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Liu Y, Song P, Yan M, Luo J, Wang Y, Fan F. Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis. Int J Mol Sci 2024; 25:3596. [PMID: 38612408 PMCID: PMC11011405 DOI: 10.3390/ijms25073596] [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: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Protein disulfide isomerase (PDI, EC 5.3.4.1) is a thiol-disulfide oxidoreductase that plays a crucial role in catalyzing the oxidation and rearrangement of disulfides in substrate proteins. In plants, PDI is primarily involved in regulating seed germination and development, facilitating the oxidative folding of storage proteins in the endosperm, and also contributing to the formation of pollen. However, the role of PDI in root growth has not been previously studied. This research investigated the impact of PDI gene deficiency in plants by using 16F16 [2-(2-Chloroacetyl)-2,3,4,9-tetrahydro-1-methyl-1H-pyrido[3,4-b]indole-1-carboxylic acid methyl ester], a small-molecule inhibitor of PDI, to remove functional redundancy. The results showed that the growth of Arabidopsis roots was significantly inhibited when treated with 16F16. To further investigate the effects of 16F16 treatment, we conducted expression profiling of treated roots using RNA sequencing and a Tandem Mass Tag (TMT)-based quantitative proteomics approach at both the transcriptomic and proteomic levels. Our analysis revealed 994 differentially expressed genes (DEGs) at the transcript level, which were predominantly enriched in pathways associated with "phenylpropane biosynthesis", "plant hormone signal transduction", "plant-pathogen interaction" and "starch and sucrose metabolism" pathways. Additionally, we identified 120 differentially expressed proteins (DEPs) at the protein level. These proteins were mainly enriched in pathways such as "phenylpropanoid biosynthesis", "photosynthesis", "biosynthesis of various plant secondary metabolites", and "biosynthesis of secondary metabolites" pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network for root shortening in Arabidopsis seedlings under 16F16 treatment, mainly involving phenylpropane biosynthesis and plant hormone signal transduction pathways. This study enhances our understanding of the significant role of PDIs in Arabidopsis root growth and provides insights into the regulatory mechanisms of root shortening following 16F16 treatment.
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Affiliation(s)
| | | | | | | | - Yingjuan Wang
- State Key Laboratory of Biotechnology of Shannxi Province, College of Life Science, Northwest University, Xi’an 710069, China; (Y.L.); (P.S.); (M.Y.); (J.L.)
| | - Fenggui Fan
- State Key Laboratory of Biotechnology of Shannxi Province, College of Life Science, Northwest University, Xi’an 710069, China; (Y.L.); (P.S.); (M.Y.); (J.L.)
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Ming Q, Wang K, Wang J, Liu J, Li X, Wei P, Guo H, Chen J, Zong J. The combination of RNA-seq transcriptomics and data-independent acquisition proteomics reveals the mechanisms underlying enhanced salt tolerance by the ZmPDI gene in Zoysia matrella [L.] Merr. FRONTIERS IN PLANT SCIENCE 2022; 13:970651. [PMID: 36003810 PMCID: PMC9393727 DOI: 10.3389/fpls.2022.970651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Zoysia matrella [L.] Merr. is one of the three most economically important Zoysia species due to its strong salt tolerance and wide application. However, the molecular mechanisms regulating salt tolerance in Z. matrella remain unknown. The protein disulfide isomerase ZmPDI of Z. matrella was obtained by salt stress screening with yeast cells, and its expression was significantly upregulated after salt stress. Based on the obtained ZmPDI overexpression transgenic Z. matrella plants, we carried out salt tolerance identification and found that ZmPDI can significantly enhance the salt tolerance of Z. matrella. Root samples of OX-ZmPDI transgenic and wild-type plants were collected at 0 and 24 h after salt treatments for RNA-seq and data-independent acquisition (DIA) proteome sequencing. Combined analysis of the transcriptome and proteome revealed that ZmPDI may enhance the salt tolerance of Z. matrella by regulating TUBB2, PXG4, PLDα2, PFK4, and 4CL1. This research presents the molecular regulatory mechanism of the ZmPDI gene in Z. matrella for resistance to salt stress and facilitates the use of molecular breeding to improve the salt tolerance of grasses.
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Affiliation(s)
- Qiang Ming
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Kai Wang
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiaohui Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Peipei Wei
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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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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Zhou Y, Fan F, Han Y, Lu D. Arabidopsis PDI11 interacts with lectin molecular chaperons calreticulin 1 and 2 through its D domain. Biochem Biophys Res Commun 2022; 588:55-60. [PMID: 34952470 DOI: 10.1016/j.bbrc.2021.12.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 02/07/2023]
Abstract
The endoplasmic reticulum (ER) is equipped with protein disulfide isomerases (PDIs), molecular chaperons, and other folding enzymes to ensure that newly synthesized proteins in the ER are properly folded. Molecular chaperons and PDIs can form complex to promote protein folding in the ER of mammalian cells. In plants, many PDIs associate with each other and function cooperatively in oxidative protein folding. As a plant unique protein disulfide isomerase, Arabidopsis thaliana PDI11 (AtPDI11) demonstrates oxidative protein folding activities and works synergistically with AtPDI2/5. However, whether AtPDI11 associates with molecular chaperons or AtPDIs in catalyzing disulfide formation remained unknown. Here, we find that AtPDI11 interacts with ER resident lectin chaperones calreticulin 1 (CRT1) and CRT2. Furthermore, the D domain, but not the a or a' domain of AtPDI11 provides the biding sites for its interaction with CRT1/2. Moreover, the P domain of CRT1 is responsible for its interaction with AtPDI11. Our work implies that Arabidopsis CRT1/2 may specifically recruit AtPDI11 to assist the folding of glycoproteins in the ER.
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Affiliation(s)
- Yuanyuan Zhou
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fenggui Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education & College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yongfeng Han
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024, Shijiazhuang, 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, Hebei, 050021, China.
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Sun JL, Li JY, Wang MJ, Song ZT, Liu JX. Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives. MOLECULAR PLANT 2021; 14:95-114. [PMID: 33137518 DOI: 10.1016/j.molp.2020.10.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/09/2020] [Accepted: 10/28/2020] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein homeostasis in these organelles, maintained by a balance between protein synthesis and degradation, is essential for cell functions during plant growth, development, and stress resistance. Nucleus-encoded chloroplast- and mitochondrion-targeted proteins and ER-resident proteins are imported from the cytosol and undergo modification and maturation within their respective organelles. Protein folding is an error-prone process that is influenced by both developmental signals and environmental cues; a number of mechanisms have evolved to ensure efficient import and proper folding and maturation of proteins in plant organelles. Misfolded or damaged proteins with nonnative conformations are subject to degradation via complementary or competing pathways: intraorganelle proteases, the organelle-associated ubiquitin-proteasome system, and the selective autophagy of partial or entire organelles. When proteins in nonnative conformations accumulate, the organelle-specific unfolded protein response operates to restore protein homeostasis by reducing protein folding demand, increasing protein folding capacity, and enhancing components involved in proteasome-associated protein degradation and autophagy. This review summarizes recent progress on the understanding of protein quality control in the ER, chloroplasts, and mitochondria in plants, with a focus on common mechanisms shared by these organelles during protein homeostasis.
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Affiliation(s)
- Jing-Liang Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Mei-Jing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Ze-Ting Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
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Fan F, Zhang Q, Lu D. Identification of N-glycosylation sites on AtERO1 and AtERO2 using a transient expression system. Biochem Biophys Res Commun 2020; 533:481-485. [PMID: 32977945 DOI: 10.1016/j.bbrc.2020.09.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023]
Abstract
N-glycosylation is an important protein modification that generally occurs at the Asn residue in an Asn-X-Ser/Thr sequon. Ero1 and its homologs play key roles in catalyzing the oxidative folding in the endoplasmic reticulum (ER). Recently, we found that Arabidopsis (Arabidopsis thaliana) ERO1 and AtERO2 displayed different characteristics in catalyzing oxidative protein folding in the ER. All known Ero1s are glycosylated proteins, including AtERO1 and AtERO2 that were analyzed when they were transiently translated in mammalian cells. However, the exact N-glycosylation sites on AtERO1 and AtERO2 remains to be determined. In this work, using a plant transient expression system, we identified the N-glycosylation sites on both AtERO1 and AtERO2. We found that AtERO1 has one N-glycosylation site, while AtERO2 contains two, all in the N-X-S/T sequons. Interestingly, we found that Ero1 homologs from human, rice, soybean and Arabidopsis, all have a conserved N-glycosylation site near the inner active site that reduces molecular oxygen and provides the oxidizing equivalents. The identification of N-glycosylation sites on AtERO1/2 proteins will help understand the function of N-glycosylation not only in AtERO1/2, but also in other Ero1 homologs.
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Affiliation(s)
- Fenggui Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education & College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China. https://orcid.org/0000-0003-4157-9330
| | - Qiao Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Dongping Lu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China.
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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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Zubieta MP, Gerhardt JA, Rubio MV, Terrasan CRF, Persinoti GF, Antoniel EP, Contesini FJ, Prade RA, Damasio A. Improvement of homologous GH10 xylanase production by deletion of genes with predicted function in the Aspergillus nidulans secretion pathway. Microb Biotechnol 2020; 13:1245-1253. [PMID: 32212325 PMCID: PMC7264891 DOI: 10.1111/1751-7915.13556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/01/2020] [Indexed: 12/20/2022] Open
Abstract
Filamentous fungi are important cell factories for large-scale enzyme production. However, production levels are often low, and this limitation has stimulated research focusing on the manipulation of genes with predicted function in the protein secretory pathway. This pathway is the major route for the delivery of proteins to the cell exterior, and a positive relationship between the production of recombinant enzymes and the unfolded protein response (UPR) pathway has been observed. In this study, Aspergillus nidulans was exposed to UPR-inducing chemicals and differentially expressed genes were identified by RNA-seq. Twelve target genes were deleted in A. nidulans recombinant strains producing homologous and heterologous GH10 xylanases. The knockout of pbnA (glycosyltransferase), ydjA (Hsp40 co-chaperone), trxA (thioredoxin) and cypA (cyclophilin) improved the production of the homologous xylanase by 78, 171, 105 and 125% respectively. Interestingly, these deletions decreased the overall protein secretion, suggesting that the production of the homologous xylanase was specifically altered. However, the production of the heterologous xylanase and the secretion of total proteins were not altered by deleting the same genes. Considering the results, this approach demonstrated the possibility of rationally increase the production of a homologous enzyme, indicating that trxA, cypA, ydjA and pbnA are involved in protein production by A. nidulans.
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Affiliation(s)
- Mariane P. Zubieta
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
- Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOKUSA
| | - Jaqueline A. Gerhardt
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Marcelo V. Rubio
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - César R. F. Terrasan
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Gabriela F. Persinoti
- Brazilian Biorenewables National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSPBrazil
| | - Everton P. Antoniel
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Fabiano J. Contesini
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Rolf A. Prade
- Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOKUSA
| | - André Damasio
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
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Physiology and proteomic analysis reveals root, stem and leaf responses to potassium deficiency stress in alligator weed. Sci Rep 2019; 9:17366. [PMID: 31758026 PMCID: PMC6874644 DOI: 10.1038/s41598-019-53916-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/05/2019] [Indexed: 11/09/2022] Open
Abstract
Alligator weed is reported to have a strong ability to adapt to potassium deficiency stress. Proteomic changes in response to this stress are largely unknown in alligator weed seedlings. In this study, we performed physiological and comparative proteomics of alligator weed seedlings between normal growth (CK) and potassium deficiency (LK) stress using 2-DE techniques, including root, stem and leaf tissues. Seedling height, soluble sugar content, PGK activity and H2O2 contents were significantly altered after 15 d of LK treatment. A total of 206 differentially expressed proteins (DEPs) were identified. There were 72 DEPs in the root, 79 in the stem, and 55 in the leaves. The proteomic results were verified using western blot and qRT-PCR assays. The most represented KEGG pathway was "Carbohydrate and energy metabolism" in the three samples. The "Protein degradation" pathway only existed in the stem and root, and the "Cell cycle" pathway only existed in the root. Protein-protein interaction analysis demonstrated that the interacting proteins detected were the most common in the stem, with 18 proteins. Our study highlights protein changes in alligator weed seedling under LK stress and provides new information on the comprehensive analysis of the protein network in plant potassium nutrition.
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Huang G, Sun J, Bai J, Han Y, Fan F, Wang S, Zhang Y, Zou Y, Han Z, Lu D. Identification of critical cysteine sites in brassinosteroid-insensitive 1 and novel signaling regulators using a transient expression system. THE NEW PHYTOLOGIST 2019; 222:1405-1419. [PMID: 30685894 DOI: 10.1111/nph.15709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/11/2019] [Indexed: 06/09/2023]
Abstract
The plant hormones brassinosteroids (BRs) modulate plant growth and development. Cysteine (Cys) residues located in the extracellular domain of a protein are of importance for protein structure by forming disulfide bonds. To date, the systematic study of the functional significance of Cys residues in BR-insensitive 1 (BRI1) is still lacking. We used brassinolide-induced exogenous bri1-EMS-Suppressor 1 (BES1) dephosphorylation in Arabidopsis thaliana protoplasts as a readout, took advantage of the dramatic decrease of BRI1 protein levels during protoplast isolation, and of the strong phosphorylation of BES1 by BR-insensitive 2 (BIN2) in protoplasts, and developed a protoplast transient system to identify critical Cys sites in BRI1. Using this system, we identified a set of critical Cys sites in BRI1, as substitution of these Cys residues with alanine residues greatly compromised the function of BRI1. Moreover, we identified two negative regulators of BR signaling, pattern-triggered immunity compromised RLCK1 (PCRK1) and PCRK2, that were previously known to positively regulate innate immunity signaling. This work not only provides insight into the functional importance of critical Cys residues in stabilizing the superhelical conformation of BRI1-leucine-rich-repeat, but also reveals that PCRK1/2 can inversely modulate BR and plant immune signaling pathways.
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Affiliation(s)
- Guozhong Huang
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhang Sun
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaojiao Bai
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufang Han
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fenggui Fan
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangfeng Wang
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingying Zhang
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
| | - Yanmin Zou
- State Key Laboratory of Plant Genomics, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
| | - Zhifu Han
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, 100084, 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, Hebei, 050021, China
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Meyer AJ, Riemer J, Rouhier N. Oxidative protein folding: state-of-the-art and current avenues of research in plants. THE NEW PHYTOLOGIST 2019; 221:1230-1246. [PMID: 30230547 DOI: 10.1111/nph.15436] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 1230 I. Introduction 1230 II. Formation and isomerization of disulfides in the ER and the Golgi apparatus 1231 III. The disulfide relay in the mitochondrial intermembrane space: why are plants different? 1236 IV. Disulfide bond formation on luminal proteins in thylakoids 1240 V. Conclusion 1242 Acknowledgements 1242 References 1242 SUMMARY: Disulfide bonds are post-translational modifications crucial for the structure and function of thousands of proteins. Their formation and isomerization, referred to as oxidative folding, require specific protein machineries found in oxidizing subcellular compartments, namely the endoplasmic reticulum and the associated endomembrane system, the intermembrane space of mitochondria and the thylakoid lumen of chloroplasts. At least one protein component is required for transferring electrons from substrate proteins to an acceptor that is usually molecular oxygen. For oxidation reactions, incoming reduced substrates are oxidized by thiol-oxidoreductase proteins (or domains in case of chimeric proteins), which are usually themselves oxidized by a single thiol oxidase, the enzyme generating disulfide bonds de novo. By contrast, the description of the molecular actors and pathways involved in proofreading and isomerization of misfolded proteins, which require a tightly controlled redox balance, lags behind. Herein we provide a general overview of the knowledge acquired on the systems responsible for oxidative protein folding in photosynthetic organisms, highlighting their particularities compared to other eukaryotes. Current research challenges are discussed including the importance and specificity of these oxidation systems in the context of the existence of reducing systems in the same compartments.
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Affiliation(s)
- Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, 53113, Bonn, Germany
| | - Jan Riemer
- Institute of Biochemistry, University of Cologne, 50674, Cologne, Germany
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