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A Proteomic Analysis for the Red Seaweed Asparagopsis taxiformis. BIOLOGY 2023; 12:biology12020167. [PMID: 36829446 PMCID: PMC9952816 DOI: 10.3390/biology12020167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
The red seaweed Asparagopsis taxiformis is a promising ruminant feed additive with anti-methanogenic properties that could contribute to global climate change solutions. Genomics has provided a strong foundation for in-depth molecular investigations, including proteomics. Here, we investigated the proteome of A. taxiformis (Lineage 6) in both sporophyte and gametophyte stages, using soluble and insoluble extraction methods. We identified 741 unique non-redundant proteins using a genome-derived database and 2007 using a transcriptome-derived database, which included numerous proteins predicted to be of fungal origin. We further investigated the genome-derived proteins to focus on seaweed-specific proteins. Ontology analysis indicated a relatively large proportion of ion-binding proteins (i.e., iron, zinc, manganese, potassium and copper), which may play a role in seaweed heavy metal tolerance. In addition, we identified 58 stress-related proteins (e.g., heat shock and vanadium-dependent haloperoxidases) and 44 photosynthesis-related proteins (e.g., phycobilisomes, photosystem I, photosystem II and ATPase), which were in general more abundantly identified from female gametophytes. Forty proteins were predicted to be secreted, including ten rhodophyte collagen-alpha-like proteins (RCAPs), which displayed overall high gene expression levels. These findings provide a comprehensive overview of expressed proteins in A. taxiformis, highlighting the potential for targeted protein extraction and functional characterisation for future biodiscovery.
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Carrillo R, Feldeverd E, Christopher DA. The Use of Fluorescent Protein Fusions to Monitor the Unfolded Protein Response and Protein Foldase-Substrate Interactions in Plant Protoplasts. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2378:69-81. [PMID: 34985694 DOI: 10.1007/978-1-0716-1732-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Endoplasmic reticulum (ER) stress and the resulting unfolded protein response (UPR) are critical stress response pathways in eukaryotes. To study these types of interactions in plants, a wide range of methods have been used, including generation of transgenic plants, subcellular immunolocalization of protein foldases, and co-immunoprecipitation (co-IP) assays. Although these more time-consuming methods have been successfully implemented, there is a need for a versatile and rapid in vivo system to investigate ER stress and UPR. Here, we describe a transient expression system that uses plant protoplasts to define in vivo subcellular localizations and protein-protein interactions of protein foldases and their substrates fused to fluorescent protein reporters. This accurate and robust assay utilizes a variety of analyses, such as subcellular localization, FLIM-FRET, co-IP, mutagenesis, and RT-PCR in the genetically amenable Arabidopsis model system. We demonstrate the methodology by using the representative protein foldase, protein disulfide isomerase-9 (PDI9), as well as subcellular markers, secretory proteins, and dithiothreitol (DTT)-mediated induction of the UPR as monitored by RT-PCR. Together, these methods yield reliable high output results for investigating subcellular localization and protein-protein interactions in plants to decipher the UPR pathways.
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Affiliation(s)
- Rina Carrillo
- Department of Molecular Biosciences & Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Elizabeth Feldeverd
- Department of Molecular Biosciences & Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - David A Christopher
- Department of Molecular Biosciences & Bioengineering, University of Hawaii, Honolulu, HI, USA.
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Expression Characterization of AtPDI11 and Functional Analysis of AtPDI11 D Domain in Oxidative Protein Folding. Int J Mol Sci 2022; 23:ijms23031409. [PMID: 35163331 PMCID: PMC8836223 DOI: 10.3390/ijms23031409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
The formation and isomerization of disulfide bonds mediated by protein disulfide isomerase (PDI) in the endoplasmic reticulum (ER) is of fundamental importance in eukaryotes. Canonical PDI structure comprises four domains with the order of a-b-b′-a′. In Arabidopsis thaliana, the PDI-S subgroup contains only one member, AtPDI11, with an a-a′-D organization, which has no orthologs in mammals or yeast. However, the expression pattern of AtPDI11 and the functioning mechanism of AtPDI11 D domain are currently unclear. In this work, we found that PDI-S is evolutionarily conserved between land plants and algal organisms. AtPDI11 is expressed in various tissues and its induction by ER stress is disrupted in bzip28/60 and ire1a/b mutants that are null mutants of key components in the unfolded protein response (UPR) signal transduction pathway, suggesting that the induction of AtPDI11 by ER stress is mediated by the UPR signaling pathway. Furthermore, enzymatic activity assays and genetic evidence showed that the D domain is crucially important for the activities of AtPDI11. Overall, this work will help to further understand the working mechanism of AtPDI11 in catalyzing disulfide formation in plants.
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Fan F, Zhang Q, Zhang Y, Huang G, Liang X, Wang CC, Wang L, Lu D. Two protein disulfide isomerase subgroups work synergistically in catalyzing oxidative protein folding. PLANT PHYSIOLOGY 2022; 188:241-254. [PMID: 34609517 PMCID: PMC8774737 DOI: 10.1093/plphys/kiab457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/31/2021] [Indexed: 05/13/2023]
Abstract
Disulfide bonds play essential roles in the folding of secretory and plasma membrane proteins in the endoplasmic reticulum (ER). In eukaryotes, protein disulfide isomerase (PDI) is an enzyme catalyzing the disulfide bond formation and isomerization in substrates. The Arabidopsis (Arabidopsis thaliana) genome encodes diverse PDIs including structurally distinct subgroups PDI-L and PDI-M/S. It remains unclear how these AtPDIs function to catalyze the correct disulfide formation. We found that one Arabidopsis ER oxidoreductin-1 (Ero1), AtERO1, can interact with multiple PDIs. PDI-L members AtPDI2/5/6 mainly serve as an isomerase, while PDI-M/S members AtPDI9/10/11 are more efficient in accepting oxidizing equivalents from AtERO1 and catalyzing disulfide bond formation. Accordingly, the pdi9/10/11 triple mutant exhibited much stronger inhibition than pdi1/2/5/6 quadruple mutant under dithiothreitol treatment, which caused disruption of disulfide bonds in plant proteins. Furthermore, AtPDI2/5 work synergistically with PDI-M/S members in relaying disulfide bonds from AtERO1 to substrates. Our findings reveal the distinct but overlapping roles played by two structurally different AtPDI subgroups in oxidative protein folding in the ER.
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Affiliation(s)
- Fenggui Fan
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education & College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Qiao Zhang
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Shijiazhuang 050024, China
| | - Yini Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guozhong Huang
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xuelian Liang
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Shijiazhuang 050024, China
| | - Chih-chen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongping Lu
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Shijiazhuang 050024, China
- Author for communication:
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Okuda A, Matsusaki M, Masuda T, Morishima K, Sato N, Inoue R, Sugiyama M, Urade R. A novel soybean protein disulphide isomerase family protein possesses dithiol oxidation activity: identification and characterization of GmPDIL6. J Biochem 2020; 168:393-405. [PMID: 32458972 DOI: 10.1093/jb/mvaa058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/02/2020] [Indexed: 01/04/2023] Open
Abstract
Secretory and membrane proteins synthesized in the endoplasmic reticulum (ER) are folded with intramolecular disulphide bonds, viz. oxidative folding, catalysed by the protein disulphide isomerase (PDI) family proteins. Here, we identified a novel soybean PDI family protein, GmPDIL6. GmPDIL6 has a single thioredoxin-domain with a putative N-terminal signal peptide and an active centre (CKHC). Recombinant GmPDIL6 forms various oligomers binding iron. Oligomers with or without iron binding and monomers exhibited a dithiol oxidase activity level comparable to those of other soybean PDI family proteins. However, they displayed no disulphide reductase and extremely low oxidative refolding activity. Interestingly, GmPDIL6 was mainly expressed in the cotyledon during synthesis of seed storage proteins and GmPDIL6 mRNA was up-regulated under ER stress. GmPDIL6 may play a role in the formation of disulphide bonds in nascent proteins for oxidative folding in the ER.
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Affiliation(s)
- Aya Okuda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Motonori Matsusaki
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Taro Masuda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Reiko Urade
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Rada P, Makki A, Žárský V, Tachezy J. Targeting of tail-anchored proteins to Trichomonas vaginalis hydrogenosomes. Mol Microbiol 2019; 111:588-603. [PMID: 30506591 DOI: 10.1111/mmi.14175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2018] [Indexed: 01/17/2023]
Abstract
Tail-anchored (TA) proteins are membrane proteins that are found in all domains of life. They consist of an N-terminal domain that performs various functions and a single transmembrane domain (TMD) near the C-terminus. In eukaryotes, TA proteins are targeted to the membranes of mitochondria, the endoplasmic reticulum (ER), peroxisomes and in plants, chloroplasts. The targeting of these proteins to their specific destinations correlates with the properties of the C-terminal domain, mainly the TMD hydrophobicity and the net charge of the flanking regions. Trichomonas vaginalis is a human parasite that has adapted to oxygen-poor environment. This adaptation is reflected by the presence of highly modified mitochondria (hydrogenosomes) and the absence of peroxisomes. The proteome of hydrogenosomes is considerably reduced; however, our bioinformatic analysis predicted 120 putative hydrogenosomal TA proteins. Seven proteins were selected to prove their localization. The elimination of the net positive charge in the C-tail of the hydrogenosomal TA4 protein resulted in its dual localization to hydrogenosomes and the ER, causing changes in ER morphology. Domain mutation and swap experiments with hydrogenosomal (TA4) and ER (TAPDI) proteins indicated that the general principles for specific targeting are conserved across eukaryotic lineages, including T. vaginalis; however, there are also significant lineage-specific differences.
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Affiliation(s)
- Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
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Onelli E, Moscatelli A, Gagliardi A, Zaninelli M, Bini L, Baldi A, Caccianiga M, Reggi S, Rossi L. Retarded germination of Nicotiana tabacum seeds following insertion of exogenous DNA mimics the seed persistent behavior. PLoS One 2017; 12:e0187929. [PMID: 29216220 PMCID: PMC5720674 DOI: 10.1371/journal.pone.0187929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/09/2017] [Indexed: 01/23/2023] Open
Abstract
Tobacco seeds show a coat-imposed dormancy in which the seed envelope tissues (testa and endosperm) impose a physical constraint on the radicle protrusion. The germination-limiting process is represented by the endosperm rupture which is induced by cell-wall weakening. Transgenic tobacco seeds, obtained by insertion of exogenous genes codifying for seed-based oral vaccines (F18 and VT2eB), showed retarded germination with respect to the wild type and modified the expression of endogenous proteins. Morphological and proteomic analyses of wild type and transgenic seeds revealed new insights into factors influencing seed germination. Our data showed that the interference of exogenous DNA influences the germination rather than the dormancy release, by modifying the maturation process. Dry seeds of F18 and VT2eB transgenic lines accumulated a higher amount of reserve and stress-related proteins with respect to the wild type. Moreover, the storage proteins accumulated in tobacco F18 and VT2eB dry seeds have structural properties that do not enable the early limited proteolysis observed in the wild type. Morphological observations by electron and light microscopy revealed a retarded mobilization of the storage material from protein and lipid bodies in transgenic seeds, thus impairing water imbibition and embryo elongation. In addition, both F18 and VT2eB dry seeds are more rounded than the wild type. Both the morphological and biochemical characteristics of transgenic seeds mimic the seed persistent profile, in which their roundness enables them to be buried in the soil, while the higher content of storage material enables the hypocotyl to elongate more and the cotyledons to emerge.
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Affiliation(s)
| | | | - Assunta Gagliardi
- Laboratory of Functional Proteomic, Department of Life Science, University of Siena, Siena, Italy
| | - Mauro Zaninelli
- Department of Human Sciences and Quality of Life Promotion, Università Telematica San Raffaele Roma, Italy, Rome, Italy
| | - Luca Bini
- Laboratory of Functional Proteomic, Department of Life Science, University of Siena, Siena, Italy
| | - Antonella Baldi
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milan, Italy
| | | | | | - Luciana Rossi
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milan, Italy
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