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Chen Y, Liu Z, Han D, Yang Q, Li C, Shi X, Zhang M, Yang C, Qiu L, Jia H, Wang S, Lu W, Ma Q, Yan L. Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:178. [PMID: 38976061 DOI: 10.1007/s00122-024-04685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
KEY MESSAGE Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.
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Affiliation(s)
- Yuehan Chen
- College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Zhi Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Qing Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Chenhui Li
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm and Biotechnology (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongchang Jia
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Shu Wang
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Wencheng Lu
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China.
| | - Qian Ma
- College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
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Zhao Y, Wang S, Ma X, He Y, Zhou J, Jiao S, Xun J, Kong X, Wu X, Bai X. GmANKTM21 Positively Regulates Drought Tolerance and Enhanced Stomatal Response through the MAPK Signaling Pathway in Soybean. Int J Mol Sci 2024; 25:6972. [PMID: 39000082 PMCID: PMC11241039 DOI: 10.3390/ijms25136972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Drought stress is one of the significant abiotic stresses that limit soybean (Glycine max [L.] Merr.) growth and production. Ankyrin repeat (ANK) proteins, being highly conserved, occupy a pivotal role in diverse biological processes. ANK genes were classified into nine subfamilies according to conserved domains in the soybean genome. However, the function of ANK-TM subfamily proteins (Ankyrin repeat proteins with a transmembrane domain) in the abiotic-stress response to soybean remains poorly understood. In this study, we first demonstrated the subcellular localization of GmANKTM21 in the cell membrane and nucleus. Drought stress-induced mRNA levels of GmANKTM21, which encodes proteins belonging to the ANK-TM subfamily, Transgenic 35S:GmANKTM21 soybean improved drought tolerance at the germination and seedling stages, with higher stomatal closure in soybean, lower water loss, lower malondialdehyde (MDA) content, and less reactive oxygen species (ROS) production compared with the wild-type soybean (Dongnong50). RNA-sequencing (RNA-seq) and RT-qPCR analysis of differentially expressed transcripts in overexpression of GmANKTM21 further identified potential downstream genes, including GmSPK2, GmSPK4, and GmCYP707A1, which showed higher expression in transgenic soybean, than those in wild-type soybean and KEGG enrichment analysis showed that MAPK signaling pathways were mostly enriched in GmANKTM21 overexpressing soybean plants under drought stress conditions. Therefore, we demonstrate that GmANKTM21 plays an important role in tolerance to drought stress in soybeans.
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Affiliation(s)
- Yue Zhao
- Northeast Agricultural University, Harbin 150001, China
| | - Sinan Wang
- Northeast Agricultural University, Harbin 150001, China
| | - Xiaofei Ma
- Northeast Agricultural University, Harbin 150001, China
| | - Yu He
- Northeast Agricultural University, Harbin 150001, China
| | - Jingwen Zhou
- Northeast Agricultural University, Harbin 150001, China
| | - Shuang Jiao
- Northeast Agricultural University, Harbin 150001, China
| | - Jianing Xun
- Northeast Agricultural University, Harbin 150001, China
| | - Xiaoyu Kong
- Northeast Agricultural University, Harbin 150001, China
| | - Xiaoxia Wu
- Northeast Agricultural University, Harbin 150001, China
| | - Xi Bai
- Northeast Agricultural University, Harbin 150001, China
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Zeng J, Wang Y, Wu G, Sun Q, He X, Zhang X, Sun X, Zhao Y, Liu W, Xu D, Dai X, Ma W. Comparative Transcriptome Analysis Reveals the Genes and Pathways Related to Wheat Root Hair Length. Int J Mol Sci 2024; 25:2069. [PMID: 38396749 PMCID: PMC10889798 DOI: 10.3390/ijms25042069] [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: 01/10/2024] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Tube-like outgrowths from root epidermal cells, known as root hairs, enhance water and nutrient absorption, facilitate microbial interactions, and contribute to plant anchorage by expanding the root surface area. Genetically regulated and strongly influenced by environmental conditions, longer root hairs generally enhance water and nutrient absorption, correlating with increased stress resistance. Wheat, a globally predominant crop pivotal for human nutrition, necessitates the identification of long root hair genotypes and their regulatory genes to enhance nutrient capture and yield potential. This study focused on 261 wheat samples of diverse genotypes during germination, revealing noticeable disparities in the length of the root hair among the genotypes. Notably, two long root hair genotypes (W106 and W136) and two short root hair genotypes (W90 and W100) were identified. Transcriptome sequencing resulted in the development of 12 root cDNA libraries, unveiling 1180 shared differentially expressed genes (DEGs). Further analyses, including GO function annotation, KEGG enrichment, MapMan metabolic pathway analysis, and protein-protein interaction (PPI) network prediction, underscored the upregulation of root hair length regulatory genes in the long root hair genotypes. These included genes are associated with GA and BA hormone signaling pathways, FRS/FRF and bHLH transcription factors, phenylpropanoid, lignin, lignan secondary metabolic pathways, the peroxidase gene for maintaining ROS steady state, and the ankyrin gene with diverse biological functions. This study contributes valuable insights into modulating the length of wheat root hair and identifies candidate genes for the genetic improvement of wheat root traits.
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Affiliation(s)
- Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yongmei Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Gang Wu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Qingyi Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xinyi Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuelian Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yan Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wenxing Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuehuan Dai
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
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Valencia-Lozano E, Herrera-Isidrón L, Flores-López JA, Recoder-Meléndez OS, Uribe-López B, Barraza A, Cabrera-Ponce JL. Exploring the Potential Role of Ribosomal Proteins to Enhance Potato Resilience in the Face of Changing Climatic Conditions. Genes (Basel) 2023; 14:1463. [PMID: 37510367 PMCID: PMC10379993 DOI: 10.3390/genes14071463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Potatoes have emerged as a key non-grain crop for food security worldwide. However, the looming threat of climate change poses significant risks to this vital food source, particularly through the projected reduction in crop yields under warmer temperatures. To mitigate potential crises, the development of potato varieties through genome editing holds great promise. In this study, we performed a comprehensive transcriptomic analysis to investigate microtuber development and identified several differentially expressed genes, with a particular focus on ribosomal proteins-RPL11, RPL29, RPL40 and RPL17. Our results reveal, by protein-protein interaction (PPI) network analyses, performed with the highest confidence in the STRING database platform (v11.5), the critical involvement of these ribosomal proteins in microtuber development, and highlighted their interaction with PEBP family members as potential microtuber activators. The elucidation of the molecular biological mechanisms governing ribosomal proteins will help improve the resilience of potato crops in the face of today's changing climatic conditions.
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Affiliation(s)
- Eliana Valencia-Lozano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
| | - Lisset Herrera-Isidrón
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Jorge Abraham Flores-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Osiel Salvador Recoder-Meléndez
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Braulio Uribe-López
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), Instituto Politécnico Nacional, Av. Mineral de Valenciana 200, Puerto Interior, Silao de la Victoria 36275, Guanajuato, Mexico
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noreste, SC., Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz CP 23096, Baja California Sur, Mexico
| | - José Luis Cabrera-Ponce
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico
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Le Provost G, Gerardin T, Plomion C, Brendel O. Molecular plasticity to soil water deficit differs between sessile oak (Quercus Petraea (Matt.) Liebl.) high- and low-water use efficiency genotypes. TREE PHYSIOLOGY 2022; 42:2546-2562. [PMID: 35867420 DOI: 10.1093/treephys/tpac087] [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: 11/08/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Water use efficiency (WUE) is an important adaptive trait for soil water deficit. The molecular and physiological bases of WUE regulation in crops have been studied in detail in the context of plant breeding. Knowledge for most forest tree species lags behind, despite the need to identify populations or genotypes able to cope with the longer, more intense drought periods likely to result from climate warming. We aimed to bridge this gap in knowledge for sessile oak (Quercus petraea (Matt.) Liebl.), one of the most ecologically and economically important tree species in Europe, using a factorial design including trees with contrasted phenotypic values (low and high WUE) and two watering regimes (control and drought). By monitoring the ecophysiological response, we first qualified genotypes for their WUE (by using instantaneous and long-term measures). We then performed RNA-seq to quantify gene expression for the three most extreme genotypes exposed to the two watering regimes. By analyzing the interaction term, we were able to capture the molecular strategy of each group of plants for coping with drought. We identified putative candidate genes potentially involved in the regulation of transpiration rate in high-WUE phenotypes. Regardless of water availability, trees from the high-WUE phenotypic class overexpressed genes associated with drought responses, and in the control of stomatal density and distribution, and displayed a downregulation of genes associated with early stomatal closure and high transpiration rate. Fine physiological screening of sessile oaks with contrasting WUE, and their molecular characterization (i) highlighted subtle differences in transcription between low- and high-WUE genotypes, identifying key molecular players in the genetic control of this trait and (ii) revealed the genes underlying the molecular strategy that evolved in each group to potentially cope with water deficit, providing new insight into the within-species diversity in drought adaptation strategies.
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Affiliation(s)
| | - Theo Gerardin
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, Nancy, France
| | | | - Oliver Brendel
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, Nancy, France
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Kulichová K, Pieters J, Kumar V, Honys D, Hafidh S. A Plastid-Bound Ankyrin Repeat Protein Controls Gametophyte and Early Embryo Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:767339. [PMID: 35350296 PMCID: PMC8958021 DOI: 10.3389/fpls.2022.767339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Proplastids are essential precursors for multi-fate plastid biogenesis, including chloroplast differentiation, a powerhouse for photosynthesis in plants. Arabidopsis ankyrin repeat protein (AKRP, AT5G66055) is a plastid-localized protein with a putative function in plastid differentiation and morphogenesis. Loss of function of akrp leads to embryo developmental arrest. Whether AKRP is critical pre-fertilization has remained unresolved. Here, using reverse genetics, we report a new allele, akrp-3, that exhibited a reduced frequency of mutant embryos (<13%) compared to previously reported alleles. akrp-3 affected both male and female gametophytes resulting in reduced viability, incompetence in pollen tube attraction, altered gametic cell fate, and embryo arrest that were depleted of chlorophyll. AKRP is widely expressed, and the AKRP-GFP fusion localized to plastids of both gametophytes, in isolated chloroplast and co-localized with a plastid marker in pollen and pollen tubes. Cell-type-specific complementation of akrp-3 hinted at the developmental timing at which AKRP might play an essential role. Our findings provide a plausible insight into the crucial role of AKRP in the differentiation of both gametophytes and coupling embryo development with chlorophyll synthesis.
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Affiliation(s)
- Katarína Kulichová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Janto Pieters
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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Wang W, Xiong H, Sun K, Zhang B, Sun MX. New insights into cell-cell communications during seed development in flowering plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:215-229. [PMID: 34473416 DOI: 10.1111/jipb.13170] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The evolution of seeds is a major reason why flowering plants are a dominant life form on Earth. The developing seed is composed of two fertilization products, the embryo and endosperm, which are surrounded by a maternally derived seed coat. Accumulating evidence indicates that efficient communication among all three seed components is required to ensure coordinated seed development. Cell communication within plant seeds has drawn much attention in recent years. In this study, we review current knowledge of cross-talk among the endosperm, embryo, and seed coat during seed development, and highlight recent advances in this field.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanxian Xiong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kaiting Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bo Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Zheng C, Xu X, Zhang L, Lu D. Liquid-Liquid Phase Separation Phenomenon on Protein Sorting Within Chloroplasts. Front Physiol 2022; 12:801212. [PMID: 35002776 PMCID: PMC8740050 DOI: 10.3389/fphys.2021.801212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
In higher plants, chloroplasts are vital organelles possessing highly complex compartmentalization. As most chloroplast-located proteins are encoded in the nucleus and synthesized in the cytosol, the correct sorting of these proteins to appropriate compartments is critical for the proper functions of chloroplasts as well as plant survival. Nuclear-encoded chloroplast proteins are imported into stroma and further sorted to distinct compartments via different pathways. The proteins predicted to be sorted to the thylakoid lumen by the chloroplast twin arginine transport (cpTAT) pathway are shown to be facilitated by STT1/2 driven liquid-liquid phase separation (LLPS). Liquid-liquid phase separation is a novel mechanism to facilitate the formation of membrane-less sub-cellular compartments and accelerate biochemical reactions temporally and spatially. In this review, we introduce the sorting mechanisms within chloroplasts, and briefly summarize the properties and significance of LLPS, with an emphasis on the novel function of LLPS in the sorting of cpTAT substrate proteins. We conclude with perspectives for the future research on chloroplast protein sorting and targeting mechanisms.
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Affiliation(s)
- Canhui Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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Xiong H, Wang W, Sun MX. Endosperm development is an autonomously programmed process independent of embryogenesis. THE PLANT CELL 2021; 33:1151-1160. [PMID: 33793916 DOI: 10.1093/plcell/koab007] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
The seeds of flowering plants contain three genetically distinct structures: the embryo, endosperm, and seed coat. The embryo and endosperm need to interact and exchange signals to ensure coordinated growth. Accumulating evidence has confirmed that embryo growth is supported by the nourishing endosperm and regulated by signals originating from the endosperm. Available data also support that endosperm development requires communication with the embryo. Here, using single-fertilization mutants, Arabidopsis thaliana dmp8 dmp9 and gex2, we demonstrate that in the absence of a zygote and embryo, endosperm initiation, syncytium formation, free nuclear cellularization, and endosperm degeneration occur as in the wild type in terms of the cytological process and time course. Although rapid embryo expansion accelerates endosperm breakdown, our findings strongly suggest that endosperm development is an autonomously organized process, independent of egg cell fertilization and embryo-endosperm communication. This work confirms both the altruistic and self-directed nature of the endosperm during coordinated embryo-endosperm development. Our findings provide insights into the intricate interaction between the two fertilization products and will help to distinguish the physiological roles of the signaling between endosperm and embryo. These findings also open new avenues in agro-biotechnology for crop improvement.
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Affiliation(s)
- Hanxian Xiong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Zhang T. Autonomous endosperm development in embryo-free seeds. THE PLANT CELL 2021; 33:1091-1092. [PMID: 35234964 PMCID: PMC8889992 DOI: 10.1093/plcell/koab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Tian Zhang
- Assistant Features Editor, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
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Cao Y, Diao Q, Chen Y, Jin H, Zhang Y, Zhang H. Development of KASP Markers and Identification of a QTL Underlying Powdery Mildew Resistance in Melon ( Cucumis melo L.) by Bulked Segregant Analysis and RNA-Seq. FRONTIERS IN PLANT SCIENCE 2021; 11:593207. [PMID: 33613580 PMCID: PMC7893098 DOI: 10.3389/fpls.2020.593207] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/28/2020] [Indexed: 05/27/2023]
Abstract
Powdery mildew (PM), caused by Podosphaera xanthii (Px), is one of the most devastating fungal diseases of melon worldwide. The use of resistant cultivars is considered to be the best and most effective approach to control this disease. In this study, an F2 segregating population derived from a cross between a resistant (wm-6) and a susceptible cultivar (12D-1) of melon was used to map major powdery mildew resistance genes using bulked segregant analysis (BSA), in combination with next-generation sequencing (NGS). A novel quantitative trait locus (QTL) named qCmPMR-12 for resistance to PM on chromosome 12 was identified, which ranged from 22.0 Mb to 22.9 Mb. RNA-Seq analysis indicated that the MELO3C002434 gene encoding an ankyrin repeat-containing protein was considered to be the most likely candidate gene that was associated with resistance to PM. Moreover, 15 polymorphic SNPs around the target area were successfully converted to Kompetitive Allele-Specific PCR (KASP) markers (P < 0.0001). The novel QTL and candidate gene identified from this study provide insights into the genetic mechanism of PM resistance in melon, and the tightly linked KASP markers developed in this research can be used for marker-assisted selection (MAS) to improve powdery mildew resistance in melon breeding programs.
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Zhang FJ, Xie YH, Jiang H, Wang X, Hao YJ, Zhang Z, You CX. The ankyrin repeat-containing protein MdANK2B regulates salt tolerance and ABA sensitivity in Malus domestica. PLANT CELL REPORTS 2021; 40:405-419. [PMID: 33331953 DOI: 10.1007/s00299-020-02642-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/23/2020] [Indexed: 05/08/2023]
Abstract
The ankyrin repeat-containing protein MdANK2B was identified to contribute to increasing resistance to salt stress and decreasing sensitivity to ABA in Malus domestica. Ankyrin (ANK) repeat-containing proteins occur widely in prokaryotes, eukaryotes, and even in some viruses and play a critical role in plant growth and development, as well as the response to biotic and abiotic stress. However, the function of ANK repeat-containing proteins in apple (Malus domestica) has not yet been investigated. Here, we identified apple MdANK2B based on homology analysis with the Arabidopsis ANK repeat-containing proteins AtAKR2A and AtAKR2B. MdANK2B was found to be localized in the cytoplasm, and its encoding gene was highly expressed in both apple leaves and fruits. In addition, MdANK2B gene expression was highly induced by salt stresses and abscisic acid (ABA). Overexpression of MdANK2B increased resistance to salt stress and decreased sensitivity to ABA in both transgenic apple calli and seedlings. In addition, overexpression of MdANK2B reduced the accumulation of reactive oxygen species (ROS) by enhancing the activity of antioxidant enzymes in response to salt stress. Our data revealed the role of MdANK2B in response to salt stress and ABA treatment in apple, which widens the known functions of ANK repeat-containing proteins in response to abiotic stress.
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Affiliation(s)
- Fu-Jun Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yin-Huan Xie
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Han Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yang ling, Shanxi, 712100, China
| | - Xun Wang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Zhenlu Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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13
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Zhao JY, Lu ZW, Sun Y, Fang ZW, Chen J, Zhou YB, Chen M, Ma YZ, Xu ZS, Min DH. The Ankyrin-Repeat Gene GmANK114 Confers Drought and Salt Tolerance in Arabidopsis and Soybean. FRONTIERS IN PLANT SCIENCE 2020; 11:584167. [PMID: 33193533 PMCID: PMC7658197 DOI: 10.3389/fpls.2020.584167] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/06/2020] [Indexed: 05/20/2023]
Abstract
Ankyrin repeat (ANK) proteins are essential in cell growth, development, and response to hormones and environmental stresses. In the present study, 226 ANK genes were identified and classified into nine subfamilies according to conserved domains in the soybean genome (Glycine max L.). Among them, the GmANK114 was highly induced by drought, salt, and abscisic acid. The GmANK114 encodes a protein that belongs to the ANK-RF subfamily containing a RING finger (RF) domain in addition to the ankyrin repeats. Heterologous overexpression of GmANK114 in transgenic Arabidopsis improved the germination rate under drought and salt treatments compared to wild-type. Homologous overexpression of GmANK114 improved the survival rate under drought and salt stresses in transgenic soybean hairy roots. In response to drought or salt stress, GmANK114 overexpression in soybean hairy root showed higher proline and lower malondialdehyde contents, and lower H2O2 and O2- contents compared control plants. Besides, GmANK114 activated transcription of several abiotic stress-related genes, including WRKY13, NAC11, DREB2, MYB84, and bZIP44 under drought and salt stresses in soybean. These results provide new insights for functional analysis of soybean ANK proteins and will be helpful for further understanding how ANK proteins in plants adapt to abiotic stress.
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Affiliation(s)
- Juan-Ying Zhao
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Zhi-Wei Lu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yue Sun
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Zheng-Wu Fang
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Dong-Hong Min
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
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Ouyang M, Li X, Zhang J, Feng P, Pu H, Kong L, Bai Z, Rong L, Xu X, Chi W, Wang Q, Chen F, Lu C, Shen J, Zhang L. Liquid-Liquid Phase Transition Drives Intra-chloroplast Cargo Sorting. Cell 2020; 180:1144-1159.e20. [PMID: 32169217 DOI: 10.1016/j.cell.2020.02.045] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 01/14/2020] [Accepted: 02/20/2020] [Indexed: 12/21/2022]
Abstract
In eukaryotic cells, organelle biogenesis is pivotal for cellular function and cell survival. Chloroplasts are unique organelles with a complex internal membrane network. The mechanisms of the migration of imported nuclear-encoded chloroplast proteins across the crowded stroma to thylakoid membranes are less understood. Here, we identified two Arabidopsis ankyrin-repeat proteins, STT1 and STT2, that specifically mediate sorting of chloroplast twin arginine translocation (cpTat) pathway proteins to thylakoid membranes. STT1 and STT2 form a unique hetero-dimer through interaction of their C-terminal ankyrin domains. Binding of cpTat substrate by N-terminal intrinsically disordered regions of STT complex induces liquid-liquid phase separation. The multivalent nature of STT oligomer is critical for phase separation. STT-Hcf106 interactions reverse phase separation and facilitate cargo targeting and translocation across thylakoid membranes. Thus, the formation of phase-separated droplets emerges as a novel mechanism of intra-chloroplast cargo sorting. Our findings highlight a conserved mechanism of phase separation in regulating organelle biogenesis.
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Affiliation(s)
- Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoyi Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jing Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Peiqiang Feng
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hua Pu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lingxi Kong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zechen Bai
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Chinese Academy of Sciences, Beijing 100086, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jianren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China.
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15
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Lopez-Ortiz C, Peña-Garcia Y, Natarajan P, Bhandari M, Abburi V, Dutta SK, Yadav L, Stommel J, Nimmakayala P, Reddy UK. The ankyrin repeat gene family in Capsicum spp: Genome-wide survey, characterization and gene expression profile. Sci Rep 2020; 10:4044. [PMID: 32132613 PMCID: PMC7055287 DOI: 10.1038/s41598-020-61057-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
The ankyrin (ANK) repeat protein family is largely distributed across plants and has been found to participate in multiple processes such as plant growth and development, hormone response, response to biotic and abiotic stresses. It is considered as one of the major markers of capsaicin content in pepper fruits. In this study, we performed a genome-wide identification and expression analysis of genes encoding ANK proteins in three Capsicum species: Capsicum baccatum, Capsicum annuum and Capsicum chinense. We identified a total of 87, 85 and 96 ANK genes in C. baccatum, C. annuum and C. chinense genomes, respectively. Next, we performed a comprehensive bioinformatics analysis of the Capsicum ANK gene family including gene chromosomal localization, Cis-elements, conserved motif identification, intron/exon structural patterns and gene ontology classification as well as profile expression. Phylogenetic and domain organization analysis grouped the Capsicum ANK gene family into ten subfamilies distributed across all 12 pepper chromosomes at different densities. Analysis of the expression of ANK genes in leaf and pepper fruits suggested that the ANKs have specific expression patterns at various developmental stages in placenta tissue. Our results provide valuable information for further studies of the evolution, classification and putative functions of ANK genes in pepper.
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Affiliation(s)
- Carlos Lopez-Ortiz
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Yadira Peña-Garcia
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.,Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India
| | - Menuka Bhandari
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Sudip Kumar Dutta
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.,ICAR RC NEH Region, Mizoram Centre, Kolasib, Mizoram, India
| | - Lav Yadav
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory (USDA, ARS), Beltsville, MD, 20705, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.
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16
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Zhang S, Sun F, Wang W, Yang G, Zhang C, Wang Y, Liu S, Xi Y. Comparative transcriptome analysis provides key insights into seedling development in switchgrass ( Panicum virgatum L.). BIOTECHNOLOGY FOR BIOFUELS 2019; 12:193. [PMID: 31402932 PMCID: PMC6683553 DOI: 10.1186/s13068-019-1534-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth. RESULTS Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development. CONCLUSIONS The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops.
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Affiliation(s)
- Shumeng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Fengli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Weiwei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Guoyu Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yongfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shudong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yajun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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17
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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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18
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Fujii S, Kobayashi K, Nakamura Y, Wada H. Inducible knockdown of MONOGALACTOSYLDIACYLGLYCEROL SYNTHASE1 reveals roles of galactolipids in organelle differentiation in Arabidopsis cotyledons. PLANT PHYSIOLOGY 2014; 166:1436-49. [PMID: 25253888 PMCID: PMC4226381 DOI: 10.1104/pp.114.250050] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 09/23/2014] [Indexed: 05/18/2023]
Abstract
Monogalactosyldiacylglycerol (MGDG) is the major lipid constituent of thylakoid membranes and is essential for chloroplast biogenesis in plants. In Arabidopsis (Arabidopsis thaliana), MGDG is predominantly synthesized by inner envelope-localized MONOGALACTOSYLDIACYLGLYCEROL SYNTHASE1 (MGD1); its knockout causes albino seedlings. Because of the lethal phenotype of the null MGD1 mutant, functional details of MGDG synthesis at seedling development have remained elusive. In this study, we used an inducible gene-suppression system to investigate the impact of MGDG synthesis on cotyledon development. We created transgenic Arabidopsis lines that express an artificial microRNA targeting MGD1 (amiR-MGD1) under the control of a dexamethasone-inducible promoter. The induction of amiR-MGD1 resulted in up to 75% suppression of MGD1 expression, although the resulting phenotypes related to chloroplast development were diverse, even within a line. The strong MGD1 suppression by continuous dexamethasone treatment caused substantial decreases in galactolipid content in cotyledons, leading to severe defects in the formation of thylakoid membranes and impaired photosynthetic electron transport. Time-course analyses of the MGD1 suppression during seedling germination revealed that MGDG synthesis at the very early germination stage is particularly important for chloroplast biogenesis. The MGD1 suppression down-regulated genes associated with the photorespiratory pathway in peroxisomes and mitochondria as well as those responsible for photosynthesis in chloroplasts and caused high expression of genes for the glyoxylate cycle. MGD1 function may link galactolipid synthesis with the coordinated transcriptional regulation of chloroplasts and other organelles during cotyledon greening.
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Affiliation(s)
- Sho Fujii
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan (S.F., K.K., H.W.);PRESTO (Y.N.) and CREST (H.W.), JST, Kawaguchi, Saitama 332-0012, Japan; andInstitute of Plant and Microbial Biology, Academia Sinica, Nankang, Tapei 11529, Taiwan (Y.N.)
| | - Koichi Kobayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan (S.F., K.K., H.W.);PRESTO (Y.N.) and CREST (H.W.), JST, Kawaguchi, Saitama 332-0012, Japan; andInstitute of Plant and Microbial Biology, Academia Sinica, Nankang, Tapei 11529, Taiwan (Y.N.)
| | - Yuki Nakamura
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan (S.F., K.K., H.W.);PRESTO (Y.N.) and CREST (H.W.), JST, Kawaguchi, Saitama 332-0012, Japan; andInstitute of Plant and Microbial Biology, Academia Sinica, Nankang, Tapei 11529, Taiwan (Y.N.)
| | - Hajime Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan (S.F., K.K., H.W.);PRESTO (Y.N.) and CREST (H.W.), JST, Kawaguchi, Saitama 332-0012, Japan; andInstitute of Plant and Microbial Biology, Academia Sinica, Nankang, Tapei 11529, Taiwan (Y.N.)
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19
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Lu X, Zhang D, Li S, Su Y, Liang Q, Meng H, Shen S, Fan Y, Liu C, Zhang C. FtsHi4 is essential for embryogenesis due to its influence on chloroplast development in Arabidopsis. PLoS One 2014; 9:e99741. [PMID: 24964212 PMCID: PMC4070914 DOI: 10.1371/journal.pone.0099741] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/17/2014] [Indexed: 12/31/2022] Open
Abstract
Chloroplast formation is associated with embryo development and seedling growth. However, the relationship between chloroplast differentiation and embryo development remains unclear. Five FtsHi genes that encode proteins with high similarity to FtsH proteins, but lack Zn2+-binding motifs, are present in the Arabidopsis genome. In this study, we showed that T-DNA insertion mutations in the Arabidopsis FtsHi4 gene resulted in embryo arrest at the globular-to-heart-shaped transition stage. Transmission electron microscopic analyses revealed abnormal plastid differentiation with a severe defect in thylakoid formation in the mutant embryos. Immunocytological studies demonstrated that FtsHi4 localized in chloroplasts as a thylakoid membrane-associated protein, supporting its essential role in thylakoid membrane formation. We further showed that FtsHi4 forms protein complexes, and that there was a significant reduction in the accumulation of D2 and PsbO (two photosystem II proteins) in mutant ovules. The role of FtsHi4 in chloroplast development was confirmed using an RNA-interfering approach. Additionally, mutations in other FtsHi genes including FtsHi1, FtsHi2, and FtsHi5 caused phenotypic abnormalities similar to ftshi4 with respect to plastid differentiation during embryogenesis. Taken together, our data suggest that FtsHi4, together with FtsHi1, FtsHi2, and FtsHi5 are essential for chloroplast development in Arabidopsis.
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Affiliation(s)
- Xiaoduo Lu
- Department of Life Sciences, Qilu Normal University, Jinan, China
| | - Dongyuan Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shipeng Li
- Department of Life Sciences, Qilu Normal University, Jinan, China
| | - Yanping Su
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, China
| | - Hongyan Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Songdong Shen
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yunliu Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, China
| | - Chunming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, China
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Kawai-Yamada M, Nagano M, Kakimoto M, Uchimiya H. Plastidic protein Cdf1 is essential in Arabidopsis embryogenesis. PLANTA 2014; 239:39-46. [PMID: 24097264 DOI: 10.1007/s00425-013-1966-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/24/2013] [Indexed: 05/22/2023]
Abstract
Arabidopsis cell growth defect factor-1 (Cdf1 in yeast, At5g23040) was originally isolated as a cell growth suppressor of yeast from genetic screening. To investigate the in vivo role of Cdf1 in plants, a T-DNA insertion line was analyzed. A homozygous T-DNA insertion mutant (cdf1/cdf1) was embryo lethal and showed arrested embryogenesis at the globular stage. The Cdf1 protein, when fused with green fluorescent protein, was localized to the plastid in stomatal guard cells and mesophyll cells. A promoter-β-glucuronidase assay found expression of Cdf1 in the early heart stage of embryogenesis, suggesting that Cdf1 was essential for Arabidopsis embryogenesis during the transition of the embryo from the globular to heart stage.
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Affiliation(s)
- Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan,
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21
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Yuan X, Zhang S, Qing X, Sun M, Liu S, Su H, Shu H, Li X. Superfamily of ankyrin repeat proteins in tomato. Gene 2013; 523:126-36. [PMID: 23587915 DOI: 10.1016/j.gene.2013.03.122] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/11/2013] [Accepted: 03/27/2013] [Indexed: 01/18/2023]
Abstract
The ankyrin repeat (ANK) protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for tomato (Solanum lycopersicum) due to the limited information on whole genome sequences. In this study, we identified a total of 130 ANK genes in tomato genome (SlANK), and these genes were distributed across all 12 chromosomes at various densities. And chromosomal localizations of SlANK genes indicated 25 SlANK genes were involved in tandem duplications. Based on their domain composition, all of the SlANK proteins were grouped into 13 subgroups. A combined phylogenetic tree was constructed with the aligned SlANK protein sequences. This tree revealed that the SlANK proteins comprise five major groups. An analysis of the expression profiles of SlANK genes in tomato in different tissues and in response to stresses showed that the SlANK proteins play roles in plant growth, development and stress responses. To our knowledge, this is the first report of a genome-wide analysis of the tomato ANK gene family. This study provides valuable information regarding the classification and putative functions of SlANK genes in tomato.
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Affiliation(s)
- Xiaowei Yuan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
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22
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Mou S, Liu Z, Guan D, Qiu A, Lai Y, He S. Functional analysis and expressional characterization of rice ankyrin repeat-containing protein, OsPIANK1, in basal defense against Magnaporthe oryzae attack. PLoS One 2013; 8:e59699. [PMID: 23555750 PMCID: PMC3608567 DOI: 10.1371/journal.pone.0059699] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/17/2013] [Indexed: 11/18/2022] Open
Abstract
The ankyrin repeat-containing protein gene OsPIANK1 (AK068021) in rice (Oryza sativa L.) was previously shown to be upregulated following infection with the rice leaf blight pathogen Xanthomonas oryzae pv oryzae (Xoo). In this study, we further characterized the role of OsPIANK1 in basal defense against Magnaporthe oryzae (M.oryzae) by 5' deletion analysis of its promoter and overexpression of the gene. The promoter of OsPIANK1 with 1,985 bps in length was sufficient to induce the OsPIANK1 response to inoculation with M.oryzae and to exogenous application of methyl jasmonate (MeJA) or salicylic acid (SA), but not to exogenous application of abscisic acid (ABA). A TCA-element present in the region between -563 bp and -249 bp may be responsible for the OsPIANK1 response to both M.oryzae infection and exogenous SA application. The JERE box, CGTCA-box, and two MYB binding sites locating in the region between -1985 bp and -907 bp may be responsible for the response of OsPIANK1 to exogenous MeJA. OsPIANK1 expression was upregulated after inoculation with M.oryzae and after treatment with exogenous SA and MeJA. Overexpression of OsPIANK1 enhanced resistance of rice to M.oryzae, although it did not confer complete resistance. The enhanced resistance to M.oryzae was accompanied by enhanced transcriptional expression of SA- and JA-dependent genes such as NH1, WKRY13, PAL, AOS2, PR1b, and PR5. This evidence suggests that OsPIANK1 acted as a positive regulator in rice basal defense mediated by SA- and JA-signaling pathways.
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Affiliation(s)
- Shaoliang Mou
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhiqin Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Deyi Guan
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ailian Qiu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yan Lai
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuilin He
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
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23
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Michalak de Jimenez MK, Bassi FM, Ghavami F, Simons K, Dizon R, Seetan RI, Alnemer LM, Denton AM, Doğramacı M, Šimková H, Doležel J, Seth K, Luo MC, Dvorak J, Gu YQ, Kianian SF. A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus. Funct Integr Genomics 2013. [PMID: 23479086 DOI: 10.1007/s10142‐013‐0318‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The species cytoplasm specific (scs) genes affect nuclear-cytoplasmic interactions in interspecific hybrids. A radiation hybrid (RH) mapping population of 188 individuals was employed to refine the location of the scs (ae) locus on Triticum aestivum chromosome 1D. "Wheat Zapper," a comparative genomics tool, was used to predict synteny between wheat chromosome 1D, Oryza sativa, Brachypodium distachyon, and Sorghum bicolor. A total of 57 markers were developed based on synteny or literature and genotyped to produce a RH map spanning 205.2 cR. A test-cross methodology was devised for phenotyping of RH progenies, and through forward genetic, the scs (ae) locus was pinpointed to a 1.1 Mb-segment containing eight genes. Further, the high resolution provided by RH mapping, combined with chromosome-wise synteny analysis, located the ancestral point of fusion between the telomeric and centromeric repeats of two paleochromosomes that originated chromosome 1D. Also, it indicated that the centromere of this chromosome is likely the result of a neocentromerization event, rather than the conservation of an ancestral centromere as previously believed. Interestingly, location of scs locus in the vicinity of paleofusion is not associated with the expected disruption of synteny, but rather with a good degree of conservation across grass species. Indeed, these observations advocate the evolutionary importance of this locus as suggested by "Maan's scs hypothesis."
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24
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Michalak de Jimenez MK, Bassi FM, Ghavami F, Simons K, Dizon R, Seetan RI, Alnemer LM, Denton AM, Doğramacı M, Šimková H, Doležel J, Seth K, Luo MC, Dvorak J, Gu YQ, Kianian SF. A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus. Funct Integr Genomics 2013; 13:19-32. [PMID: 23479086 DOI: 10.1007/s10142-013-0318-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
The species cytoplasm specific (scs) genes affect nuclear-cytoplasmic interactions in interspecific hybrids. A radiation hybrid (RH) mapping population of 188 individuals was employed to refine the location of the scs (ae) locus on Triticum aestivum chromosome 1D. "Wheat Zapper," a comparative genomics tool, was used to predict synteny between wheat chromosome 1D, Oryza sativa, Brachypodium distachyon, and Sorghum bicolor. A total of 57 markers were developed based on synteny or literature and genotyped to produce a RH map spanning 205.2 cR. A test-cross methodology was devised for phenotyping of RH progenies, and through forward genetic, the scs (ae) locus was pinpointed to a 1.1 Mb-segment containing eight genes. Further, the high resolution provided by RH mapping, combined with chromosome-wise synteny analysis, located the ancestral point of fusion between the telomeric and centromeric repeats of two paleochromosomes that originated chromosome 1D. Also, it indicated that the centromere of this chromosome is likely the result of a neocentromerization event, rather than the conservation of an ancestral centromere as previously believed. Interestingly, location of scs locus in the vicinity of paleofusion is not associated with the expected disruption of synteny, but rather with a good degree of conservation across grass species. Indeed, these observations advocate the evolutionary importance of this locus as suggested by "Maan's scs hypothesis."
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25
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Yin T, Pan G, Liu H, Wu J, Li Y, Zhao Z, Fu T, Zhou Y. The chloroplast ribosomal protein L21 gene is essential for plastid development and embryogenesis in Arabidopsis. PLANTA 2012; 235:907-21. [PMID: 22105802 DOI: 10.1007/s00425-011-1547-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 10/31/2011] [Indexed: 05/22/2023]
Abstract
Embryogenesis in higher plants is controlled by a complex gene network. Identification and characterization of genes essential for embryogenesis will provide insights into the early events in embryo development. In this study, a novel mutant with aborted seed development (asd) was identified in Arabidopsis. The asd mutant produced about 25% of albino seeds at the early stage of silique development. The segregation of normal and albino seeds was inherited as a single recessive embryo-lethal trait. The gene disrupted in the asd mutant was isolated through map-based cloning. The mutated gene contains a single base change (A to C) in the coding region of RPL21C (At1g35680) that is predicted to encode the chloroplast 50S ribosomal protein L21. Allele test with other two T-DNA insertion lines in RPL21C and a complementation test demonstrated that the mutation in RPL21C was responsible for the asd phenotype. RPL21C exhibits higher expression in leaves and flowers compared with expression levels in roots and developing seeds. The RPL21C-GFP fusion protein was localized in chloroplasts. Cytological observations showed that the asd embryo development was arrested at the globular stage. There were no plastids with normal thylakoids and as a result no normal chloroplasts formed in mutant cells, indicating an indispensable role of the ASD gene in chloroplasts biogenesis. Our studies suggest that the chloroplast ribosomal protein L21 gene is required for chloroplast development and embryogenesis in Arabidopsis.
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Affiliation(s)
- Tuanzhang Yin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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26
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Hsu SC, Belmonte MF, Harada JJ, Inoue K. Indispensable Roles of Plastids in Arabidopsis thaliana Embryogenesis. Curr Genomics 2011; 11:338-49. [PMID: 21286311 PMCID: PMC2944999 DOI: 10.2174/138920210791616716] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/18/2010] [Accepted: 05/25/2010] [Indexed: 11/22/2022] Open
Abstract
The plastid is an organelle vital to all photosynthetic and some non-photosynthetic eukaryotes. In the model plant Arabidopsis thaliana, a number of nuclear genes encoding plastid proteins have been found to be necessary for embryo development. However, the exact roles of plastids in this process remain largely unknown. Here we use publicly available datasets to obtain insights into the relevance of plastid activities to A. thaliana embryogenesis. By searching the SeedGenes database (http://www.seedgenes.org) and recent literature, we found that, of the 339 non-redundant genes required for proper embryo formation, 108 genes likely encode plastid-targeted proteins. Nineteen of these genes are necessary for development of preglobular embryos and/or their conversion to globular embryos, of which 13 genes encode proteins involved in non-photosynthetic metabolism. By contrast, among 38 genes which are dispensable for globular embryo formation but necessary for further development, only one codes for a protein involved in metabolism. Products of 21 of the 38 genes play roles in plastid gene expression and maintenance. Examination of RNA profiles of embryos at distinct growth stages obtained in laser-capture microdissection coupled with DNA microarray experiments revealed that most of the identified genes are expressed throughout embryo morphogenesis and maturation. These findings suggest that metabolic activities are required at preglobular and throughout all stages of embryo development, whereas plastid gene expression becomes necessary during and/or after the globular stage to sustain various activities of the organelle including photosynthetic electron transport.
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Affiliation(s)
- Shih-Chi Hsu
- Department of Plant Sciences, University of California, Davis, CA, USA
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27
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Candela H, Pérez-Pérez JM, Micol JL. Uncovering the post-embryonic functions of gametophytic- and embryonic-lethal genes. TRENDS IN PLANT SCIENCE 2011; 16:336-345. [PMID: 21420345 DOI: 10.1016/j.tplants.2011.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/09/2011] [Accepted: 02/17/2011] [Indexed: 05/30/2023]
Abstract
An estimated 500-1 000 Arabidopsis (Arabidopsis thaliana) genes mutate to embryonic lethality. In addition, several hundred mutations have been identified that cause gametophytic lethality. Thus, a significant fraction of the ∼25,000 protein-coding genes in Arabidopsis are indispensable to the early stages of the diploid phase or to the haploid gametophytic phase. The expression patterns of many of these genes indicate that they also act later in development but, because the mutants die at such early stages, conventional methods limit the study of their roles in adult diploid plants. Here, we describe the toolset that allows researchers to assess the post-embryonic functions of plant genes for which only gametophytic- and embryonic-lethal alleles have been isolated.
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Affiliation(s)
- Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
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28
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ANK6, a mitochondrial ankyrin repeat protein, is required for male-female gamete recognition in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2010; 107:22332-7. [PMID: 21123745 DOI: 10.1073/pnas.1015911107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Double fertilization in angiosperms involves several successive steps, including guidance and reception of the pollen tube and male-female gamete recognition. Each step entails extensive communication and interaction between two different reproductive cell or tissue types. Extensive research has focused on the pollen tube, namely, its interaction with the stigma and reception by maternal cells. Little is known, however, about the mechanism by which the gametes recognize each other and interact to form a zygote. We report that an ankyrin repeat protein (ANK6) is essential for fertilization, specifically for gamete recognition. ANK6 (At5g61230) was highly expressed in the male and female gametophytes before and during but not after fertilization. Genetic analysis of a T-DNA insertional mutant suggested that loss of function of ANK6 results in embryonic lethality. Moreover, male-female gamete recognition was found to be impaired only when an ank6 male gamete reached an ank6 female gamete, thereby preventing formation of homozygous zygotes. ANK6 was localized to the mitochondria, where it interacted with SIG5, a transcription initiation factor previously found to be essential for fertility. These results show that ANK6 plays a central role in male-female gamete recognition, possibly by regulating mitochondrial gene expression.
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29
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Liang Q, Lu X, Jiang L, Wang C, Fan Y, Zhang C. EMB1211 is required for normal embryo development and influences chloroplast biogenesis in Arabidopsis. PHYSIOLOGIA PLANTARUM 2010; 140:380-394. [PMID: 20738804 DOI: 10.1111/j.1399-3054.2010.01407.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chloroplast biogenesis is tightly linked with embryogenesis and seedling development. A growing body of work has been done on the molecular mechanisms underlying chloroplast development; however, the molecular components involved in chloroplast biogenesis during embryogenesis remain largely uncharacterized. In this paper, we show that an Arabidopsis mutant carrying a T-DNA insertion in a gene encoding a multiple membrane occupation and recognition nexus (MORN)-containing protein exhibits severe defects during embryogenesis, producing abnormal embryos and thereby leading to a lethality of young seedlings. Genetic and microscopic studies reveal that the mutation is allelic to a previously designated Arabidopsis embryo-defective 1211 mutant (emb1211). The emb1211 +/- mutant plants produce approximately 25% of white-colored ovules with abnormal embryos since late globular stage when primary chloroplast biogenesis takes place, while the wild-type plants produce all green ovules. Transmission electron microscopic analysis reveals the absence of normal chloroplast development, both in the mutant embryos and in the mutant seedlings, that contributes to the albinism. The EMB1211 gene is preferentially expressed in developing embryos as revealed in the EMB1211::GUS transgenic plants. Taken together, the data indicate that EMB1211 has an important role during embryogenesis and chloroplast biogenesis in Arabidopsis.
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Affiliation(s)
- Qiuju Liang
- Department of Plant Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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30
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Andriotis VME, Pike MJ, Bunnewell S, Hills MJ, Smith AM. The plastidial glucose-6-phosphate/phosphate antiporter GPT1 is essential for morphogenesis in Arabidopsis embryos. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:128-39. [PMID: 20659277 DOI: 10.1111/j.1365-313x.2010.04313.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: 05/24/2023]
Abstract
The glucose-6-phosphate/phosphate antiporter GPT1 is a major route of entry of carbon into non-photosynthetic plastids. To discover its importance in oilseeds, we used a seed-specific promoter to generate lines of Arabidopsis thaliana with reduced levels of GPT1 in developing embryos. Strong reductions resulted in seed abortion at the end of the globular stage of embryo development, when proplastids in normal embryos differentiate and acquire chlorophyll. Seed abortion was partly dependent on the light level during silique development. Embryos in seeds destined for abortion failed to undergo normal morphogenesis and were 'raspberry-like' in appearance. They had ultrastructural and biochemical defects including proliferation of peroxisomes and starch granules, and altered expression of genes involved in starch turnover and the oxidative pentose phosphate pathway. We propose that GPT1 is necessary for early embryo development because it catalyses import into plastids of glucose-6-phosphate as the substrate for NADPH generation via the oxidative pentose phosphate pathway. We suggest that low NADPH levels during plastid differentiation and chlorophyll synthesis may result in generation of reactive oxygen species and triggering of embryo cell death.
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Affiliation(s)
- Vasilios M E Andriotis
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK
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31
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Wang X, Xue L, Sun J, Zuo J. The Arabidopsis BE1 gene, encoding a putative glycoside hydrolase localized in plastids, plays crucial roles during embryogenesis and carbohydrate metabolism. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:273-288. [PMID: 20377688 DOI: 10.1111/j.1744-7909.2010.00930.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Carbohydrate metabolism is central to plant growth and development. However, little is known about its role in embryogenesis. Here, we report the characterization of multiple alleles of the BRANCHING ENZYME1 (BE1) gene (also known as EMB2729). The weak allele of be1-3, characterized by positional cloning, carries a single-nucleotide substitution in an exon-intron junction and shows various developmental defects during post-germination growth. This mutation causes a reduced level of BE1 mRNA that, likely generated from cryptically spliced pre-mRNA, contains a Glu-to-Lys substitution at codon 366. In four null alleles, BE1 is disrupted by T-DNA insertions, causing embryo developmental arrests at the heart stage. Light microscopy reveals reduced cell divisions and abnormal cell differentiation, thereby leading to defects in setting up the shoot apical meristem, embryonic vascular tissues and cotyledons. Overexpression of BE1 results in a pleiotropic phenotype, indicating that the fine-tuned BE1 level is crucial for plant growth and development. BE1 encodes a putative glycoside hydrolase that is highly conserved in higher plants. A BE1-GFP fusion protein, which is fully functional in complementing be1 mutants, is localized in plastids. The be1-3 phenotype can be partially rescued by glucose, fructose or sucrose, implying the involvement of BE1 in carbohydrate metabolism in plastids.
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Affiliation(s)
- Xingchun Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
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32
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Meinke D, Sweeney C, Muralla R. Integrating the genetic and physical maps of Arabidopsis thaliana: identification of mapped alleles of cloned essential (EMB) genes. PLoS One 2009; 4:e7386. [PMID: 19812694 PMCID: PMC2754112 DOI: 10.1371/journal.pone.0007386] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 09/15/2009] [Indexed: 12/23/2022] Open
Abstract
The classical genetic map of Arabidopsis includes more than 130 genes with an embryo-defective (emb) mutant phenotype. Many of these essential genes remain to be cloned. Hundreds of additional EMB genes have been cloned and catalogued (www.seedgenes.org) but not mapped. To facilitate EMB gene identification and assess the current level of saturation, we updated the classical map, compared the physical and genetic locations of mapped loci, and performed allelism tests between mapped (but not cloned) and cloned (but not mapped) emb mutants with similar chromosome locations. Two hundred pairwise combinations of genes located on chromosomes 1 and 5 were tested and more than 1100 total crosses were screened. Sixteen of 51 mapped emb mutants examined were found to be disrupted in a known EMB gene. Alleles of a wide range of published EMB genes (YDA, GLA1, TIL1, AtASP38, AtDEK1, EMB506, DG1, OEP80) were discovered. Two EMS mutants isolated 30 years ago, T-DNA mutants with complex insertion sites, and a mutant with an atypical, embryo-specific phenotype were resolved. The frequency of allelism encountered was consistent with past estimates of 500 to 1000 EMB loci. New EMB genes identified among mapped T-DNA insertion mutants included CHC1, which is required for chromatin remodeling, and SHS1/AtBT1, which encodes a plastidial nucleotide transporter similar to the maize Brittle1 protein required for normal endosperm development. Two classical genetic markers (PY, ALB1) were identified based on similar map locations of known genes required for thiamine (THIC) and chlorophyll (PDE166) biosynthesis. The alignment of genetic and physical maps presented here should facilitate the continued analysis of essential genes in Arabidopsis and further characterization of a broad spectrum of mutant phenotypes in a model plant.
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Affiliation(s)
- David Meinke
- Department of Botany, Oklahoma State University, Stillwater, Oklahoma, United States of America.
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33
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Huang J, Zhao X, Yu H, Ouyang Y, Wang L, Zhang Q. The ankyrin repeat gene family in rice: genome-wide identification, classification and expression profiling. PLANT MOLECULAR BIOLOGY 2009; 71:207-226. [PMID: 19609685 DOI: 10.1007/s11103-009-9518-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2009] [Accepted: 06/12/2009] [Indexed: 05/28/2023]
Abstract
Ankyrin repeat (ANK) containing proteins comprise a large protein family. Although many members of this family have been implicated in plant growth, development and signal transduction, only a few ANK genes have been reported in rice. In this study, we analyzed the structures, phylogenetic relationship, genome localizations and expression profiles of 175 ankyrin repeat genes identified in rice (OsANK). Domain composition analysis suggested OsANK proteins can be classified into ten subfamilies. Chromosomal localizations of OsANK genes indicated nine segmental duplication events involving 17 genes and 65 OsANK genes were involved in tandem duplications. The expression profiles of 158 OsANK genes were analyzed in 24 tissues covering the whole life cycle of two rice genotypes, Minghui 63 and Zhenshan 97. Sixteen genes showed preferential expression in given tissues compared to all the other tissues in Minghui 63 and Zhenshan 97. Nine genes were preferentially expressed in stamen of 1 day before flowering, suggesting that these genes may play important roles in pollination and fertilization. Expression data of OsANK genes were also obtained with tissues of seedlings subjected to three phytohormone (NAA, GA3 and KT) and light/dark treatments. Eighteen genes showed differential expression with at least one phytohormone treatment while under light/dark treatments, 13 OsANK genes showed differential expression. Our data provided a very useful reference for cloning and functional analysis of members of this gene family in rice.
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Affiliation(s)
- Jianyan Huang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070 Wuhan, China.
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34
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Muñoz-Amatriaín M, Svensson JT, Castillo AM, Close TJ, Vallés MP. Microspore embryogenesis: assignment of genes to embryo formation and green vs. albino plant production. Funct Integr Genomics 2009; 9:311-23. [PMID: 19229567 PMCID: PMC2700865 DOI: 10.1007/s10142-009-0113-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 01/16/2009] [Accepted: 01/24/2009] [Indexed: 11/30/2022]
Abstract
Plant microspores can be reprogrammed from their normal pollen development to an embryogenic route in a process termed microspore embryogenesis or androgenesis. Stress treatment has a critical role in this process, inducing the dedifferentiation of microspores and conditioning the following androgenic response. In this study, we have used three barley doubled haploid lines with similar genetic background but different androgenic response. The Barley1 GeneChip was used for transcriptome comparison of these lines after mannitol stress treatment, allowing the identification of 213 differentially expressed genes. Most of these genes belong to the functional categories "cell rescue, defense, and virulence"; "metabolism"; "transcription"; and "transport". These genes were grouped into clusters according to their expression profiles among lines. A principal component analysis allowed us to associate specific gene expression clusters to phenotypic variables. Genes associated with the ability of microspores to divide and form embryos were mainly involved in changes in the structure and function of membranes, efficient use of available energy sources, and cell fate. Genes related to stress response, transcription and translation regulation, and degradation of pollen-specific proteins were associated with green plant production, while expression of genes related to plastid development was associated with albino plant regeneration.
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Affiliation(s)
- M. Muñoz-Amatriaín
- Departamento de Genética y Producción Vegetal, Estación Experimental Aula Dei, Consejo Superior de Investigaciones Científicas, Apdo 13034, 50080 Zaragoza, Spain
| | - J. T. Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - A. M. Castillo
- Departamento de Genética y Producción Vegetal, Estación Experimental Aula Dei, Consejo Superior de Investigaciones Científicas, Apdo 13034, 50080 Zaragoza, Spain
| | - T. J. Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - M. P. Vallés
- Departamento de Genética y Producción Vegetal, Estación Experimental Aula Dei, Consejo Superior de Investigaciones Científicas, Apdo 13034, 50080 Zaragoza, Spain
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A novel chloroplast-localized protein EMB1303 is required for chloroplast development in Arabidopsis. Cell Res 2009; 19:1205-16. [DOI: 10.1038/cr.2009.84] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Zhang X, Li D, Zhang H, Wang X, Zheng Z, Song F. Molecular characterization of rice OsBIANK1, encoding a plasma membrane-anchored ankyrin repeat protein, and its inducible expression in defense responses. Mol Biol Rep 2009; 37:653-60. [PMID: 19288292 DOI: 10.1007/s11033-009-9507-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 03/04/2009] [Indexed: 10/21/2022]
Abstract
A rice gene, OsBIANK1, encoding a protein containing a typical ankyrin repeat domain, was cloned and identified. The OsBIANK1 protein, consisting of 329 amino acids, contains a conserved ankyrin repeat domain with two ankyrin repeats organized in tandem and was showed to be localized on cytoplasmic membrane during transient expression in onion epidermal cells. Expression of OsBIANK1 was induced by treatment with benzothiadiazole (BTH), a chemical inducer capable of inducing disease resistance response in rice. In BTH-treated rice seedlings, expression of OsBIANK1 was further induced by infection with Magnaporthe grisea, the rice blast fungus, as compared with those in water-treated seedlings. Our preliminary results confirm previous evidences that OsBIANK1 may be involved in regulation of disease resistance response in rice.
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Affiliation(s)
- Xinchun Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 310029, Hangzhou, Zhejiang, People's Republic of China
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