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Istomina EA, Korostyleva TV, Kovtun AS, Slezina MP, Odintsova TI. Transcriptome-Wide Identification and Expression Analysis of Genes Encoding Defense-Related Peptides of Filipendula ulmaria in Response to Bipolaris sorokiniana Infection. J Fungi (Basel) 2024; 10:258. [PMID: 38667929 PMCID: PMC11050963 DOI: 10.3390/jof10040258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/06/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Peptides play an essential role in plant development and immunity. Filipendula ulmaria, belonging to the Rosaceae family, is a medicinal plant which exhibits valuable pharmacological properties. F. ulmaria extracts in vitro inhibit the growth of a variety of plant and human pathogens. The role of peptides in defense against pathogens in F. ulmaria remains unknown. The objective of this study was to explore the repertoire of antimicrobial (AMPs) and defense-related signaling peptide genes expressed by F. ulmaria in response to infection with Bipolaris sorokiniana using RNA-seq. Transcriptomes of healthy and infected plants at two time points were sequenced on the Illumina HiSeq500 platform and de novo assembled. A total of 84 peptide genes encoding novel putative AMPs and signaling peptides were predicted in F. ulmaria transcriptomes. They belong to known, as well as new, peptide families. Transcriptional profiling in response to infection disclosed complex expression patterns of peptide genes and identified both up- and down-regulated genes in each family. Among the differentially expressed genes, the vast majority were down-regulated, suggesting suppression of the immune response by the fungus. The expression of 13 peptide genes was up-regulated, indicating their possible involvement in triggering defense response. After functional studies, the encoded peptides can be used in the development of novel biofungicides and resistance inducers.
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Affiliation(s)
- Ekaterina A. Istomina
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (E.A.I.); (T.V.K.); (M.P.S.)
| | - Tatyana V. Korostyleva
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (E.A.I.); (T.V.K.); (M.P.S.)
| | - Alexey S. Kovtun
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia;
| | - Marina P. Slezina
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (E.A.I.); (T.V.K.); (M.P.S.)
| | - Tatyana I. Odintsova
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (E.A.I.); (T.V.K.); (M.P.S.)
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Opdensteinen P, Knödler M, Buyel JF. Production of enzymes for the removal of odorous substances in plant biomass. Protein Expr Purif 2024; 214:106379. [PMID: 37816475 DOI: 10.1016/j.pep.2023.106379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023]
Abstract
Residual plant biomass collected from agricultural, technical or biopharmaceutical processes contains odorous substances. The latter are often unacceptable for customers if the biomass is used in sustainable products such as building materials, paints, glues or flame-resistant foils. The objective of this study was to identify enzymes that can prevent the formation or facilitate the degradation of odorous substances such as butanol, eugenol or ethyl acetate and their derivatives in residual biomass. We used plant cell packs (PCPs) as a small-scale screening platform to assess the expression of enzymes that break down odorous substances in tobacco biomass. First, we compiled a list of volatile compounds in residual plant biomass that may give rise to undesirable odors, refining the list to 10 diverse compounds representing a range of odors. We then selected five monomeric enzymes (a eugenol oxidase, laccase, oxidase, alkane mono-oxidase and ethyl acetate hydrolase) with the potential to degrade these substances. We transiently expressed the proteins in PCPs, targeting different subcellular compartments to identify optimal production conditions. The maximum yield we achieved was ∼20 mg kg-1 for Trametes hirsute laccase targeted to the chloroplast. Our results confirm that enzymes for the removal of odorous substances can be produced in plant systems, facilitating the upcycling of residual biomass as an ingredient for sustainable products.
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Affiliation(s)
- Patrick Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074, Aachen, Germany; Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074, Aachen, Germany.
| | - Matthias Knödler
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074, Aachen, Germany; Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074, Aachen, Germany.
| | - Johannes F Buyel
- Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074, Aachen, Germany; Institute of Bioprocess Science and Engineering (IBSE), Department of Biotechnology (DBT), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, A-1190, Vienna, Austria.
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3
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Qiu C, Halterman D, Zhang H, Liu Z. Multifunctionality of AsCFEM6 and AsCFEM12 effectors from the potato early blight pathogen Alternaria solani. Int J Biol Macromol 2024; 257:128575. [PMID: 38048930 DOI: 10.1016/j.ijbiomac.2023.128575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/31/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Plant pathogens secrete fungal-specific common in several fungal extracellular membrane (CFEM) effectors to manipulate host immunity and contribute to their virulence. Little is known about effectors and their functions in Alternaria solani, the necrotrophic fungal pathogen causing potato early blight. To identify candidate CFEM effector genes, we mined A. solani genome databases. This led to the identification of 12 genes encoding CFEM proteins (termed AsCFEM1-AsCFEM12) and 6 of them were confirmed to be putative secreted effectors. In planta expression revealed that AsCFEM6 and AsCFEM12 have elicitor function that triggers plant defense response including cell death in different botanical families. Targeted gene disruption of AsCFEM6 and AsCFEM12 resulted in a change in spore development, significant reduction of virulence on potato and eggplant susceptible cultivars, increased resistance to fungicide stress, variation in iron acquisition and utilization, and the involvement in 1,8-dihydroxynaphthalene (DHN) melanin biosynthesis pathway. Using maximum likelihood method, we found that positive selection likely caused the polymorphism within AsCFEM6 and AsCFEM12 homologs in different Alternaria spp. Site-directed mutagenesis analysis indicated that positive selection sites within their CFEM domains are required for cell death induction in Nicotiana benthamiana and are critical for response to abiotic stress in yeast. These results demonstrate that AsCFEM effectors possess additional functions beyond their roles in host plant immune response and pathogen virulence.
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Affiliation(s)
- Chaodong Qiu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
| | - Huajian Zhang
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei 230036, China.
| | - Zhenyu Liu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei 230036, China.
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Figueiredo R, Costa M, Moreira D, Moreira M, Noble J, Pereira LG, Melo P, Palanivelu R, Coimbra S, Pereira AM. JAGGER localization and function are dependent on GPI anchor addition. PLANT REPRODUCTION 2024:10.1007/s00497-024-00495-w. [PMID: 38294499 DOI: 10.1007/s00497-024-00495-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE GPI anchor addition is important for JAGGER localization and in vivo function. Loss of correct GPI anchor addition in JAGGER, negatively affects its localization and function. In flowering plants, successful double fertilization requires the correct delivery of two sperm cells to the female gametophyte inside the ovule. The delivery of a single pair of sperm cells is achieved by the entrance of a single pollen tube into one female gametophyte. To prevent polyspermy, Arabidopsis ovules avoid the attraction of multiple pollen tubes to one ovule-polytubey block. In Arabidopsis jagger mutants, a significant number of ovules attract more than one pollen tube to an ovule due to an impairment in synergid degeneration. JAGGER encodes a putative arabinogalactan protein which is predicted to be anchored to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor. Here, we show that JAGGER fused to citrine yellow fluorescent protein (JAGGER-cYFP) is functional and localizes mostly to the periphery of ovule integuments and transmitting tract cells. We further investigated the importance of GPI-anchor addition domains for JAGGER localization and function. Different JAGGER proteins with deletions in predicted ω-site regions and GPI attachment signal domain, expected to compromise the addition of the GPI anchor, led to disruption of JAGGER localization in the cell periphery. All JAGGER proteins with disrupted localization were also not able to rescue the polytubey phenotype, pointing to the importance of GPI-anchor addition to in vivo function of the JAGGER protein.
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Affiliation(s)
- Raquel Figueiredo
- LAQV/REQUIMTE, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Mónica Costa
- LAQV/REQUIMTE, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Diana Moreira
- LAQV/REQUIMTE, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Miguel Moreira
- LAQV/REQUIMTE, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Jennifer Noble
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Luís Gustavo Pereira
- GreenUPorto - Sustainable Agrifood Production Research Centre, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Paula Melo
- GreenUPorto - Sustainable Agrifood Production Research Centre, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | | | - Sílvia Coimbra
- LAQV/REQUIMTE, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Ana Marta Pereira
- LAQV/REQUIMTE, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
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Nagasato D, Sugita Y, Tsuno Y, Tanaka R, Fukuda M, Matsuoka K. Glycosylphosphatidylinositol-anchoring is required for the proper transport and extensive glycosylation of a classical arabinogalactan protein precursor in tobacco BY-2 cells. Biosci Biotechnol Biochem 2023; 87:991-1008. [PMID: 37348475 DOI: 10.1093/bbb/zbad081] [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: 03/31/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
Many precursors of plant arabinogalactan proteins (AGPs) contain a C-terminal glycosylphosphatidylinositol (GPI)-anchoring signal. Using NtAGP1, a classical tobacco AGP, as a model, and green fluorescent protein (GFP) and sweet potato sporamin (SPO) as tags, we analyzed the localization and modification of AGP and its mutant without GPI-anchoring signal (AGPΔC) in tobacco BY-2 cells. The NtAGP1 fusion proteins migrated as large smear on SDS-polyacrylamide gel, and these proteins also localized preferentially to the plasma membrane. In contrast, fusions of AGPΔC with GFP and SPO yielded several forms: The largest were secreted, whereas others were recovered in the endomembrane organelles, including vacuoles. Comparison of the glycan structures of the microsomal SPO-AGP and the secreted SPO-AGPΔC using antibodies against the glycan epitopes of AGP indicated that the glycan structures of these proteins are different. These observations indicate that GPI-anchoring is required for the proper transport and glycosylation of the AGP precursor.
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Affiliation(s)
- Daiki Nagasato
- Graduate School of Bioresource and Bioenvironmental Science, Kyushu University, Fukuoka, Japan
| | - Yuto Sugita
- Graduate School of Bioresource and Bioenvironmental Science, Kyushu University, Fukuoka, Japan
| | - Yuhei Tsuno
- Graduate School of Bioresource and Bioenvironmental Science, Kyushu University, Fukuoka, Japan
| | | | - Maki Fukuda
- School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Ken Matsuoka
- Graduate School of Bioresource and Bioenvironmental Science, Kyushu University, Fukuoka, Japan
- School of Agriculture, Kyushu University, Fukuoka, Japan
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Mueller KK, Pfeifer L, Schuldt L, Szövényi P, de Vries S, de Vries J, Johnson KL, Classen B. Fern cell walls and the evolution of arabinogalactan proteins in streptophytes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:875-894. [PMID: 36891885 DOI: 10.1111/tpj.16178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 05/27/2023]
Abstract
Significant changes have occurred in plant cell wall composition during evolution and diversification of tracheophytes. As the sister lineage to seed plants, knowledge on the cell wall of ferns is key to track evolutionary changes across tracheophytes and to understand seed plant-specific evolutionary innovations. Fern cell wall composition is not fully understood, including limited knowledge of glycoproteins such as the fern arabinogalactan proteins (AGPs). Here, we characterize the AGPs from the leptosporangiate fern genera Azolla, Salvinia, and Ceratopteris. The carbohydrate moiety of seed plant AGPs consists of a galactan backbone including mainly 1,3- and 1,3,6-linked pyranosidic galactose, which is conserved across the investigated fern AGPs. Yet, unlike AGPs of angiosperms, those of ferns contained the unusual sugar 3-O-methylrhamnose. Besides terminal furanosidic arabinose, Ara (Araf), the main linkage type of Araf in the ferns was 1,2-linked Araf, whereas in seed plants 1,5-linked Araf is often dominating. Antibodies directed against carbohydrate epitopes of AGPs supported the structural differences between AGPs of ferns and seed plants. Comparison of AGP linkage types across the streptophyte lineage showed that angiosperms have rather conserved monosaccharide linkage types; by contrast bryophytes, ferns, and gymnosperms showed more variability. Phylogenetic analyses of glycosyltransferases involved in AGP biosynthesis and bioinformatic search for AGP protein backbones revealed a versatile genetic toolkit for AGP complexity in ferns. Our data reveal important differences across AGP diversity of which the functional significance is unknown. This diversity sheds light on the evolution of the hallmark feature of tracheophytes: their elaborate cell walls.
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Affiliation(s)
- Kim-Kristine Mueller
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lukas Pfeifer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lina Schuldt
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008, Zurich, Switzerland
- Zurich-Basel Plant Science Center (PSC), ETH Zürich, Tannenstrasse 1, 8092, Zürich, Switzerland
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtsr. 1, 37077, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Kim L Johnson
- Department of Animal, Plant and Soil Science, La Trobe Institute for Agriculture & Food, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Birgit Classen
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
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Genome-Wide Comparative Analysis of the Fasciclin-like Arabinogalactan Proteins (FLAs) in Salicacea and Identification of Secondary Tissue Development-Related Genes. Int J Mol Sci 2023; 24:ijms24021481. [PMID: 36675002 PMCID: PMC9862198 DOI: 10.3390/ijms24021481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/24/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) containing both AGP-like glycated domains and fasciclin (FAS) domains, which are involved in plant growth and development and synthesis of the cell wall. However, these proteins have not been identified or analyzed in willow, Salix, the sister genus of Populus. In this study, we performed a whole genome study of the FLA gene family of Salix suchowensis and compared it with the FLA gene family of Populus deltoides. The results showed the presence of 40 and 46 FLA genes in P. deltoides and S. suchowensis, distributed on 17 and 16 chromosomes, respectively. Four pairs of tandem repeat genes were found in willow, while poplar had no tandem repeat genes. Twelve and thirteen pairs of duplicated gene fragments were identified in poplar and willow, respectively. The multispecies phylogenetic tree showed that the FLA gene family could be divided into four groups (I-IV), with Group 1 showing significant expansion in woody plants. A gene expression analysis showed that PdeFLA19/27 in Group I of poplar was highly expressed, specifically during the secondary growth period of the stem and the rapid elongation of seed hairs. In the Group I genes of S. suchowensis, SsuFLA25/26/28 was also highly expressed during the secondary growth period, whereas increased expression of SsuFLA35 was associated with seed hair tissue. These results provide important clues about the differences in the FLA gene family during the evolution of herbs and woody plants, and suggest that the FLA gene family may play an essential role in regulating the secondary growth of woody plants. It also provides a reference for further studies on the regulation of secondary growth and seed hair development by FLA genes in poplar and willow.
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Cas9/gRNA-Mediated Mutations in PtrFLA40 and PtrFLA45 Reveal Redundant Roles in Modulating Wood Cell Size and SCW Synthesis in Poplar. Int J Mol Sci 2022; 24:ijms24010427. [PMID: 36613871 PMCID: PMC9820481 DOI: 10.3390/ijms24010427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/14/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Fasciclin-like arabinogalactan proteins (FLAs) play an important role in plant development and adaptation to the environment. However, the roles of FLAs in wood formation remain poorly understood. Here, we identified a total of 50 PtrFLA genes in poplar. They were classified into four groups: A to D, among which group A was the largest group with 28 members clustered into four branches. Most PtrFLAs of group A were dominantly expressed in developing xylem based on microarray and RT-qPCR data. The roles of PtrFLA40 and PtrFLA45 in group A were investigated via the Cas9/gRNA-induced mutation lines. Loss of PtrFLA40 and PtrFLA45 increased stem length and diameter in ptrfla40ptrfla45 double mutants, but not in ptrfla40 or ptrfla45 single mutants. Further, our findings indicated that the ptrfla40ptrfla45 mutants enlarged the cell size of xylem fibers and vessels, suggesting a negative modulation in stem xylem cell size. In addition, wood lignin content in the ptrfla40fla45 mutants was increased by nearly 9%, and the lignin biosynthesis-related genes were significantly up-regulated in the ptrfla40fla45 mutants, in agreement with the increase in wood lignin content. Overall, Cas9/gRNA-mediated mutations in PtrFLA40 and PtrFLA45 reveal redundant roles in modulating wood cell size and secondary cell wall (SCW) synthesis in poplar.
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Zhou K. The regulation of the cell wall by glycosylphosphatidylinositol-anchored proteins in Arabidopsis. Front Cell Dev Biol 2022; 10:904714. [PMID: 36036018 PMCID: PMC9412048 DOI: 10.3389/fcell.2022.904714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/04/2022] [Indexed: 12/04/2022] Open
Abstract
A polysaccharides-based cell wall covers the plant cell, shaping it and protecting it from the harsh environment. Cellulose microfibrils constitute the cell wall backbone and are embedded in a matrix of pectic and hemicellulosic polysaccharides and glycoproteins. Various environmental and developmental cues can regulate the plant cell wall, and diverse glycosylphosphatidylinositol (GPI)-anchored proteins participate in these regulations. GPI is a common lipid modification on eukaryotic proteins, which covalently tethers the proteins to the membrane lipid bilayer. Catalyzed by a series of enzymic complexes, protein precursors are post-translationally modified at their hydrophobic carboxyl-terminus in the endomembrane system and anchored to the lipid bilayer through an oligosaccharidic GPI modification. Ultimately, mature proteins reach the plasma membrane via the secretory pathway facing toward the apoplast and cell wall in plants. In Arabidopsis, more than three hundred GPI-anchored proteins (GPI-APs) have been predicted, and many are reported to be involved in diverse regulations of the cell wall. In this review, we summarize GPI-APs involved in cell wall regulation. GPI-APs are proposed to act as structural components of the cell wall, organize cellulose microfibrils at the cell surface, and during cell wall integrity signaling transduction. Besides regulating protein trafficking, the GPI modification is potentially governed by a GPI shedding system that cleaves and releases the GPI-anchored proteins from the plasma membrane into the cell wall.
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10
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GhENODL6 Isoforms from the Phytocyanin Gene Family Regulated Verticillium Wilt Resistance in Cotton. Int J Mol Sci 2022; 23:ijms23062913. [PMID: 35328334 PMCID: PMC8955391 DOI: 10.3390/ijms23062913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/28/2022] Open
Abstract
Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae, currently devastates cotton fiber yield and quality seriously, yet few resistance germplasm resources have been discovered in Gossypium hirsutum. The cotton variety Nongda601 with suitable VW resistance and high yield was developed in our lab, which supplied elite resources for discovering resistant genes. Early nodulin-like protein (ENODL) is mainly related to nodule formation, and its role in regulating defense response has been seldom studied. Here, 41 conserved ENODLs in G. hirsutum were identified and characterized, which could divide into four subgroups. We found that GhENODL6 was upregulated under V. dahliae stress and hormonal signal and displayed higher transcript levels in resistant cottons than the susceptible. The GhENODL6 was proved to positively regulate VW resistance via overexpression and gene silencing experiments. Overexpression of GhENODL6 significantly enhanced the expressions of salicylic acid (SA) hormone-related transcription factors and pathogenicity-related (PR) protein genes, as well as hydrogen peroxide (H2O2) and SA contents, resulting in improved VW resistance in transgenic Arabidopsis. Correspondingly, in the GhENODL6 silenced cotton, the expression levels of both phenylalanine ammonia lyase (PAL) and 4-coumarate-CoA ligase (4CL) genes significantly decreased, leading to the reduced SA content mediating by the phenylalanine ammonia lyase pathway. Taken together, GhENODL6 played a crucial role in VW resistance by inducing SA signaling pathway and regulating the production of reactive oxygen species (ROS). These findings broaden our understanding of the biological roles of GhENODL and the molecular mechanisms underlying cotton disease resistance.
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Zhang MJ, Zhao TY, Ouyang XK, Zhao XY, Dai X, Gao XQ. Pollen-specific gene SKU5-SIMILAR 13 enhances growth of pollen tubes in the transmitting tract in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:696-710. [PMID: 34626184 DOI: 10.1093/jxb/erab448] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Pollen tube growth and penetration in female tissues are essential for the transfer of sperm to the embryo sac during plant pollination. Despite its importance during pollination, little is known about the mechanisms that mediate pollen tube growth in female tissues. In this study, we identified an Arabidopsis thaliana pollen/pollen tube-specific gene, SKU5-SIMILAR 13 (SKS13), which was critical for the growth of pollen tubes in the transmitting tract. The SKS13 protein was distributed throughout the cytoplasm and pollen tube walls at the apical region. In comparison with wild-type pollen tubes, those of the sks13 mutants burst more frequently when grown in vitro. Additionally, the growth of sks13 pollen tubes was retarded in the transmitting tract, thereby resulting in decreased male fertility. The accumulation of pectin and cellulose in the cell wall of sks13 pollen tubes was altered, and the content of jasmonic acid (JA) in sks13 pollen was reduced. The pollen tubes treated with an inhibitor of JA biosynthesis grew much more slowly and had an altered distribution of pectin, which is similar to the pollen tube phenotypes of the SKS13 mutation. Our results suggest that SKS13 is essential for pollen tube growth in the transmitting tract by mediating the biosynthesis of JA that modifies the components of pollen tube cell walls.
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Affiliation(s)
- Ming Jun Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China271018
| | - Tian Yi Zhao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China271018
| | - Xiu Ke Ouyang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China271018
| | - Xin-Ying Zhao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China271018
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China100091
| | - Xin-Qi Gao
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China271018
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Schultz CJ, Wu Y, Baumann U. A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina. MYCORRHIZA 2022; 32:45-66. [PMID: 35031894 PMCID: PMC8786786 DOI: 10.1007/s00572-021-01066-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Diversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.
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Affiliation(s)
- Carolyn J Schultz
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
| | - Yue Wu
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ute Baumann
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
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Shin YJ, Vavra U, Strasser R. Proper protein folding in the endoplasmic reticulum is required for attachment of a glycosylphosphatidylinositol anchor in plants. PLANT PHYSIOLOGY 2021; 186:1878-1892. [PMID: 33930152 PMCID: PMC8331152 DOI: 10.1093/plphys/kiab181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/04/2021] [Indexed: 05/31/2023]
Abstract
Endoplasmic reticulum (ER) quality control processes recognize and eliminate misfolded proteins to maintain cellular protein homeostasis and prevent the accumulation of defective proteins in the secretory pathway. Glycosylphosphatidylinositol (GPI)-anchored proteins carry a glycolipid modification, which provides an efficient ER export signal and potentially prevents the entry into ER-associated degradation (ERAD), which is one of the major pathways for clearance of terminally misfolded proteins from the ER. Here, we analyzed the degradation routes of different misfolded glycoproteins carrying a C-terminal GPI-attachment signal peptide in Arabidopsis thaliana. We found that a fusion protein consisting of the misfolded extracellular domain from Arabidopsis STRUBBELIG and the GPI-anchor attachment sequence of COBRA1 was efficiently targeted to hydroxymethylglutaryl reductase degradation protein 1 complex-mediated ERAD without the detectable attachment of a GPI anchor. Non-native variants of the GPI-anchored lipid transfer protein 1 (LTPG1) that lack a severely misfolded domain, on the other hand, are modified with a GPI anchor and targeted to the vacuole for degradation. Impaired processing of the GPI-anchoring signal peptide by mutation of the cleavage site or in a GPI-transamidase-compromised mutant caused ER retention and routed the non-native LTPG1 to ERAD. Collectively, these results indicate that for severely misfolded proteins, ER quality control processes are dominant over ER export. For less severely misfolded proteins, the GPI anchor provides an efficient ER export signal resulting in transport to the vacuole.
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Affiliation(s)
- Yun-Ji Shin
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Ulrike Vavra
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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Slezina MP, Istomina EA, Korostyleva TV, Kovtun AS, Kasianov AS, Konopkin AA, Shcherbakova LA, Odintsova TI. Molecular Insights into the Role of Cysteine-Rich Peptides in Induced Resistance to Fusarium oxysporum Infection in Tomato Based on Transcriptome Profiling. Int J Mol Sci 2021; 22:ijms22115741. [PMID: 34072144 PMCID: PMC8198727 DOI: 10.3390/ijms22115741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022] Open
Abstract
Cysteine-rich peptides (CRPs) play an important role in plant physiology. However, their role in resistance induced by biogenic elicitors remains poorly understood. Using whole-genome transcriptome sequencing and our CRP search algorithm, we analyzed the repertoire of CRPs in tomato Solanum lycopersicum L. in response to Fusarium oxysporum infection and elicitors from F. sambucinum. We revealed 106 putative CRP transcripts belonging to different families of antimicrobial peptides (AMPs), signaling peptides (RALFs), and peptides with non-defense functions (Major pollen allergen of Olea europaea (Ole e 1 and 6), Maternally Expressed Gene (MEG), Epidermal Patterning Factor (EPF)), as well as pathogenesis-related proteins of families 1 and 4 (PR-1 and 4). We discovered a novel type of 10-Cys-containing hevein-like AMPs named SlHev1, which was up-regulated both by infection and elicitors. Transcript profiling showed that F. oxysporum infection and F. sambucinum elicitors changed the expression levels of different overlapping sets of CRP genes, suggesting the diversification of functions in CRP families. We showed that non-specific lipid transfer proteins (nsLTPs) and snakins mostly contribute to the response of tomato plants to the infection and the elicitors. The involvement of CRPs with non-defense function in stress reactions was also demonstrated. The results obtained shed light on the mode of action of F. sambucinum elicitors and the role of CRP families in the immune response in tomato.
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Affiliation(s)
- Marina P. Slezina
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Ekaterina A. Istomina
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Tatyana V. Korostyleva
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Alexey S. Kovtun
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia;
| | - Artem S. Kasianov
- Laboratory of Plant Genomics, Institute for Information Transmission Problems RAS, 127051 Moscow, Russia;
| | - Alexey A. Konopkin
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
| | - Larisa A. Shcherbakova
- Laboratory of Physiological Plant Pathology, All-Russian Research Institute of Phytopathology, B. Vyazyomy, 143050 Moscow, Russia;
| | - Tatyana I. Odintsova
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia; (M.P.S.); (E.A.I.); (T.V.K.); (A.A.K.)
- Correspondence:
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Abstract
Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall proteins that function in diverse aspects of plant growth and development. This superfamily consists of three members: arabinogalactan-proteins (AGPs), extensins (EXTs), and proline-rich proteins (PRPs). Hybrid and chimeric HRGPs also exist. A bioinformatic software program, BIO OHIO 2.0, was developed to expedite the genome-wide identification and classification of AGPs, EXTs, and PRPs based on characteristic HRGP motifs and biased amino acid compositions. This chapter explains the principles of identifying HRGPs and provides a stepwise tutorial for using the BIO OHIO 2.0 program with genomic/proteomic data. Here, as an example, the genome/proteome of the common bean (Phaseolus vulgaris) is analyzed using the BIO OHIO 2.0 program to identify and characterize its set of HRGPs.
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Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don). Sci Rep 2021; 11:1496. [PMID: 33452328 PMCID: PMC7810747 DOI: 10.1038/s41598-020-80688-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022] Open
Abstract
Identifying causative genes for a target trait in conifer reproduction is challenging for species lacking whole-genome sequences. In this study, we searched for the male-sterility gene (MS1) in Cryptomeria japonica, aiming to promote marker-assisted selection (MAS) of male-sterile C. japonica to reduce the pollinosis caused by pollen dispersal from artificial C. japonica forests in Japan. We searched for mRNA sequences expressed in male strobili and found the gene CJt020762, coding for a lipid transfer protein containing a 4-bp deletion specific to male-sterile individuals. We also found a 30-bp deletion by sequencing the entire gene of another individual with the ms1. All nine breeding materials with the allele ms1 had either a 4-bp or 30-bp deletion in gene CJt020762, both of which are expected to result in faulty gene transcription and function. Furthermore, the 30-bp deletion was detected from three of five individuals in the Ishinomaki natural forest. From our findings, CJt020762 was considered to be the causative gene of MS1. Thus, by performing MAS using two deletion mutations as a DNA marker, it will be possible to find novel breeding materials of C. japonica with the allele ms1 adapted to the unique environment of each region of the Japanese archipelago.
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Silva J, Ferraz R, Dupree P, Showalter AM, Coimbra S. Three Decades of Advances in Arabinogalactan-Protein Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:610377. [PMID: 33384708 PMCID: PMC7769824 DOI: 10.3389/fpls.2020.610377] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/23/2020] [Indexed: 05/18/2023]
Abstract
Arabinogalactan-proteins (AGPs) are a large, complex, and highly diverse class of heavily glycosylated proteins that belong to the family of cell wall hydroxyproline-rich glycoproteins. Approximately 90% of the molecules consist of arabinogalactan polysaccharides, which are composed of arabinose and galactose as major sugars and minor sugars such as glucuronic acid, fucose, and rhamnose. About half of the AGP family members contain a glycosylphosphatidylinositol (GPI) lipid anchor, which allows for an association with the outer leaflet of the plasma membrane. The mysterious AGP family has captivated the attention of plant biologists for several decades. This diverse family of glycoproteins is widely distributed in the plant kingdom, including many algae, where they play fundamental roles in growth and development processes. The journey of AGP biosynthesis begins with the assembly of amino acids into peptide chains of proteins. An N-terminal signal peptide directs AGPs toward the endoplasmic reticulum, where proline hydroxylation occurs and a GPI anchor may be added. GPI-anchored AGPs, as well as unanchored AGPs, are then transferred to the Golgi apparatus, where extensive glycosylation occurs by the action of a variety glycosyltransferase enzymes. Following glycosylation, AGPs are transported by secretory vesicles to the cell wall or to the extracellular face of the plasma membrane (in the case of GPI-anchored AGPs). GPI-anchored proteins can be released from the plasma membrane into the cell wall by phospholipases. In this review, we present an overview of the accumulated knowledge on AGP biosynthesis over the past three decades. Particular emphasis is placed on the glycosylation of AGPs as the sugar moiety is essential to their function. Recent genetics and genomics approaches have significantly contributed to a broader knowledge of AGP biosynthesis. However, many questions remain to be elucidated in the decades ahead.
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Affiliation(s)
- Jessy Silva
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Ricardo Ferraz
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Allan M. Showalter
- Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
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Desnoyer N, Palanivelu R. Bridging the GAPs in plant reproduction: a comparison of plant and animal GPI-anchored proteins. PLANT REPRODUCTION 2020; 33:129-142. [PMID: 32945906 DOI: 10.1007/s00497-020-00395-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/07/2020] [Indexed: 05/29/2023]
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins (GAPs) are a unique type of membrane-associated proteins in eukaryotes. GPI and GAP biogenesis and function have been well studied in non-plant models and play an important role in the fertility of mouse sperm and egg. Although GPI and GAP biogenesis and function in plants are less known, they are critical for flowering plant reproduction because of their essential roles in the fertility of the male and female gametophytes. In Eukaryotes, GPI, a glycolipid molecule, can be post-translationally attached to proteins to serve as an anchor in the plasma membrane. GPI-anchoring, compared to other modes of membrane attachment and lipidation processes, localizes proteins to the extracellular portion of the plasma membrane and confers several unique attributes including specialized sorting during secretion, molecular painting onto membranes, and enzyme-mediated release of protein through anchor cleavage. While the biosynthesis, structure, and role of GPI are mostly studied in mammals, yeast and protists, the function of GPI and GAPs in plants is being discovered, particularly in gametophyte development and function. Here, we review GPI biosynthesis, protein attachment, and remodeling in plants with insights about this process in mammals. Additionally, we summarize the reproductive phenotypes of all loss of function mutations in Arabidopsis GPI biosynthesis and GAP genes and compare these to the reproductive phenotypes seen in mice to serve as a framework to identify gaps in our understanding of plant GPI and GAPs. In addition, we present an analysis on the gametophyte expression of all Arabidopsis GAPs to assist in further research on the role of GPI and GAPs in all aspects of the gametophyte generation in the life cycle of a plant.
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Affiliation(s)
- Nicholas Desnoyer
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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Beihammer G, Maresch D, Altmann F, Strasser R. Glycosylphosphatidylinositol-Anchor Synthesis in Plants: A Glycobiology Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:611188. [PMID: 33312189 PMCID: PMC7704450 DOI: 10.3389/fpls.2020.611188] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/30/2020] [Indexed: 05/02/2023]
Abstract
More than 200 diverse secretory proteins from Arabidopsis thaliana carry a glycosylphosphatidylinositol (GPI) lipid anchor covalently attached to their carboxyl-terminus. The GPI-anchor contains a lipid-linked glycan backbone that is preassembled in the endoplasmic reticulum (ER) of plants and subsequently transferred to distinct proteins, which provides them with specific features. The GPI-anchored proteins exit the ER and are transported through the Golgi apparatus to the plasma membrane. In the Golgi, the glycan moiety can be further modified by the specific attachment of sugar residues. While these biosynthetic steps are already quite well understood in mammals and yeast, comparatively little is known in plants. In this perspective, we discuss the current knowledge about the biosynthesis of the GPI-anchor glycan moiety in the light of recent findings for mammalian GPI-anchor glycan modifications.
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Affiliation(s)
- Gernot Beihammer
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Friedrich Altmann
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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Genome-wide identification of fasciclin-like arabinogalactan proteins in jute and their expression pattern during fiber formation. Mol Biol Rep 2020; 47:7815-7829. [PMID: 33011893 DOI: 10.1007/s11033-020-05858-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022]
Abstract
Fasciclin-like arabinogalactan proteins (FLAs), a class of arabinogalactan proteins (AGPs) are involved in plant growth and development via cell communication and adhesion. FLAs were also associated with fiber and wood formation in plants but no information is available about the roles of FLA proteins during fibre development of jute. Here, we performed molecular characterization, evolutionary relationship and expression profiling of FLAs proteins in jute (Corchorus olitorius). In total, nineteen CoFLA genes have been identified in jute genome, which were divided into four classes like FLAs of other species based on protein structure and similarity. All CoFLAs have N-terminal signal peptide and one or two FAS domain while two FLAs lack well defined AGP region and eight FLAs were devoid of C-terminal glycosylphosphatidylinositol (GPI) anchor. Expression analysis of different regions of jute stem suggested their involvement in different fiber development stages. Four genes CoFLA 11, 12, 20, and 23 were highly or predominately expressed in fiber containing bark tissues while the expression levels of six CoFLA genes 02, 03, 04, 06, 14 and 19 were comparatively higher in stick. Higher transcripts levels of CoFLA 12 and 20 in the middle bark tissues suggest their involvement in fiber elongation. In contrast, the CoFLA 11 and 23 were more expressed in bottom bark tissues suggesting their potential involvement in secondary cell wall synthesis. Our study can serve as solid foundation for further functional exploration of FLAs and in future breeding program of jute aiming fiber improvement.
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Su CTT, Sinha S, Eisenhaber B, Eisenhaber F. Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biol Direct 2020; 15:14. [PMID: 32993792 PMCID: PMC7522609 DOI: 10.1186/s13062-020-00266-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Background The transamidase complex is a molecular machine in the endoplasmic reticulum of eukaryotes that attaches a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins after cleaving a C-terminal propeptide with a defined sequence signal. Its five subunits are very hydrophobic; thus, solubility, heterologous expression and complex reconstruction are difficult. Therefore, theoretical approaches are currently the main source of insight into details of 3D structure and of the catalytic process. Results In this work, we generated model 3D structures of the lumenal domain of human GPAA1, the M28-type metallo-peptide-synthetase subunit of the transamidase, including zinc ion and model substrate positions. In comparative molecular dynamics (MD) simulations of M28-type structures and our GPAA1 models, we estimated the metal ion binding energies with evolutionary conserved amino acid residues in the catalytic cleft. We find that canonical zinc binding sites 2 and 3 are strongest binders for Zn1 and, where a second zinc is available, sites 2 and 4 for Zn2. Zinc interaction of site 5 with Zn1 enhances upon substrate binding in structures with only one zinc. Whereas a previously studied glutaminyl cyclase structure, the best known homologue to GPAA1, binds only one zinc ion at the catalytic site, GPAA1 can sterically accommodate two. The M28-type metallopeptidases segregate into two independent branches with regard to one/two zinc ion binding modality in a phylogenetic tree where the GPAA1 family is closer to the joint origin of both groups. For GPAA1 models, MD studies revealed two large loops (flaps) surrounding the active site being involved in an anti-correlated, breathing-like dynamics. Conclusions In the light of combined sequence-analytic and phylogenetic arguments as well as 3D structural modelling results, GPAA1 is most likely a single zinc ion metallopeptidase. Two large flaps environ the catalytic site restricting access to large substrates. Reviewers This article was reviewed by Thomas Dandekar (MD) and Michael Gromiha.
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Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Swati Sinha
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Genome-wide identification and expression analysis of extensin genes in tomato. Genomics 2020; 112:4348-4360. [PMID: 32712296 DOI: 10.1016/j.ygeno.2020.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 02/05/2023]
Abstract
Extensins (EXTs) are major protein components in plant cell walls that play crucial roles in higher plants. The function of EXTs has been reported in several plants but is limited in tomato, especially in fruit ripening. In this study, we identified 83 EXTs in tomato, and divided them into seven groups. The gene intron-exon structure and protein-motif composition of SlEXTs were similar within each group but different among groups. SlEXT genes showed different expression patterns in roots, leaves, flowers and fruits, and some SlEXT gene expressions in flowers could be regulated by treatments of auxin, gibberellic acid and jasmonic acid. In particular, SlSEXT8 had higher and increased expression during tomato fruit ripening, and its expression could be induced by ethylene, suggesting SlSEXT8 may be involved in tomato fruit softening. The result provides insights into the function of EXTs, and will facilitate to further study EXT roles in tomato fruit ripening.
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Plant Cell Wall Proteomes: Bioinformatics and Cell Biology Tools to Assess the Bona Fide Cell Wall Localization of Proteins. Methods Mol Biol 2020. [PMID: 32617950 DOI: 10.1007/978-1-0716-0621-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The purification of plant cell walls is challenging because they constitute an open compartment which is not limited by a membrane like the cell organelles. Different strategies have been established to limit the contamination by proteins of other compartments in cell wall proteomics studies. Non-destructive methods rely on washing intact cells with various types of solutions without disrupting the plasma membrane in order to elute cell wall proteins. In contrast, destructive protocols involve the purification of cell walls prior to the extraction of proteins with salt solutions. In both cases, proteins known to be intracellular have been identified by mass spectrometry in cell wall proteomes. The aim of this chapter is to provide tools to assess the subcellular localization of the proteins identified in cell wall proteomics studies, including: (1) bioinformatic predictions, (2) immunocytolocalization of proteins of interest on tissue sections and (3) in muro observation of proteins of interest fused to reporter fluorescent proteins by confocal microscopy. Finally, a qualitative assessment of the work can be performed and the strategy used to prepare the samples can be optimized if necessary.
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Noman A, Aqeel M, Irshad MK, Qari SH, Hashem M, Alamri S, AbdulMajeed AM, Al-Sadi AM. Elicitins as molecular weapons against pathogens: consolidated biotechnological strategy for enhancing plant growth. Crit Rev Biotechnol 2020; 40:821-832. [PMID: 32546015 DOI: 10.1080/07388551.2020.1779174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To fight against pathogens, defense systems in plants mainly depend upon preformed as well as induced responses. Pathogen detection activates induced responses and signals are transmitted for coordinated cellular events in order to restrict infection and spread. In spite of significant developments in manipulating genes, transcription factors and proteins for their involvement in immunity, absolute tolerance/resistance to pathogens has not been seen in plants/crops. Defense responses, among diverse plant types, to different pathogens involve modifications at the physio-biochemical and molecular levels. Secreted by oomycetes, elicitins are small, highly conserved and sterol-binding extracellular proteins with PAMP (pathogen associated molecular patterns) functions and are capable of eliciting plant defense reactions. Belonging to multigene families in oomycetes, elicitins are different from other plant proteins and show a different affinity for binding sterols and other lipids. These function for sterols binding to catalyze their inter-membrane and intra- as well as inter-micelle transport. Importantly, elicitins protect plants by inducing HR (hypersensitive response) and systemic acquired resistance. Despite immense metabolic significance and the involvement in defense activities, elicitins have not yet been fully studied and many questions regarding their functional activities remain to be explained. In order to address multiple questions associated with the role of elicitins, we have reviewed the understanding and topical advancements in plant defense mechanisms with a particular interest in elicitin-based defense actions and metabolic activities. This article offers potential attributes of elicitins as the biological control of plant diseases and can be considered as a baseline toward a more profound understanding of elicitins.
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Affiliation(s)
- Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Science, Lanzhou University, Lanzhou, Gansu, PR China
| | - Muhammad Kashif Irshad
- Department of Environmental Sciences, Government College University, Faisalabad, Pakistan
| | - Sameer H Qari
- Biology Department, Aljumum University College, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed Hashem
- College of Science, Department of Biology, King Khalid University, Abha, Saudi Arabia.,Faculty of Science, Botany and Microbiology Department, Assiut University, Assiut, Egypt
| | - Saad Alamri
- College of Science, Department of Biology, King Khalid University, Abha, Saudi Arabia.,Prince Sultan Ben Abdulaziz Center for Environmental and Tourism Research and Studies, King Khalid University, Abha, Saudi Arabia
| | - Awatif M AbdulMajeed
- Biology Department, Faculty of Science, University of Tabook, Umluj, Saudi Arabia
| | - Abdullah M Al-Sadi
- College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
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Meng J, Hu B, Yi G, Li X, Chen H, Wang Y, Yuan W, Xing Y, Sheng Q, Su Z, Xu C. Genome-wide analyses of banana fasciclin-like AGP genes and their differential expression under low-temperature stress in chilling sensitive and tolerant cultivars. PLANT CELL REPORTS 2020; 39:693-708. [PMID: 32128627 DOI: 10.1007/s00299-020-02524-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Thirty MaFLAs vary in their molecular features. MaFLA14/18/27/29 are likely to be involved in banana chilling tolerance by facilitating the cold signaling pathway and enhancing the cell wall biosynthesis. Although several studies have identified the molecular functions of individual fasciclin-like arabinogalactan protein (FLA) genes in plant growth and development, little information is available on their involvement in plant tolerance to low-temperature (LT) stress, and the related underlying mechanism is far from clear. In this study, the different expression of FLAs of banana (Musa acuminata) (MaFLAs) in the chilling-sensitive (CS) and chilling-tolerant (CT) banana cultivars under natural LT was investigated. Based on the latest banana genome database, a genome-wide identification of this gene family was done and the molecular features were analyzed. Thirty MaFLAs were distributed in 10 out of 11 chromosomes and these clustered into four major phylogenetic groups based on shared gene structure. Twenty-four MaFLAs contained N-terminal signal, 19 possessed predicted glycosylphosphatidylinositol (GPI), while 16 had both. Most MaFLAs were downregulated by LT stress. However, MaFLA14/18/29 were upregulated by LT in both cultivars with higher expression level recorded in the CT cultivar. Interestingly, MaFLA27 was significantly upregulated in the CT cultivar, but the opposite occurred for the CS cultivar. MaFLA27 possessed only N-terminal signal, MaFLA18 contained only GPI anchor, MaFLA29 possessed both, while MaFLA14 had neither. Thus, it was suggested that the accumulation of these FLAs in banana under LT could improve banana chilling tolerance through facilitating cold signal pathway and thereafter enhancing biosynthesis of plant cell wall components. The results provide background information of MaFLAs, suggest their involvement in plant chilling tolerance and their potential as candidate genes to be targeted when breeding CT banana.
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Affiliation(s)
- Jian Meng
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bei Hu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoquan Li
- Institute of Biotechnology, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Houbin Chen
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yingying Wang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Weina Yuan
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yanqing Xing
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiming Sheng
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Zuxiang Su
- Institute of Biotechnology, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Chunxiang Xu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Shafee T, Bacic A, Johnson K. Evolution of Sequence-Diverse Disordered Regions in a Protein Family: Order within the Chaos. Mol Biol Evol 2020; 37:2155-2172. [DOI: 10.1093/molbev/msaa096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Approaches for studying the evolution of globular proteins are now well established yet are unsuitable for disordered sequences. Our understanding of the evolution of proteins containing disordered regions therefore lags that of globular proteins, limiting our capacity to estimate their evolutionary history, classify paralogs, and identify potential sequence–function relationships. Here, we overcome these limitations by using new analytical approaches that project representations of sequence space to dissect the evolution of proteins with both ordered and disordered regions, and the correlated changes between these. We use the fasciclin-like arabinogalactan proteins (FLAs) as a model family, since they contain a variable number of globular fasciclin domains as well as several distinct types of disordered regions: proline (Pro)-rich arabinogalactan (AG) regions and longer Pro-depleted regions.
Sequence space projections of fasciclin domains from 2019 FLAs from 78 species identified distinct clusters corresponding to different types of fasciclin domains. Clusters can be similarly identified in the seemingly random Pro-rich AG and Pro-depleted disordered regions. Sequence features of the globular and disordered regions clearly correlate with one another, implying coevolution of these distinct regions, as well as with the N-linked and O-linked glycosylation motifs. We reconstruct the overall evolutionary history of the FLAs, annotated with the changing domain architectures, glycosylation motifs, number and length of AG regions, and disordered region sequence features. Mapping these features onto the functionally characterized FLAs therefore enables their sequence–function relationships to be interrogated. These findings will inform research on the abundant disordered regions in protein families from all kingdoms of life.
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Affiliation(s)
- Thomas Shafee
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
| | - Kim Johnson
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
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Xia X, Zhang HM, Offler CE, Patrick JW. Enzymes contributing to the hydrogen peroxide signal dynamics that regulate wall labyrinth formation in transfer cells. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:219-233. [PMID: 31587068 PMCID: PMC6913738 DOI: 10.1093/jxb/erz443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 05/31/2023]
Abstract
Transfer cells are characterized by an amplified plasma membrane area supported on a wall labyrinth composed of a uniform wall layer (UWL) from which wall ingrowth (WI) papillae arise. Adaxial epidermal cells of developing Vicia faba cotyledons, when placed in culture, undergo a rapid (hours) trans-differentiation to a functional epidermal transfer cell (ETC) phenotype. The trans-differentiation event is controlled by a signalling cascade comprising auxin, ethylene, apoplasmic reactive oxygen species (apoROS), and cytosolic Ca2+. Apoplasmic hydrogen peroxide (apoH2O2) was confirmed as the apoROS regulating UWL and WI papillae formation. Informed by an ETC-specific transcriptome, a pharmacological approach identified a temporally changing cohort of H2O2 biosynthetic enzymes. The cohort contained a respiratory burst oxidase homologue, polyamine oxidase, copper amine oxidase, and a suite of class III peroxidases. Collectively these generated two consecutive bursts in apoH2O2 production. Spatial organization of biosynthetic/catabolic enzymes was deduced from responses to pharmacologically blocking their activities on the cellular and subcellular distribution of apoH2O2. The findings were consistent with catalase activity constraining the apoH2O2 signal to the outer periclinal wall of the ETCs. Strategic positioning of class III peroxidases in this outer domain shaped subcellular apoH2O2 signatures that differed during assembly of the UWL and WI papillae.
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Affiliation(s)
- Xue Xia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
- School of Life Sciences, Henan University, Kaifeng, Henan, China
- International Joint Center for Biomedical Innovation, Henan University, Kaifeng, Henan, China
- Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, China
| | - Hui-Ming Zhang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Christina E Offler
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - John W Patrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
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Costa M, Pereira AM, Pinto SC, Silva J, Pereira LG, Coimbra S. In silico and expression analyses of fasciclin-like arabinogalactan proteins reveal functional conservation during embryo and seed development. PLANT REPRODUCTION 2019; 32:353-370. [PMID: 31501923 PMCID: PMC6820600 DOI: 10.1007/s00497-019-00376-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/29/2019] [Indexed: 05/31/2023]
Abstract
KEY MESSAGE The fasciclin-like arabinogalactan proteins organization into four groups is conserved and may be related to specific roles in developmental processes across angiosperms. Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs), which contain fasciclin-like domains in addition to typical AGP domains. FLAs are present across all embryophytes, and despite their low overall sequence similarity, conserved regions that define the fasciclin functional domain (FAS) have been identified, suggesting that the cell adhesion property is also conserved. FLAs in Arabidopsis have been organized into four subgroups according to the number and distribution of functional domains. Recent studies associated FLAs with cell wall-related processes where domain organization seemed to be related to functional roles. In Arabidopsis, FLAs containing a single FAS domain were found to be important for the integrity and elasticity of the plant cell wall matrix, and FLAs with two FAS domains and two AGP domains were found to be involved in maintaining proper cell expansion under salt stress conditions. The main purpose of the present work was to elucidate the expression pattern of selected FLA genes during embryo and seed development using RT-qPCR. AtFLA8 and AtFLA10, two Arabidopsis genes that stood out in previous microarray studies of embryo development, were further examined using promoter-driven gene reporter analyses. We also studied the expression of cork oak FLA genes and found that their expression partially parallels the expression patterns of the putative AtFLA orthologs. We propose that the functional organization of FLAs is conserved and may be related to fundamental aspects of embryogenesis and seed development across angiosperms. Phylogenetic studies were performed, and we show that the same basic four-subgroup organization described for Arabidopsis FLA gene classification is valid for most Arabidopsis FLA orthologs of several plant species, namely poplar, corn and cork oak.
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Affiliation(s)
- Mário Costa
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Ana Marta Pereira
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Milan, Italy
| | - Sara Cristina Pinto
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Jessy Silva
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Luís Gustavo Pereira
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- GreenUPorto Sustainable Agrifood Production Research Centre, Porto, Portugal
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal.
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Non-Specific Lipid Transfer Proteins in Triticum kiharae Dorof. et Migush.: Identification, Characterization and Expression Profiling in Response to Pathogens and Resistance Inducers. Pathogens 2019; 8:pathogens8040221. [PMID: 31694319 PMCID: PMC6963497 DOI: 10.3390/pathogens8040221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 01/14/2023] Open
Abstract
Non-specific lipid-transfer proteins (nsLTPs) represent a family of plant antimicrobial peptides (AMPs) implicated in diverse physiological processes. However, their role in induced resistance (IR) triggered by non-pathogenic fungal strains and their metabolites is poorly understood. In this work, using RNA-seq data and our AMP search pipeline, we analyzed the repertoire of nsLTP genes in the wheat Triticum kiharae and studied their expression in response to Fusarium oxysporum infection and treatment with the intracellular metabolites of Fusarium sambucinum FS-94. A total of 243 putative nsLTPs were identified, which were classified into five structural types and characterized. Expression analysis showed that 121 TkLTPs including sets of paralogs with identical mature peptides displayed specific expression patters in response to different treatments pointing to their diverse roles in resistance development. We speculate that upregulated nsLTP genes are involved in protection due to their antimicrobial activity or signaling functions. Furthermore, we discovered that in IR-displaying plants, a vast majority of nsLTP genes were downregulated, suggesting their role as negative regulators of immune mechanisms activated by the FS-94 elicitors. The results obtained add to our knowledge of the role of nsLTPs in IR and provide candidate molecules for genetic engineering of crops to enhance disease resistance.
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31
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Wang C, Chen L, Yang H, Yang S, Wang J. Genome-wide identification, expression and functional analysis of Populus xylogen-like genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110191. [PMID: 31481222 DOI: 10.1016/j.plantsci.2019.110191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 05/26/2023]
Abstract
As an extracellular arabinogalactan protein (AGP) containing a non-specific lipid transfer protein (nsLTP) domain, xylogen mediates the local intercellular communication required for tracheary element (TE) differentiation in Zinnia cell culture. Although XYLP (xylogen-like protein) gene families have been reported in Arabidopsis and rice, no comprehensive analysis has been performed in woody plants. In this work, 31 XYLP genes in five phylogenetic groups were identified from Populus trichocarpa genome and a comprehensive bioinformatic analysis including gene and protein structures, chromosomal locations and duplication events were conducted. In-silico data and qRT-PCR results indicated that PtXYLP1 is predominantly expressed in poplar apex, young leaves and roots, while PtXYLP2 is uniformly expressed across a variety of tissues with a low abundance. Analysis on PtXYLP1pro:GUS and PtXYLP2pro:GUS in Arabidopsis revealed their differential expression patterns during seed germination and specific inductions by exogenously applied phytohormones including auxin, cytokinin and GA. When overexpressed in Arabidopsis, PtXYLP1 but not PtXYLP2 resulted in cotyledons with defective venation patterns and interrupted secondary (2°) vein loops, which phenotype was underpinned by the down-regulation of genes indispensably required by embryonic venation development at procambium and/or vessel level.
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Affiliation(s)
- Caili Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Lincai Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Heyu Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.
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32
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Dragićević MB, Paunović DM, Bogdanović MD, Todorović SI, Simonović AD. ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. Glycobiology 2019; 30:cwz072. [PMID: 31508799 DOI: 10.1093/glycob/cwz072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 06/19/2019] [Accepted: 08/29/2019] [Indexed: 11/12/2022] Open
Abstract
Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R's rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.
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Affiliation(s)
- Milan B Dragićević
- Institute for Biological Research"Siniša Stanković", Department of Plant Physiology, Bul. Despota Stefana 142, University of Belgrade, 11000 Belgrade, Serbia
| | - Danijela M Paunović
- Institute for Biological Research"Siniša Stanković", Department of Plant Physiology, Bul. Despota Stefana 142, University of Belgrade, 11000 Belgrade, Serbia
| | - Milica D Bogdanović
- Institute for Biological Research"Siniša Stanković", Department of Plant Physiology, Bul. Despota Stefana 142, University of Belgrade, 11000 Belgrade, Serbia
| | - Slađana I Todorović
- Institute for Biological Research"Siniša Stanković", Department of Plant Physiology, Bul. Despota Stefana 142, University of Belgrade, 11000 Belgrade, Serbia
| | - Ana D Simonović
- Institute for Biological Research"Siniša Stanković", Department of Plant Physiology, Bul. Despota Stefana 142, University of Belgrade, 11000 Belgrade, Serbia
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Cao S, Guo M, Wang C, Xu W, Shi T, Tong G, Zhen C, Cheng H, Yang C, Elsheery NI, Cheng Y. Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation. BMC PLANT BIOLOGY 2019; 19:276. [PMID: 31234799 PMCID: PMC6591973 DOI: 10.1186/s12870-019-1865-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/03/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined. RESULTS A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAPpromoter::GUS techniques, the activities of PtAP66 promoters were observed only in fiber cells, not in the vessels of stems as the xylem and leaf veins developed in the transgenic Populus tree, and strong GUS signals were detected in interfascicular fiber cells, roots, anthers and sepals of PtAP17promoter::GUS transgenic plants. Intensive GUS activities in various secondary tissues implied that PtAP66 and PtAP17 could function in wood formation. In addition, most of the PtAP proteins were predicted to contain N- and (or) O-glycosylation sites, and the integration of PNGase F digestion and western blotting revealed that the PtAP17 and PtAP66 proteins were N-glycosylated in Populus. CONCLUSIONS Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.
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Affiliation(s)
- Shenquan Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Mengjie Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Chong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Wenjing Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Tianyuan Shi
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Guimin Tong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Cheng Zhen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Hao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | | | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
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34
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He J, Zhao H, Cheng Z, Ke Y, Liu J, Ma H. Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. Int J Mol Sci 2019; 20:E1945. [PMID: 31010036 PMCID: PMC6514703 DOI: 10.3390/ijms20081945] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 01/03/2023] Open
Abstract
The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the FLA gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 FLA genes are identified with gene copy numbers ranging from one (Chondrus crispus) to 49 (Populus trichocarpa). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in FLA genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of FLA gene families. The duplicated gene pairs in FLA gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the FLA gene family and help us understand their functions during the process of evolution.
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Affiliation(s)
- Jiadai He
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Hua Zhao
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Zhilu Cheng
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Yuwei Ke
- College of Life Sciences, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Jiaxi Liu
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Haoli Ma
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
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35
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Kouidri A, Baumann U, Okada T, Baes M, Tucker EJ, Whitford R. Wheat TaMs1 is a glycosylphosphatidylinositol-anchored lipid transfer protein necessary for pollen development. BMC PLANT BIOLOGY 2018; 18:332. [PMID: 30518316 PMCID: PMC6280385 DOI: 10.1186/s12870-018-1557-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 11/21/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND In flowering plants, lipid biosynthesis and transport within anthers is essential for male reproductive success. TaMs1, a dominant wheat fertility gene located on chromosome 4BS, has been previously fine mapped and identified to encode a glycosylphosphatidylinositol (GPI)-anchored non-specific lipid transfer protein (nsLTP). Although this gene is critical for pollen exine development, details of its function remains poorly understood. RESULTS In this study, we report that TaMs1 is only expressed from the B sub-genome, with highest transcript abundance detected in anthers containing microspores undergoing pre-meiosis through to meiosis. β-glucuronidase transcriptional fusions further revealed that TaMs1 is expressed throughout all anther cell-types. TaMs1 was identified to be expressed at an earlier stage of anther development relative to genes reported to be necessary for sporopollenin precursor biosynthesis. In anthers missing a functional TaMs1 (ms1c deletion mutant), these same genes were not observed to be mis-regulated, indicating an independent function for TaMs1 in pollen development. Exogenous hormone treatments on GUS reporter lines suggest that TaMs1 expression is increased by both indole-3-acetic acid (IAA) and abscisic acid (ABA). Translational fusion constructs showed that TaMs1 is targeted to the plasma membrane. CONCLUSIONS In summary, TaMs1 is a wheat fertility gene, expressed early in anther development and encodes a GPI-LTP targeted to the plasma membrane. The work presented provides a new insight into the process of wheat pollen development.
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Affiliation(s)
- Allan Kouidri
- University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Urrbrae, South Australia 5064 Australia
| | - Ute Baumann
- University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Urrbrae, South Australia 5064 Australia
| | - Takashi Okada
- University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Urrbrae, South Australia 5064 Australia
| | - Mathieu Baes
- University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Urrbrae, South Australia 5064 Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Waite Campus, Urrbrae, South Australia 5064 Australia
| | - Elise J. Tucker
- University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Urrbrae, South Australia 5064 Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Waite Campus, Urrbrae, South Australia 5064 Australia
| | - Ryan Whitford
- University of Adelaide, School of Agriculture, Food and Wine, Waite Campus, Urrbrae, South Australia 5064 Australia
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36
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Kouidri A, Whitford R, Suchecki R, Kalashyan E, Baumann U. Genome-wide identification and analysis of non-specific Lipid Transfer Proteins in hexaploid wheat. Sci Rep 2018; 8:17087. [PMID: 30459322 PMCID: PMC6244205 DOI: 10.1038/s41598-018-35375-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/26/2018] [Indexed: 01/17/2023] Open
Abstract
Non-specific Lipid Transfer Proteins (nsLTPs) are involved in numerous biological processes. To date, only a fraction of wheat (Triticum aestivum L.) nsLTPs (TaLTPs) have been identified, and even fewer have been functionally analysed. In this study, the identification, classification, phylogenetic reconstruction, chromosome distribution, functional annotation and expression profiles of TaLTPs were analysed. 461 putative TaLTPs were identified from the wheat genome and classified into five types (1, 2, C, D and G). Phylogenetic analysis of the TaLTPs along with nsLTPs from Arabidopsis thaliana and rice, showed that all five types were shared across species, however, some type 2 TaLTPs formed wheat-specific clades. Gene duplication analysis indicated that tandem duplications contributed to the expansion of this gene family in wheat. Analysis of RNA sequencing data showed that TaLTPs were expressed in most tissues and stages of wheat development. Further, we refined the expression profile of anther-enriched expressed genes, and identified potential cis-elements regulating their expression specificity. This analysis provides a valuable resource towards elucidating the function of TaLTP family members during wheat development, aids our understanding of the evolution and expansion of the TaLTP gene family and, additionally, provides new information for developing wheat male-sterile lines with application to hybrid breeding.
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Affiliation(s)
- Allan Kouidri
- University of Adelaide, School of Agriculture, Food & Wine, Waite Campus, Urrbrae, South Australia, 5064, Australia
| | - Ryan Whitford
- University of Adelaide, School of Agriculture, Food & Wine, Waite Campus, Urrbrae, South Australia, 5064, Australia
| | - Radoslaw Suchecki
- University of Adelaide, School of Agriculture, Food & Wine, Waite Campus, Urrbrae, South Australia, 5064, Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Waite Campus, Urrbrae, South Australia, 5064, Australia
| | - Elena Kalashyan
- University of Adelaide, School of Agriculture, Food & Wine, Waite Campus, Urrbrae, South Australia, 5064, Australia
| | - Ute Baumann
- University of Adelaide, School of Agriculture, Food & Wine, Waite Campus, Urrbrae, South Australia, 5064, Australia.
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Lamport DTA, Tan L, Held M, Kieliszewski MJ. The Role of the Primary Cell Wall in Plant Morphogenesis. Int J Mol Sci 2018; 19:E2674. [PMID: 30205598 PMCID: PMC6165521 DOI: 10.3390/ijms19092674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 01/16/2023] Open
Abstract
Morphogenesis remains a riddle, wrapped in a mystery, inside an enigma. It remains a formidable problem viewed from many different perspectives of morphology, genetics, and computational modelling. We propose a biochemical reductionist approach that shows how both internal and external physical forces contribute to plant morphogenesis via mechanical stress⁻strain transduction from the primary cell wall tethered to the plasma membrane by a specific arabinogalactan protein (AGP). The resulting stress vector, with direction defined by Hechtian adhesion sites, has a magnitude of a few piconewtons amplified by a hypothetical Hechtian growth oscillator. This paradigm shift involves stress-activated plasma membrane Ca2+ channels and auxin-activated H⁺-ATPase. The proton pump dissociates periplasmic AGP-glycomodules that bind Ca2+. Thus, as the immediate source of cytosolic Ca2+, an AGP-Ca2+ capacitor directs the vectorial exocytosis of cell wall precursors and auxin efflux (PIN) proteins. In toto, these components comprise the Hechtian oscillator and also the gravisensor. Thus, interdependent auxin and Ca2+ morphogen gradients account for the predominance of AGPs. The size and location of a cell surface AGP-Ca2+ capacitor is essential to differentiation and explains AGP correlation with all stages of morphogenetic patterning from embryogenesis to root and shoot. Finally, the evolutionary origins of the Hechtian oscillator in the unicellular Chlorophycean algae reflect the ubiquitous role of chemiosmotic proton pumps that preceded DNA at the dawn of life.
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Affiliation(s)
- Derek T A Lamport
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
| | - Li Tan
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Michael Held
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA.
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Ji J, Lv H, Yang L, Fang Z, Zhuang M, Zhang Y, Liu Y, Li Z. Genome-wide identification and characterization of non-specific lipid transfer proteins in cabbage. PeerJ 2018; 6:e5379. [PMID: 30128186 PMCID: PMC6089208 DOI: 10.7717/peerj.5379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/14/2018] [Indexed: 12/28/2022] Open
Abstract
Plant non-specific lipid transfer proteins (nsLTPs) are a group of small, secreted proteins that can reversibly bind and transport hydrophobic molecules. NsLTPs play an important role in plant development and resistance to stress. To date, little is known about the nsLTP family in cabbage. In this study, a total of 89 nsLTP genes were identified via comprehensive research on the cabbage genome. These cabbage nsLTPs were classified into six types (1, 2, C, D, E and G). The gene structure, physical and chemical characteristics, homology, conserved motifs, subcellular localization, tertiary structure and phylogeny of the cabbage nsLTPs were comprehensively investigated. Spatial expression analysis revealed that most of the identified nsLTP genes were positively expressed in cabbage, and many of them exhibited patterns of differential and tissue-specific expression. The expression patterns of the nsLTP genes in response to biotic and abiotic stresses were also investigated. Numerous nsLTP genes in cabbage were found to be related to the resistance to stress. Moreover, the expression patterns of some nsLTP paralogs in cabbage showed evident divergence. This study promotes the understanding of nsLTPs characteristics in cabbage and lays the foundation for further functional studies investigating cabbage nsLTPs.
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Affiliation(s)
- Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yumei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhansheng Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Luo S, Hu W, Wang Y, Liu B, Yan H, Xiang Y. Genome-wide identification, classification, and expression of phytocyanins in Populus trichocarpa. PLANTA 2018; 247:1133-1148. [PMID: 29383450 DOI: 10.1007/s00425-018-2849-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/17/2018] [Indexed: 05/19/2023]
Abstract
74 phytocyanin genes were identified in the Populus trichocarpa genome. Phylogenetic analysis grouped the PC proteins into four subfamilies (UCs, PLCs, SCs, and ENODLs). Closely related PC proteins share similar motifs, implying similar functions. Expression profiles of PtPC genes were analyzed in response to drought and salt-stress. Phytocyanins (PCs) are blue copper proteins associated with electron carrier activity that have a large influence on plant growth and resistance. The majority of PCs are chimeric arabinogalactan proteins (AGPs). In this work, we identified 74 PC genes in Populus trichocarpa and analyzed them comprehensively. Based on the ligands composition of copper-binding sites, glycosylation state, the domain structure and spectral characteristics of PC genes, PCs were divided into four subfamilies [uclacyanins (UCs), plantacyanins (PLCs), stellacyanins (SCs) and early nodulin-like proteins (ENODLs)], and phylogenetic relationship analysis classified them into seven groups. All PtPCs are randomly distributed on 17 of the 19 poplar chromosomes, and they appear to have undergone expansion via segmental duplication. Eight PtPCs do not contain introns, and each group has a similar conserved motif structure. Promoter analysis revealed cis-elements related to growth, development and stress responses, and established orthology relationships of PCs between Arabidopsis and poplar by synteny analysis. Expression profile analysis and qRT-PCR analysis showed that PtPCs were expressed widely in various tissues. Quantitative real-time RT-PCR analysis of PC genes expression in response to salt and drought stress revealed their stress-responses profiles. This work provides a theoretical basis for a further study of stress resistance mechanisms and the function of PC genes in poplar growth and development.
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Affiliation(s)
- Shuangshuang Luo
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Wenfang Hu
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yue Wang
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Bin Liu
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Hanwei Yan
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China.
| | - Yan Xiang
- Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China.
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Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum. BMC Genomics 2018; 19:269. [PMID: 29673315 PMCID: PMC5907747 DOI: 10.1186/s12864-018-4612-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum. RESULTS Using shotgun sequencing, a 38,660,329 bp F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome. In comparison to F. graminearum, the predicted gene count of 13,946 was slightly lower. The F. venenatum centromeres were found to be 25% smaller compared to F. graminearum. Chromosome length was 2.8% greater in F. venenatum, primarily due to an increased abundance of repetitive elements and transposons, but not transposon diversity. On chromosome 3 a major sequence rearrangement was found, but its overall gene content was relatively unchanged. Unlike homothallic F. graminearum, heterothallic F. venenatum possessed the MAT1-1 type locus, but lacked the MAT1-2 locus. The F. venenatum genome has the type A trichothecene mycotoxin TRI5 cluster, whereas F. graminearum has type B. From the F. venenatum gene set, 786 predicted proteins were species-specific versus NCBI. The annotated F. venenatum genome was predicted to possess more genes coding for hydrolytic enzymes and species-specific genes involved in the breakdown of polysaccharides than F. graminearum. Comparison of the two genomes reduced the previously defined F. graminearum-specific gene set from 741 to 692 genes. A comparison of the F. graminearum versus F. venenatum proteomes identified 15 putative secondary metabolite gene clusters (SMC), 109 secreted proteins and 38 candidate effectors not found in F. venenatum. Five of the 15 F. graminearum-specific SMCs that were either absent or highly divergent in the F. venenatum genome showed increased in planta expression. In addition, two predicted F. graminearum transcription factors previously shown to be required for fungal virulence on wheat plants were absent or exhibited high sequence divergence. CONCLUSIONS This study identifies differences between the F. venenatum and F. graminearum genomes that may contribute to contrasting lifestyles, and highlights the repertoire of F. graminearum-specific candidate genes and SMCs potentially required for pathogenesis.
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Das PK, Biswas R, Anjum N, Das AK, Maiti MK. Rice matrix metalloproteinase OsMMP1 plays pleiotropic roles in plant development and symplastic-apoplastic transport by modulating cellulose and callose depositions. Sci Rep 2018; 8:2783. [PMID: 29426868 PMCID: PMC5807377 DOI: 10.1038/s41598-018-20070-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/12/2018] [Indexed: 11/12/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are well-known proteolytic enzymes in animal systems and play roles in tissue differentiation, growth, and defence. Although a few plant MMPs have been reported, their exact functions in development and growth remain elusive. In this study, we characterized the promoter and coding sequence of OsMMP1, one of the putative MMP genes in rice (Oryza sativa). The OsMMP1 catalytic domain is structurally similar to human MMPs with respect to cofactor orientation as predicted by homology modeling. Bacterially expressed recombinant OsMMP1 showed protease activity with bovine serum albumin and gelatin as substrates. Analyses of transcript accumulation and promoter-reporter gene expression revealed that OsMMP1 is spatio-temporally expressed in vegetative and reproductive parts of plants. The plasma membrane-localized OsMMP1 protease affected plant development upon heterologous expression in tobacco and endogenous gene silencing in rice. Transgenic tobacco plants expressing OsMMP1 showed enhanced deposition of cellulose and callose, leading to impairment of symplastic and apoplastic translocations. Moreover, transgenic tobacco tissues exhibited tolerance to oxidative stress-inducing agent by confining the area of tissue death owing to callose lining. Collectively, these findings demonstrate the involvement of a plant MMP in growth, organ differentiation, and development in relation to cell wall modification.
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Affiliation(s)
- Prabir Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Rupam Biswas
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Nazma Anjum
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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Li WQ, Zhang MJ, Gan PF, Qiao L, Yang SQ, Miao H, Wang GF, Zhang MM, Liu WT, Li HF, Shi CH, Chen KM. CLD1/SRL1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:904-923. [PMID: 28960566 DOI: 10.1111/tpj.13728] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 08/29/2017] [Accepted: 09/22/2017] [Indexed: 05/20/2023]
Abstract
Leaf rolling is considered as one of the most important agronomic traits in rice breeding. It has been previously reported that SEMI-ROLLED LEAF 1 (SRL1) modulates leaf rolling by regulating the formation of bulliform cells in rice (Oryza sativa); however, the regulatory mechanism underlying SRL1 has yet to be further elucidated. Here, we report the functional characterization of a novel leaf-rolling mutant, curled leaf and dwarf 1 (cld1), with multiple morphological defects. Map-based cloning revealed that CLD1 is allelic with SRL1, and loses function in cld1 through DNA methylation. CLD1/SRL1 encodes a glycophosphatidylinositol (GPI)-anchored membrane protein that modulates leaf rolling and other aspects of rice growth and development. The cld1 mutant exhibits significant decreases in cellulose and lignin contents in secondary cell walls of leaves, indicating that the loss of function of CLD1/SRL1 affects cell wall formation. Furthermore, the loss of CLD1/SRL1 function leads to defective leaf epidermis such as bulliform-like epidermal cells. The defects in leaf epidermis decrease the water-retaining capacity and lead to water deficits in cld1 leaves, which contribute to the main cause of leaf rolling. As a result of the more rapid water loss and lower water content in leaves, cld1 exhibits reduced drought tolerance. Accordingly, the loss of CLD1/SRL1 function causes abnormal expression of genes and proteins associated with cell wall formation, cuticle development and water stress. Taken together, these findings suggest that the functional roles of CLD1/SRL1 in leaf-rolling regulation are closely related to the maintenance of cell wall formation, epidermal integrity and water homeostasis.
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Affiliation(s)
- Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Min-Juan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peng-Fei Gan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lei Qiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuai-Qi Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hai Miao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Gang-Feng Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mao-Mao Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hai-Feng Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chun-Hai Shi
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Hozumi A, Bera S, Fujiwara D, Obayashi T, Yokoyama R, Nishitani K, Aoki K. Arabinogalactan Proteins Accumulate in the Cell Walls of Searching Hyphae of the Stem Parasitic Plants, Cuscuta campestris and Cuscuta japonica. PLANT & CELL PHYSIOLOGY 2017; 58:1868-1877. [PMID: 29016904 DOI: 10.1093/pcp/pcx121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/17/2017] [Indexed: 05/06/2023]
Abstract
Stem parasitic plants (Cuscuta spp.) develop a specialized organ called a haustorium to penetrate their hosts' stem tissues. To reach the vascular tissues of the host plant, the haustorium needs to overcome the physical barrier of the cell wall, and the parasite-host interaction via the cell wall is a critical process. However, the cell wall components responsible for the establishment of parasitic connections have not yet been identified. In this study, we investigated the spatial distribution patterns of cell wall components at a parasitic interface using parasite-host complexes of Cuscuta campestris-Arabidopsis thaliana and Cuscuta japonica-Glycine max. We focused on arabinogalactan proteins (AGPs), because AGPs accumulate in the cell walls of searching hyphae of both C. campestris and C. japonica. We found more AGPs in elongated haustoria than in pre haustoria, indicating that AGP accumulation is developmentally regulated. Using in situ hybridization, we identified five genes in C. campestris that encode hyphal-expressed AGPs that belong to the fasciclin-like AGP (FLA) family, which were named CcFLA genes. Three of the five CcFLA genes were expressed in the holdfast, which develops on the Cuscuta stem epidermis at the attachment site for the host's stem epidermis. Our results suggest that AGPs are involved in hyphal elongation and adhesion to host cells, and in the adhesion between the epidermal tissues of Cuscuta and its host.
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Affiliation(s)
- Akitaka Hozumi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
| | - Subhankar Bera
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
| | - Daiki Fujiwara
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
| | - Takeshi Obayashi
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Ryusuke Yokoyama
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Kazuhiko Nishitani
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
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Guerriero G, Mangeot-Peter L, Legay S, Behr M, Lutts S, Siddiqui KS, Hausman JF. Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): in silico analyses and gene expression patterns in different tissues. BMC Genomics 2017; 18:741. [PMID: 28931375 PMCID: PMC5606014 DOI: 10.1186/s12864-017-3970-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to participate in plant growth, development, defense against abiotic stresses and, notably, cell wall biosynthesis. Although some studies are available on the characterization of FLA genes from different species, both woody and herbaceous, no detailed information is available on the FLA family of textile hemp (Cannabis sativa L.), an economically important fibre crop. RESULTS By searching the Cannabis genome and EST databases, 23 CsaFLAs have been here identified which are divided into four phylogenetic groups. A real-time qPCR analysis performed on stem tissues (isolated bast fibres and shivs sampled at three heights), hypocotyls (6-9-12-15-17-20 days-old), whole seedlings, roots, leaves and female/male flowers of the monoecious fibre variety Santhica 27, indicates that the identified FLA genes are differentially expressed. Interestingly, some hemp FLAs are expressed during early phases of fibre growth (elongation), while others are more expressed in the middle and base of the stem and thus potentially involved in secondary cell wall formation (fibre thickening). The bioinformatic analysis of the promoter regions shows that the FLAs upregulated in the younger regions of the stem share a conserved motif related to flowering control and regulation of photoperiod perception. The promoters of the FLA genes expressed at higher levels in the older stem regions, instead, share a motif putatively recognized by MYB3, a transcriptional repressor belonging to the MYB family subgroup S4. CONCLUSIONS These results point to the existence of a transcriptional network fine-tuning the expression of FLA genes in the older and younger regions of the stem, as well as in the bast fibres/shivs of textile hemp. In summary, our study paves the way for future analyses on the biological functions of FLAs in an industrially relevant fibre crop.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg.
| | - Lauralie Mangeot-Peter
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
- Present address: Institut National de la Recherche Agronomique, Université de Lorraine, UMR 1136, Interactions Arbres-Microorganismes, Champenoux, France
| | - Sylvain Legay
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
| | - Marc Behr
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Khawar Sohail Siddiqui
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362, Esch/Alzette, Luxembourg
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Ray A, Jatana N, Thukral L. Lipidated proteins: Spotlight on protein-membrane binding interfaces. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:74-84. [DOI: 10.1016/j.pbiomolbio.2017.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 01/21/2023]
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Plattner H. Evolutionary Cell Biology of Proteins from Protists to Humans and Plants. J Eukaryot Microbiol 2017; 65:255-289. [PMID: 28719054 DOI: 10.1111/jeu.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 01/10/2023]
Abstract
During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H+ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in Paramecium. One of the most flexible proteins is centrin when its intracellular localization and function throughout evolution is traced. There are many more examples documenting evolutionary flexibility of translation products depending on requirements and potential for implantation within the actual cellular context at different levels of evolution. From estimates of gene and protein numbers per organism, it appears that much of the basic inventory of protozoan precursors could be transmitted to highest eukaryotic levels, with some losses and also with important additional "inventions."
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Affiliation(s)
- Helmut Plattner
- Department of Biology, University of Konstanz, P. O. Box M625, Konstanz, 78457, Germany
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Xue H, Veit C, Abas L, Tryfona T, Maresch D, Ricardi MM, Estevez JM, Strasser R, Seifert GJ. Arabidopsis thaliana FLA4 functions as a glycan-stabilized soluble factor via its carboxy-proximal Fasciclin 1 domain. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:613-630. [PMID: 28482115 PMCID: PMC5575511 DOI: 10.1111/tpj.13591] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 05/12/2023]
Abstract
Fasciclin-like arabinogalactan proteins (FLAs) are involved in numerous important functions in plants but the relevance of their complex structure to physiological function and cellular fate is unresolved. Using a fully functional fluorescent version of Arabidopsis thaliana FLA4 we show that this protein is localized at the plasma membrane as well as in endosomes and soluble in the apoplast. FLA4 is likely to be GPI-anchored, is highly N-glycosylated and carries two O-glycan epitopes previously associated with arabinogalactan proteins. The activity of FLA4 was resistant against deletion of the amino-proximal fasciclin 1 domain and was unaffected by removal of the GPI-modification signal, a highly conserved N-glycan or the deletion of predicted O-glycosylation sites. Nonetheless these structural changes dramatically decreased endoplasmic reticulum (ER)-exit and plasma membrane localization of FLA4, with N-glycosylation acting at the level of ER-exit and O-glycosylation influencing post-secretory fate. We show that FLA4 acts predominantly by molecular interactions involving its carboxy-proximal fasciclin 1 domain and that its amino-proximal fasciclin 1 domain is required for stabilization of plasma membrane localization. FLA4 functions as a soluble glycoprotein via its carboxy-proximal Fas1 domain and its normal cellular trafficking depends on N- and O-glycosylation.
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Affiliation(s)
- Hui Xue
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Christiane Veit
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Lindy Abas
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Theodora Tryfona
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QWUK
| | - Daniel Maresch
- Department of ChemistryUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Martiniano M. Ricardi
- Biología Molecular y Neurociencias–Consejo Nacional de Investigaciones Científicas y Técnicas(IFIByNE‐CONICET)Instituto de FisiologíaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresC1428EGAArgentina
| | - José Manuel Estevez
- Biología Molecular y Neurociencias–Consejo Nacional de Investigaciones Científicas y Técnicas(IFIByNE‐CONICET)Instituto de FisiologíaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresC1428EGAArgentina
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos AiresBuenos Aires CPC1405BWEArgentina
| | - Richard Strasser
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Georg J. Seifert
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
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Johnson KL, Cassin AM, Lonsdale A, Bacic A, Doblin MS, Schultz CJ. Pipeline to Identify Hydroxyproline-Rich Glycoproteins. PLANT PHYSIOLOGY 2017; 174:886-903. [PMID: 28446635 PMCID: PMC5462032 DOI: 10.1104/pp.17.00294] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/21/2017] [Indexed: 05/14/2023]
Abstract
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three-dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signaling, and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive posttranslational modifications (glycosylation), and they have been implicated in many biological functions. HRGPs are evolutionarily ancient, having been isolated from the protein-rich walls of chlorophyte algae to the cellulose-rich walls of embryophytes. Examination of HRGPs in a range of plant species should provide valuable insights into how they have evolved. Commonly divided into the arabinogalactan proteins, extensins, and proline-rich proteins, in reality, a continuum of structures exists within this diverse and heterogenous superfamily. An inability to accurately classify HRGPs leads to inconsistent gene ontologies limiting the identification of HRGP classes in existing and emerging omics data sets. We present a novel and robust motif and amino acid bias (MAAB) bioinformatics pipeline to classify HRGPs into 23 descriptive subclasses. Validation of MAAB was achieved using available genomic resources and then applied to the 1000 Plants transcriptome project (www.onekp.com) data set. Significant improvement in the detection of HRGPs using multiple-k-mer transcriptome assembly methodology was observed. The MAAB pipeline is readily adaptable and can be modified to optimize the recovery of IDPs from other organisms.
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Affiliation(s)
- Kim L Johnson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew M Cassin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew Lonsdale
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Monika S Doblin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Carolyn J Schultz
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
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Johnson KL, Cassin AM, Lonsdale A, Wong GKS, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ. Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes. PLANT PHYSIOLOGY 2017; 174:904-921. [PMID: 28446636 PMCID: PMC5462033 DOI: 10.1104/pp.17.00295] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/21/2017] [Indexed: 05/19/2023]
Abstract
The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SPn EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots.
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Affiliation(s)
- Kim L Johnson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew M Cassin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Andrew Lonsdale
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Gane Ka-Shu Wong
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Douglas E Soltis
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Nicholas W Miles
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Michael Melkonian
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Barbara Melkonian
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Michael K Deyholos
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - James Leebens-Mack
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Carl J Rothfels
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Dennis W Stevenson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Sean W Graham
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Xumin Wang
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Shuangxiu Wu
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - J Chris Pires
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Patrick P Edger
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Eric J Carpenter
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Monika S Doblin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.)
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.)
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.)
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.)
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.)
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.)
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.)
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.)
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.)
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.)
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
| | - Carolyn J Schultz
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (K.L.J., A.M.C., A.L., A.B., M.S.D.);
- Departments of Biological Sciences and Medicine, University of Alberta, Edmonton, Alberta, Canada, and BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China (G.K.-S.W., E.J.C.);
- Florida Museum of Natural History, Department of Biology, University of Florida, Gainsville, Florida 32611 (D.E.S., N.W.M.);
- Botanical Institute, Cologne Biocenter, University of Cologne, D50674 Cologne, Germany (M.M., B.M.);
- Department of Biology, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada (M.K.D.)
- Department of Plant Biology, University of Georgia, Athens, Georgia 3062 (J.L.-M.);
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California 94720 (C.J.R.);
- New York Botanical Garden, Bronx, New York 10458 (D.W.S.);
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (S.W.G.);
- Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China (X.W., S.W.);
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211 (J.C.P.);
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48823 (P.P.E.); and
- School of Agriculture, Food, and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia 5064, Australia (C.J.S.)
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Liu C, Zhang T. Expansion and stress responses of the AP2/EREBP superfamily in cotton. BMC Genomics 2017; 18:118. [PMID: 28143399 PMCID: PMC5282909 DOI: 10.1186/s12864-017-3517-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 01/26/2017] [Indexed: 11/24/2022] Open
Abstract
Background The allotetraploid cotton originated from one hybridization event between an extant progenitor of Gosssypium herbaceum (A1) or G. arboreum (A2) and another progenitor, G. raimondii Ulbrich (D5) 1–1.5 million years ago (Mya). The APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plants. They are characterized by their AP2 domain, which comprises 60–70 amino acids, and are classified into four main subfamilies: the APETALA2 (AP2), Related to ABI3/VP1 (RAV), Dehydration-Responsive Element Binding protein (DREB) and Ethylene-Responsive Factor (ERF) subfamilies. The AP2/EREBP genes play crucial roles in plant growth, development and biotic and abiotic stress responses. Hence, understanding the molecular characteristics of cotton stress tolerance and gene family expansion would undoubtedly facilitate cotton resistance breeding and evolution research. Results A total of 269 AP2/EREBP genes were identified in the G. raimondii (D5) cotton genome. The protein domain architecture and intron/exon structure are simple and relatively conserved within each subfamily. They are distributed throughout all chromosomes but are clustered on various chromosomes due to genomic tandem duplication. We identified 73 tandem duplicated genes and 221 segmental duplicated gene pairs which contributed to the expansion of AP2/EREBP superfamily. Of them, tandem duplication was the most important force of the expansion of the B3 group. Transcriptome analysis showed that 504 AP2/EREBP genes were expressed in at least one tested G. hirsutum TM-1 tissues. In G. hirsutum, 151 non-repeated genes of the DREB and ERF subfamily genes were responsive to different stresses: 132 genes were induced by cold, 63 genes by drought and 94 genes by heat. qRT-PCR confirmed that 13 GhDREB and 15 GhERF genes were induced by cold and/or drought. No transcripts detected for 53 of the 111 tandem duplicated genes in TM-1. In addition, some homoeologous genes showed biased expression toward either A-or D-subgenome. Conclusions The AP2/EREBP genes were obviously expanded in Gossypium. The GhDREB and GhERF genes play crucial roles in cotton stress responses. Our genome-wide analysis of AP2/EREBP genes in cotton provides valuable information for characterizing the molecular functions of AP2/EREBP genes and reveals insights into their evolution in polyploid plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3517-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunxiao Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.
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