana and (cereal) crops, presents novel insights into elements that are currently hardly addressed and provides new tools and technologies to study various aspects of root system architecture. This introduction gives a broad overview of the importance of the root system and provides a snapshot of the molecular control mechanisms associated with root branching and responses to the environment in A. thaliana and cereal crops.
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Affiliation(s)
- Stephanie Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
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36
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Mei Y, Gao HB, Yuan M, Xue HW. The Arabidopsis ARCP protein, CSI1, which is required for microtubule stability, is necessary for root and anther development. THE PLANT CELL 2012; 24:1066-80. [PMID: 22427339 PMCID: PMC3336141 DOI: 10.1105/tpc.111.095059] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 01/21/2012] [Accepted: 03/01/2012] [Indexed: 05/18/2023]
Abstract
Armadillo repeat-containing proteins (ARCPs) are conserved across eukaryotic kingdoms and function in various processes. Regulation of microtubule stability by ARCPs exists widely in mammals and algae, but little is known in plants. Here, we present the functional characterization of an Arabidopsis thaliana ARCP, which was previously identified as Cellulose synthase-interactive protein1 (CSI1), and prove its crucial role in anther and root development. CSI1 is highly expressed in floral tissues, and knockout mutants of CSI1 (three allelic lines) accordingly exhibit defective anther dehiscence, which can be partially rescued by mammalian microtubule-stabilizer MAP4, suggesting that CSI1 functions by stabilizing the microtubular cytoskeleton. CSI1 binds microtubules in vitro, and immunofluorescence and coimmunoprecipitation studies confirmed the physical interactions between CSI1 and microtubules in vivo. Analysis using oryzalin, a microtubule-disrupting drug, further revealed the destabilized microtubules under CSI1 deficiency and confirmed the crucial role of CSI1 in microtubule stability. The dynamic change of CSI1 in response to dehydration strongly suggests the important function of CSI1 in dehydration-induced microtubule depolymerization and reorganization, which is crucial for anther development. These results indicate the pivotal role of CSI1 in anther development by regulating microtubule stability and hence cell morphogenesis.
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Affiliation(s)
- Yu Mei
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Bo Gao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ming Yuan
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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37
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Gardiner J, Overall R, Marc J. Plant microtubule cytoskeleton complexity: microtubule arrays as fractals. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:635-42. [PMID: 22016422 DOI: 10.1093/jxb/err312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Biological systems are by nature complex and this complexity has been shown to be important in maintaining homeostasis. The plant microtubule cytoskeleton is a highly complex system, with contributing factors through interactions with microtubule-associated proteins (MAPs), expression of multiple tubulin isoforms, and post-translational modification of tubulin and MAPs. Some of this complexity is specific to microtubules, such as a redundancy in factors that regulate microtubule depolymerization. Plant microtubules form partial helical fractals that play a key role in development. It is suggested that, under certain cellular conditions, other categories of microtubule fractals may form including isotropic fractals, triangular fractals, and branched fractals. Helical fractal proteins including coiled-coil and armadillo/beta-catenin repeat proteins and the actin cytoskeleton are important here too. Either alone, or in combination, these fractals may drive much of plant development.
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Affiliation(s)
- John Gardiner
- The School of Biological Sciences, The University of Sydney 2006, Australia.
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Dubrovsky JG, Forde BG. Quantitative analysis of lateral root development: pitfalls and how to avoid them. THE PLANT CELL 2012; 24:4-14. [PMID: 22227889 PMCID: PMC3289558 DOI: 10.1105/tpc.111.089698] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/04/2011] [Accepted: 10/12/2011] [Indexed: 05/17/2023]
Abstract
The advent of the postgenomics era has led to increased interest in exploring the role of gene networks and signaling pathways in controlling plant development. The last two decades have seen a particular increase in the number of studies focusing on the development of the Arabidopsis thaliana root system. However, the investigation of such a seemingly simple system as an Arabidopsis root can lead to problems in quantification and errors in interpretation if knowledge of root organization is lacking. In this article, we identify a number of these problems and give examples of potentially erroneous and correct determinations of lateral root parameters. Our aim is to bring this important issue to the attention of the plant science community and to suggest ways in which the problems inherent in quantifying the process of lateral root development can be avoided.
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Affiliation(s)
- Joseph G Dubrovsky
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250 Cuernavaca, Morelos, Mexico.
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Gardiner J, Overall R, Marc J. PDZ domain proteins: 'dark matter' of the plant proteome? MOLECULAR PLANT 2011; 4:933-937. [PMID: 21653283 DOI: 10.1093/mp/ssr043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PDZ domain proteins in metazoans function in diverse roles, and in conjunction with PDZ domain-binding proteins form macromolecular complexes for signaling at synapses and cell junctions. Bioinformatics approaches using the SMART tool indicate there are only a modest number of Arabidopsis PDZ proteins. However, there are hundreds of proteins predicted to possess PDZ domain-binding motifs, suggesting that there are many PDZ domain proteins not detectable by conventional bioinformatic approaches. Our Scansite analysis of PDZ domain-binding proteins indicates that PDZ domain proteins may play key roles in cytoskeletal organization including actin microfilaments, microtubules, and nuclear cytoskeletal proteins, and in the organization of macromolecular complexes involved in cell-to-cell signaling, transport, and cell wall formation.
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Affiliation(s)
- John Gardiner
- School of Biological Sciences, University of Sydney, Sydney 2006, Australia.
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Kutuzov MA, Andreeva AV. Prediction of biological functions of Shewanella-like protein phosphatases (Shelphs) across different domains of life. Funct Integr Genomics 2011; 12:11-23. [DOI: 10.1007/s10142-011-0254-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Revised: 09/07/2011] [Accepted: 09/13/2011] [Indexed: 12/12/2022]
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41
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Jia Y, Gu H, Wang X, Chen Q, Shi S, Zhang J, Ma L, Zhang H, Ma H. Molecular cloning and characterization of an F-box family gene CarF-box1 from chickpea (Cicer arietinum L.). Mol Biol Rep 2011; 39:2337-45. [PMID: 21667242 DOI: 10.1007/s11033-011-0984-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/28/2011] [Indexed: 11/30/2022]
Abstract
F-box protein family has been found to play important roles in plant development and abiotic stress responses via the ubiquitin pathway. In this study, an F-box gene CarF-box1 (for Cicer arietinum F-box gene 1, Genbank accession no. GU247510) was isolated based on a cDNA library constructed with chickpea seedling leaves treated by polyethylene glycol. CarF-box1 encoded a putative protein with 345 amino acids and contained no intron within genomic DNA sequence. CarF-box1 is a KFB-type F-box protein, having a conserved F-box domain in the N-terminus and a Kelch repeat domain in the C-terminus. CarF-box1 was localized in the nucleus. CarF-box1 exhibited organ-specific expression and showed different expression patterns during seed development and germination processes, especially strongly expressed in the blooming flowers. In the leaves, CarF-box1 could be significantly induced by drought stress and slightly induced by IAA treatment, while in the roots, CarF-box1 could be strongly induced by drought, salinity and methyl jasmonate stresses. Our results suggest that CarF-box1 encodes an F-box protein and may be involved in various plant developmental processes and abiotic stress responses.
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Affiliation(s)
- Yuying Jia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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42
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A Molecular Switch for Initiating Cell Differentiation in Arabidopsis. Curr Biol 2011; 21:999-1008. [DOI: 10.1016/j.cub.2011.04.041] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 11/20/2022]
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43
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El Kayal W, Allen CCG, Ju CJT, Adams E, King-Jones S, Zaharia LI, Abrams SR, Cooke JEK. Molecular events of apical bud formation in white spruce, Picea glauca. PLANT, CELL & ENVIRONMENT 2011; 34:480-500. [PMID: 21118421 DOI: 10.1111/j.1365-3040.2010.02257.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome-level changes that occur during bud formation of white spruce [Picea glauca (Moench) Voss], a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day-induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod-responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for abscisic acid (ABA), cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues. These findings provide a temporal roadmap of bud formation in white spruce.
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Affiliation(s)
- Walid El Kayal
- University of Alberta, Department of Biological Sciences, Edmonton, Alberta, Canada T6G2E9
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Jia L, Wu Z, Hao X, Carrie C, Zheng L, Whelan J, Wu Y, Wang S, Wu P, Mao C. Identification of a novel mitochondrial protein, short postembryonic roots 1 (SPR1), involved in root development and iron homeostasis in Oryza sativa. THE NEW PHYTOLOGIST 2011; 189:843-855. [PMID: 21039568 DOI: 10.1111/j.1469-8137.2010.03513.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
• A rice mutant, Oryza sativa short postembryonic roots 1 (Osspr1), has been characterized. It has short postembryonic roots, including adventitious and lateral roots, and a lower iron content in its leaves. • OsSPR1 was identified by map-based cloning. It encodes a novel mitochondrial protein with the Armadillo-like repeat domain. • Osspr1 mutants exhibited decreased root cell elongation. The iron content of the mutant shoots was significantly altered compared with that of wild-type shoots. A similar pattern of alteration of manganese and zinc concentrations in shoots was also observed. Complementation of the mutant confirmed that OsSPR1 is involved in post-embryonic root elongation and iron homeostasis in rice. OsSPR1 was found to be ubiquitously expressed in various tissues throughout the plant. The transcript abundance of various genes involved in iron uptake and signaling via both strategies I and II was similar in roots of wild-type and mutant plants, but was higher in the leaves of mutant plants. • Thus, a novel mitochondrial protein that is involved in root elongation and plays a role in metal ion homeostasis has been identified.
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Affiliation(s)
- Liqiang Jia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Zhongchang Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Xi Hao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Chris Carrie
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009 WA, Australia
- Joint Laboratory in Genomics and Nutriomics, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Libin Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, 6009 WA, Australia
- Joint Laboratory in Genomics and Nutriomics, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Yunrong Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Shoufeng Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Ping Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
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Nibau C, Gibbs DJ, Bunting KA, Moody LA, Smiles EJ, Tubby JA, Bradshaw SJ, Coates JC. ARABIDILLO proteins have a novel and conserved domain structure important for the regulation of their stability. PLANT MOLECULAR BIOLOGY 2011; 75:77-92. [PMID: 21052782 DOI: 10.1007/s11103-010-9709-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 10/20/2010] [Indexed: 05/10/2023]
Abstract
ARABIDILLO proteins are F-box-Armadillo (ARM) proteins that regulate root branching in Arabidopsis. Many F-box proteins in plants, yeast and mammals are unstable. In plants, the mechanism for this instability has not been fully investigated. Here, we show that a conserved family of plant ARABIDILLO-related proteins has a unique domain structure consisting of an F-box and leucine-rich repeats (LRRs) followed by ARM-repeats. The LRRs are similar to those found in other plant and animal F-box proteins, including cell cycle proteins and hormone receptors. We demonstrate that the LRRs are required for ARABIDILLO1 function in vivo. ARABIDILLO1 protein is unstable: we show that ARABIDILLO1 protein is associated with ubiquitin and is turned over by the proteasome. Both the F-box and LRR regions of ARABIDILLO1 appear to enable this turnover to occur. Application of known lateral root-regulating signals has no effect on ARABIDILLO1 stability. In addition, plants that lack or overexpress ARABIDILLO proteins respond normally to known lateral root-regulating signals. Thus, we suggest that the signal(s) regulating ARABIDILLO stability in vivo may be either highly specific or novel. The structural conservation between ARABIDILLOs and other plant and animal F-box proteins suggests that the stability of other F-box proteins may be controlled by similar mechanisms.
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Affiliation(s)
- Cândida Nibau
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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Delis C, Krokida A, Georgiou S, Peña-Rodríguez LM, Kavroulakis N, Ioannou E, Roussis V, Osbourn AE, Papadopoulou KK. Role of lupeol synthase in Lotus japonicus nodule formation. THE NEW PHYTOLOGIST 2011; 189:335-46. [PMID: 20868395 DOI: 10.1111/j.1469-8137.2010.03463.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
• Triterpenes are plant secondary metabolites, derived from the cyclization of 2,3-oxidosqualene by oxidosqualene cyclases (OSCs). Here, we investigated the role of lupeol synthase, encoded by OSC3, and its product, lupeol, in developing roots and nodules of the model legume Lotus japonicus. • The expression patterns of OSC3 in different developmental stages of uninfected roots and in roots infected with Mesorhizobium loti were determined. The tissue specificity of OSC3 expression was analysed by in situ hybridization. Functional analysis, in which transgenic L. japonicus roots silenced for OSC3 were generated, was performed. The absence of lupeol in the silenced plant lines was determined by GC-MS. • The expression of ENOD40, a marker gene for nodule primordia initiation, was increased significantly in the OSC3-silenced plant lines, suggesting that lupeol influences nodule formation. Silenced plants also showed a more rapid nodulation phenotype, consistent with this. Exogenous application of lupeol to M. loti-infected wild-type plants provided further evidence for a negative regulatory effect of lupeol on the expression of ENOD40. • The synthesis of lupeol in L. japonicus roots and nodules can be solely attributed to OSC3. Taken together, our data suggest a role for lupeol biosynthesis in nodule formation through the regulation of ENOD40 gene expression.
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Affiliation(s)
- Costas Delis
- Department of Biochemistry & Biotechnology, University of Thessaly, Larissa, Greece
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Abstract
The posttranslational addition of ubiquitin (Ub) helps control the half-life, localization, and action of many intracellular plant proteins. A primary function is the degradation of ubiquitylated proteins by the 26S proteasome, which in turn plays important housekeeping and regulatory roles by removing aberrant polypeptides and various normal short-lived regulators. Strikingly, both genetic and genomic studies reveal that Ub conjugation is extraordinarily complex in plants, with more than 1500 Ub-protein ligases (or E3s) possible that could direct the final transfer of the Ub moiety to an equally large number of targets. The cullin-RING ligases (CRLs) are a highly polymorphic E3 collection composed of a cullin backbone onto which binds carriers of activated Ub and a diverse assortment of adaptors that recruit appropriate substrates for ubiquitylation. Here, we review our current understanding of the organization and structure of CRLs in plants and their dynamics, substrates, potential functions, and evolution. The importance of CRLs is exemplified by their ability to serve as sensors of hormones and light; their essential participation in various signaling pathways; their control of the cell cycle, transcription, the stress response, self-incompatibility, and pathogen defense; and their dramatically divergent evolutionary histories in many plant lineages. Given both their organizational complexities and their critical influences, CRLs likely impact most, if not all, aspects of plant biology.
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Affiliation(s)
- Zhihua Hua
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706-1574, USA.
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Drechsel G, Bergler J, Wippel K, Sauer N, Vogelmann K, Hoth S. C-terminal armadillo repeats are essential and sufficient for association of the plant U-box armadillo E3 ubiquitin ligase SAUL1 with the plasma membrane. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:775-85. [PMID: 20956359 PMCID: PMC3003819 DOI: 10.1093/jxb/erq313] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 09/13/2010] [Indexed: 05/21/2023]
Abstract
Ubiquitination plays important roles in plant growth and development. Whereas ubiquitin-dependent protein degradation and modulation in the cytoplasm and nucleus are well established in plants, ubiquitination events mediated by E3 ubiquitin ligases at the plasma membrane are largely unknown. Here, it is demonstrated that the suppressor of premature senescence and cell death SENESCENCE-ASSOCIATED UBIQUITIN LIGASE 1 (SAUL1), a plant U-box armadillo repeat (PUB-ARM) E3 ubiquitin ligase, localizes at the plasma membrane. Among the members of the PUB-ARM protein family, this localization is unique to SAUL1 and its two closest homologues. A novel armadillo repeat domain was identified at the SAUL1 C-terminus that directs specific association with the plasma membrane and is crucial for SAUL1 function in vivo. The data suggest that a small subgroup of PUB-ARM proteins including SAUL1 have functions at the plasma membrane probably by modifying target proteins by ubiquitination.
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Affiliation(s)
| | | | | | | | | | - Stefan Hoth
- To whom correspondence should be addressed. E-mail:
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Molecular analysis and expression of a floral organ-relative F-box gene isolated from 'Zigui shatian' pummelo (Citrus grandis Osbeck). Mol Biol Rep 2010; 38:4429-36. [PMID: 21125334 DOI: 10.1007/s11033-010-0571-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 11/19/2010] [Indexed: 10/18/2022]
Abstract
F-box proteins are a large family of eukaryotic proteins that contained a conserved motif of approximately 40 amino acids. They play an important role in the processing of degradation of cellular regulatory proteins. In this study we isolated a full-length of cDNA encoding a putative F-box protein from Citrus grandis Osbeck CV 'Zigui shatian' pummelo and designated as CgF-box. The cDNA sequence of CgF-box was 920 bp containing a 585 bp open reading frame encoding a precursor protein of 194 amino acid residues. The deduced protein comprised a conserved F-box domain at the position from the 40th to 84th amino acids. Cluster analysis suggested that CgF-box was more closely related to the grape F-Box protein. Southern hybridization verified CgF-box existed in the genome as multiple copies. The expression analysis revealed that the expression level of CgF-box gene remarkably increases during the flower developmental process of 'Zigui shatian' pummelo, such as high level of expression was noted in style, petal and anther, on the other hand low level of expression was found in ovary and leaf. For further verifying the different expression in different tissue of this gene, in situ hybridization was conducted, strong expression signal could be observed in the style, stigma and anther, low even no signal was observed in ovary. According to their findings we can conclude that CgF-box was not only involved in flower maturation, but also showed different roles in different tissue.
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Gu Y, Somerville C. Cellulose synthase interacting protein: a new factor in cellulose synthesis. PLANT SIGNALING & BEHAVIOR 2010; 5:1571-4. [PMID: 21150290 PMCID: PMC3115106 DOI: 10.4161/psb.5.12.13621] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 09/14/2010] [Indexed: 05/17/2023]
Abstract
Cellulose is the most abundant biopolymer on earth. The great abundance of cellulose places it at the forefront as a primary source of biomass for renewable biofuels. However, the knowledge of how plant cells make cellulose remains very rudimentary. Cellulose microfibrils are synthesized at the plasma membrane by hexameric protein complexes, also known as cellulose synthase complexes. The only known components of cellulose synthase complexes are cellulose synthase (CESA) proteins until the recent identification of a novel component. CSI1, which encodes CESA interacting protein 1 (CSI1) in Arabidopsis. CSI1, as the first non-CESA proteins associated with cellulose synthase complexes, opens up many opportunities.
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Affiliation(s)
- Ying Gu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
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