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Díaz-Cruz GA, Bignell DRD. Exploring the specialized metabolome of the plant pathogen Streptomyces sp. 11-1-2. Sci Rep 2024; 14:10414. [PMID: 38710735 DOI: 10.1038/s41598-024-60630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Streptomyces bacteria are notable for producing chemically diverse specialized metabolites that exhibit various bioactivities and mediate interactions with different organisms. Streptomyces sp. 11-1-2 is a plant pathogen that produces nigericin and geldanamycin, both of which display toxic effects against various plants. Here, the 'One Strain Many Compounds' approach was used to characterize the metabolic potential of Streptomyces sp. 11-1-2. Organic extracts were prepared from 11-1-2 cultures grown on six different agar media, and the extracts were tested in antimicrobial and plant bioassays and were subjected to untargeted metabolomics and molecular networking. Most extracts displayed strong bioactivity against Gram-positive bacteria and yeast, and they exhibited phytotoxic activity against potato tuber tissue and radish seedlings. Several known specialized metabolites, including musacin D, galbonolide B, guanidylfungin A, meridamycins and elaiophylin, were predicted to be present in the extracts along with closely related compounds with unknown structure and bioactivity. Targeted detection confirmed the presence of elaiophylin in the extracts, and bioassays using pure elaiophylin revealed that it enhances the phytotoxic effects of geldanamycin and nigericin on potato tuber tissue. Overall, this study reveals novel insights into the specialized metabolites that may mediate interactions between Streptomyces sp. 11-1-2 and other bacteria and eukaryotic organisms.
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Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
- Phytopathology Department, Plant Protection Research Center (CIPROC), Agronomy School, Universidad de Costa Rica, San Jose, Costa Rica
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
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2
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Yang D, Li Y, Zhu M, Cui R, Gao J, Shu Y, Lu X, Zhang H, Zhang K. Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses. Genes (Basel) 2023; 14:2006. [PMID: 38002948 PMCID: PMC10671320 DOI: 10.3390/genes14112006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The FKBP (FK506-binding protein) gene family is an important member of the PPlase protease family and plays a vital role during the processes of plant growth and development. However, no studies of the FKBP gene family have been reported in cucumber. In this study, 19 FKBP genes were identified in cucumber, which were located on chromosomes 1, 3, 4, 6, and 7. Phylogenetic analysis divided the cucumber FKBP genes into three subgroups. The FKBP genes in the same subgroup exhibited similar structures and conserved motifs. The cis-acting elements analysis revealed that the promoters of cucumber FKBP genes contained hormone-, stress-, and development-related cis-acting elements. Synteny analysis of the FKBP genes among cucumber, Arabidopsis, and rice showed that 12 kinds of syntenic relationships were detected between cucumber and Arabidopsis FKBP genes, and 3 kinds of syntenic relationships were observed between cucumber and rice FKBP genes. The tissue-specific expression analysis showed that some FKBP genes were expressed in all tissues, while others were only highly expressed in part of the 10 types of tissues. The expression profile analysis of cucumber FKBP genes under 13 types of stresses showed that the CsaV3_1G007080 gene was differentially expressed under abiotic stresses (high temperature, NaCl, silicon, and photoperiod) and biotic stresses (downy mildew, green mottle mosaic virus, Fusarium wilt, phytophthora capsica, angular leaf spot, and root-knot nematode), which indicated that the CsaV3_1G007080 gene plays an important role in the growth and development of cucumber. The interaction protein analysis showed that most of the proteins in the FKBP gene family interacted with each other. The results of this study will lay the foundation for further research on the molecular biological functions of the cucumber FKBP gene family.
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Affiliation(s)
- Dekun Yang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yahui Li
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Mengdi Zhu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Rongjing Cui
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Jiong Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Yingjie Shu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Xiaomin Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei 235000, China;
| | - Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (D.Y.); (M.Z.); (R.C.); (J.G.); (Y.S.); (X.L.)
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Genome-Wide Identification and Analysis of FKBP Gene Family in Wheat ( Triticum asetivum). Int J Mol Sci 2022; 23:ijms232314501. [PMID: 36498828 PMCID: PMC9739119 DOI: 10.3390/ijms232314501] [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: 10/17/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
FK506-binding protein (FKBP) genes have been found to play vital roles in plant development and abiotic stress responses. However, limited information is available about this gene family in wheat (Triticum aestivum L.). In this study, a total of 64 FKBP genes were identified in wheat via a genome-wide analysis involving a homologous search of the latest wheat genome data, which was unevenly distributed in 21 chromosomes, encoded 152 to 649 amino acids with molecular weights ranging from 16 kDa to 72 kDa, and was localized in the chloroplast, cytoplasm, nucleus, mitochondria, peroxisome and endoplasmic reticulum. Based on sequence alignment and phylogenetic analysis, 64 TaFKBPs were divided into four different groups or subfamilies, providing evidence of an evolutionary relationship with Aegilops tauschii, Brachypodium distachyon, Triticum dicoccoides, Arabidopsis thaliana and Oryza sativa. Hormone-related, abiotic stress-related and development-related cis-elements were preferentially presented in promoters of TaFKBPs. The expression levels of TaFKBP genes were investigated using transcriptome data from the WheatExp database, which exhibited tissue-specific expression patterns. Moreover, TaFKBPs responded to drought and heat stress, and nine of them were randomly selected for validation by qRT-PCR. Yeast cells expressing TaFKBP19-2B-2 or TaFKBP18-6B showed increased influence on drought stress, indicating their negative roles in drought tolerance. Collectively, our results provide valuable information about the FKBP gene family in wheat and contribute to further characterization of FKBPs during plant development and abiotic stress responses, especially in drought stress.
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Duarte KE, Basso MF, de Oliveira NG, da Silva JCF, de Oliveira Garcia B, Cunha BADB, Cardoso TB, Nepomuceno AL, Kobayashi AK, Santiago TR, de Souza WR, Molinari HBC. MicroRNAs expression profiles in early responses to different levels of water deficit in Setaria viridis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1607-1624. [PMID: 36389096 PMCID: PMC9530107 DOI: 10.1007/s12298-022-01226-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Water deficit is a major constraint for crops of economic importance in almost all agricultural regions. However, plants have an active defense system to adapt to these adverse conditions, acting in the reprogramming of gene expression responsible for encoding microRNAs (miRNAs). These miRNAs promote the regulation to the target gene expression by the post-transcriptional (PTGS) and transcriptional gene silencing (TGS), modulating several pathways including defense response to water deficit. The broader knowledge of the miRNA expression profile and its regulatory networks in response to water deficit can provide evidence for the development of new biotechnological tools for genetic improvement of several important crops. In this study, we used Setaria viridis accession A10.1 as a C4 model plant to widely investigate the miRNA expression profile in early responses to different levels of water deficit. Ecophysiological studies in Setaria viridis under water deficit and after rewatering demonstrated a drought tolerant accession, capable of a rapid recovery from the stress. Deep small RNA sequencing and degradome studies were performed in plants submitted to drought to identify differentially expressed miRNA genes and their predicted targets, using in silico analysis. Our findings showed that several miRNAs were differentially modulated in response to distinctive levels of water deficit and after rewatering. The predicted mRNA targets mainly corresponded to genes related to cell wall remodeling, antioxidant system and drought-related transcription factors, indicating that these genes are rapidly regulated in early responses to drought stress. The implications of these modulations are extensively discussed, and higher-effect miRNAs are suggested as major players for potential use in genetic engineering to improve drought tolerance in economically important crops, such as sugarcane, maize, and sorghum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01226-z.
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Affiliation(s)
- Karoline Estefani Duarte
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of ABC, Santo André, SP 09210-580 Brazil
| | - Marcos Fernando Basso
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- BIOMOL/BIOTEC Laboratory, Mato Grosso Cotton Institute (IMAmt), Rondonópolis, MT 78740-970 Brazil
| | | | | | - Bruno de Oliveira Garcia
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of Lavras, Lavras, MG 37200-900 Brazil
| | | | | | | | | | - Thaís Ribeiro Santiago
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- University of Brasília, Brasília, DF 70910-900 Brazil
| | - Wagner Rodrigo de Souza
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of ABC, Santo André, SP 09210-580 Brazil
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Folimonova SY, Sun YD. Citrus Tristeza Virus: From Pathogen to Panacea. Annu Rev Virol 2022; 9:417-435. [DOI: 10.1146/annurev-virology-100520-114412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Citrus tristeza virus (CTV) is the most destructive viral pathogen of citrus. During the past century, CTV induced grave epidemics in citrus-growing areas worldwide that have resulted in a loss of more than 100 million trees. At present, the virus continues to threaten citrus production in many different countries. Research on CTV is accompanied by distinctive challenges stemming from the large size of its RNA genome, the narrow host range limited to slow-growing Citrus species and relatives, and the complexity of CTV populations. Despite these hurdles, remarkable progress has been made in understanding the CTV-host interactions and in converting the virus into a tool for crop protection and improvement. This review focuses on recent advances that have shed light on the mechanisms underlying CTV infection. Understanding these mechanisms is pivotal for the development of means to control CTV diseases and, ultimately, turn this virus into an ally. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Svetlana Y. Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, USA
| | - Yong-Duo Sun
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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Chang H, Lee C, Chang C, Jan F. FKBP-type peptidyl-prolyl cis-trans isomerase interacts with the movement protein of tomato leaf curl New Delhi virus and impacts viral replication in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2022; 23:561-575. [PMID: 34984809 PMCID: PMC8916215 DOI: 10.1111/mpp.13181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/29/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Begomoviruses belonging to the family Geminiviridae are plant-infecting DNA viruses. Begomoviral movement protein (MP) has been reported to be required for virus movement, host range determination, and symptom development. In the present study, the FK506-binding protein (FKBP)-type peptidyl-prolyl cis-trans isomerase (NbFKPPIase) of Nicotiana benthamiana was identified by a yeast two-hybrid screening system using the MP of tomato leaf curl New Delhi virus (ToLCNDV) oriental melon (OM) isolate (MPOM ) as bait. Transient silencing of the gene encoding NbFKPPIase increased replication of three test begomoviruses, and transient overexpression decreased viral replication, indicating that NbFKPPIase plays a role in defence against begomoviruses. However, infection of N. benthamiana by ToLCNDV-OM or overexpression of the gene encoding MPOM drastically reduced the expression of the gene encoding NbFKPPIase. Fluorescence resonance energy transfer analysis revealed that MPOM interacted with NbFKPPIase in the periphery of cells. Expression of the gene encoding NbFKPPIase was induced by salicylic acid but not by methyl jasmonate or ethylene. Moreover, the expression of the gene encoding NbFKPPIase was down-regulated in response to 6-benzylaminopurine and up-regulated in response to gibberellin or indole-3-acetic acid, suggesting a role of NbFKPPIase in plant development. Transcriptome analysis and comparison of N. benthamiana transient silencing and overexpression of the gene encoding MPOM led to the identification of several differentially expressed genes whose functions are probably associated with cell cycle regulation. Our results indicate that begomoviruses could suppress NbFKPPIase-mediated defence and biological functions by transcriptional inhibition and physical interaction between MP and NbFKPPIase to facilitate infection.
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Affiliation(s)
- Ho‐Hsiung Chang
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan
| | - Chia‐Hwa Lee
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan
- Ph.D. Program in Microbial GenomicsNational Chung Hsing University and Academia SinicaTaichung and TaipeiTaiwan
| | - Chung‐Jan Chang
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan
- Department of Plant PathologyUniversity of GeorgiaGriffinGeorgiaUSA
| | - Fuh‐Jyh Jan
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan
- Ph.D. Program in Microbial GenomicsNational Chung Hsing University and Academia SinicaTaichung and TaipeiTaiwan
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
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7
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Moreno P, López C, Ruiz-Ruiz S, Peña L, Guerri J. From the smallest to the largest subcellular plant pathogen: Citrus tristeza virus and its unique p23 protein. Virus Res 2022; 314:198755. [PMID: 35341876 DOI: 10.1016/j.virusres.2022.198755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
Abstract
Knowledge on diseases caused by Citrus tristeza virus (CTV) has greatly increased in last decades after their etiology was demonstrated in the past seventies. Professor Ricardo Flores substantially contributed to these advances in topics like: i) improvement of virus purification to obtain biologically active virions, ii) sequencing mild CTV isolates for genetic comparisons with sequences of moderate or severe isolates and genetic engineering, iii) analysis of genetic variation of both CTV genomic RNA ends and features of the highly variable 5' end that allow accommodating this variation within a conserved secondary structure, iv) studies on the structure, subcellular localization and biological functions of the CTV-unique p23 protein, and v) potential use of p23 and other 3'-proximal regions of the CTV genome to develop transgenic citrus resistant to the virus. Here we review his main achievements on these topics and how they contributed to deeper understanding of CTV biology and to new potential measures for disease control.
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Affiliation(s)
- Pedro Moreno
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113-Valencia, Spain. (Retired).
| | - Carmelo López
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, 46022-Valencia, Spain
| | - Susana Ruiz-Ruiz
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46022-Valencia, Spain
| | - Leandro Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), 46022-Valencia, Spain
| | - José Guerri
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113-Valencia, Spain. (Retired)
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Su X, Cao D, Pan X, Shi L, Liu Z, Dall'Osto L, Bassi R, Zhang X, Li M. Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana. MOLECULAR PLANT 2022; 15:454-467. [PMID: 35123031 DOI: 10.1016/j.molp.2022.01.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants.
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Affiliation(s)
- Xiaodong Su
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Xiaowei Pan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China; College of Life Science, Capital Normal University, Beijing 100101, P.R. China.
| | - Lifang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Luca Dall'Osto
- Dipartimento di Biotecnologie, Università di Verona, 37134 Verona, Italy
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, 37134 Verona, Italy
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China; Center for Biological Imaging, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.
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Vakilian M. A review on the effect of prolyl isomerization on immune response aberration and hypersensitivity reactions: A unifying hypothesis. Clin Immunol 2021; 234:108896. [PMID: 34848356 DOI: 10.1016/j.clim.2021.108896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/01/2022]
Abstract
Little is known about the causes and mechanisms of ectopic immune responses, including different types of hypersensitivity, superantigens, and cytokine storms. Two of the most questionable phenomena observed in immunology are why the intensity and extent of immune responses to different antigens are different, and why some self-antigens are attacked as foreign. The secondary structure of the peptides involved in the immune system, such as the epitope-paratope interfaces plays a pivotal role in the resulting immune responses. Prolyl cis/trans isomerization plays a fundamental role in the form of the secondary structure and the folding of proteins. This review covers some of the emerging evidence indicating the impact of prolyl isomerization on protein conformation, aberration of immune responses, and the development of hypersensitivity reactions.
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Affiliation(s)
- Mehrdad Vakilian
- Department of Cell Biology, Genetics and Physiology, University of Malaga (UMA), The Institute of Biomedical Research in Malaga (IBIMA), Málaga, Spain.
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Characterization of the Free and Membrane-Associated Fractions of the Thylakoid Lumen Proteome in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22158126. [PMID: 34360890 PMCID: PMC8346976 DOI: 10.3390/ijms22158126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
The thylakoid lumen houses proteins that are vital for photosynthetic electron transport, including water-splitting at photosystem (PS) II and shuttling of electrons from cytochrome b6f to PSI. Other lumen proteins maintain photosynthetic activity through biogenesis and turnover of PSII complexes. Although all lumen proteins are soluble, these known details have highlighted interactions of some lumen proteins with thylakoid membranes or thylakoid-intrinsic proteins. Meanwhile, the functional details of most lumen proteins, as well as their distribution between the soluble and membrane-associated lumen fractions, remain unknown. The current study isolated the soluble free lumen (FL) and membrane-associated lumen (MAL) fractions from Arabidopsis thaliana, and used gel- and mass spectrometry-based proteomics methods to analyze the contents of each proteome. These results identified 60 lumenal proteins, and clearly distinguished the difference between the FL and MAL proteomes. The most abundant proteins in the FL fraction were involved in PSII assembly and repair, while the MAL proteome was enriched in proteins that support the oxygen-evolving complex (OEC). Novel proteins, including a new PsbP domain-containing isoform, as well as several novel post-translational modifications and N-termini, are reported, and bi-dimensional separation of the lumen proteome identified several protein oligomers in the thylakoid lumen.
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Differential Response to Single and Combined Salt and Heat Stresses: Impact on Accumulation of Proteins and Metabolites in Dead Pericarps of Brassica juncea. Int J Mol Sci 2021; 22:ijms22137076. [PMID: 34209216 PMCID: PMC8267682 DOI: 10.3390/ijms22137076] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Dead organs enclosing embryos, such as seed coats and pericarps, are emerging as important maternally-derived components of the dispersal unit that affect seed performance and fate. In the face of climate change and increased incidents of heatwaves, we sought to investigate the effect of salinity (S), short episodes of high temperature (HS), and combination of S + HS (SHS), at the reproductive phase, on the properties of dead pericarps of Brassica juncea. Proteome and metabolome analyses revealed multiple proteins and metabolites stored in dead pericarps whose levels and composition were altered under single and combined stress conditions. The protein profile of SHS showed a higher correlation with salt than with HS indicating the dominant effect of salt over heat stress. On the other hand, the analysis of metabolites showed that the profile of SHS has better correlation with HS than with salt. The integration of metabolic and proteomic data showed that changes in TCA cycle intermediates and certain amino acids (e.g., proline) under salt treatments (S and SHS) are highly correlated with changes in proteins involved in their biosynthetic pathways. Thus, accumulation of proteins and metabolites in dead pericarps is differently affected by single and combination of salt and heat stresses. Salinity appears to dominate plant response to combined stresses at the protein level, while heat appears to be the major factor affecting metabolite accumulation in dead pericarps.
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12
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Yang Z, Zhang Y, Wang G, Wen S, Wang Y, Li L, Xiao F, Hong N. The p23 of Citrus Tristeza Virus Interacts with Host FKBP-Type Peptidyl-Prolylcis-Trans Isomerase 17-2 and Is Involved in the Intracellular Movement of the Viral Coat Protein. Cells 2021; 10:934. [PMID: 33920690 PMCID: PMC8073322 DOI: 10.3390/cells10040934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022] Open
Abstract
Citrus tristeza virus is a member of the genus Closterovirus in the family Closteroviridae. The p23 of citrus tristeza virus (CTV) is a multifunctional protein and RNA silencing suppressor. In this study, we identified a p23 interacting partner, FK506-binding protein (FKBP) 17-2, from Citrus aurantifolia (CaFKBP17-2), a susceptible host, and Nicotiana benthamiana (NbFKBP17-2), an experimental host for CTV. The interaction of p23 with CaFKBP17-2 and NbFKBP17-2 were individually confirmed by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Subcellular localization tests showed that the viral p23 translocated FKBP17-2 from chloroplasts to the plasmodesmata of epidermal cells of N. benthamiana leaves. The knocked-down expression level of NbFKBP17-2 mRNA resulted in a decreased CTV titer in N. benthamiana plants. Further, BiFC and Y2H assays showed that NbFKBP17-2 also interacted with the coat protein (CP) of CTV, and the complexes of CP/NbFKBP17-2 rapidly moved in the cytoplasm. Moreover, p23 guided the CP/NbFKBP17-2 complexes to move along the cell wall. To the best of our knowledge, this is the first report of viral proteins interacting with FKBP17-2 encoded by plants. Our results provide insights for further revealing the mechanism of the CTV CP protein movement.
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Affiliation(s)
- Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Yongle Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- National Biopesticide Engineering Research Centre, Hubei Biopesticide Engineering Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Liu Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Feng Xiao
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
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13
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Singh AK, Datta A, Jobichen C, Luan S, Vasudevan D. AtFKBP53: a chimeric histone chaperone with functional nucleoplasmin and PPIase domains. Nucleic Acids Res 2020; 48:1531-1550. [PMID: 31807785 PMCID: PMC7026663 DOI: 10.1093/nar/gkz1153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 12/23/2022] Open
Abstract
FKBP53 is one of the seven multi-domain FK506-binding proteins present in Arabidopsis thaliana, and it is known to get targeted to the nucleus. It has a conserved PPIase domain at the C-terminus and a highly charged N-terminal stretch, which has been reported to bind to histone H3 and perform the function of a histone chaperone. To better understand the molecular details of this PPIase with histone chaperoning activity, we have solved the crystal structures of its terminal domains and functionally characterized them. The C-terminal domain showed strong PPIase activity, no role in histone chaperoning and revealed a monomeric five-beta palm-like fold that wrapped over a helix, typical of an FK506-binding domain. The N-terminal domain had a pentameric nucleoplasmin-fold; making this the first report of a plant nucleoplasmin structure. Further characterization revealed the N-terminal nucleoplasmin domain to interact with H2A/H2B and H3/H4 histone oligomers, individually, as well as simultaneously, suggesting two different binding sites for H2A/H2B and H3/H4. The pentameric domain assists nucleosome assembly and forms a discrete complex with pre-formed nucleosomes; wherein two pentamers bind to a nucleosome.
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Affiliation(s)
- Ajit Kumar Singh
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Aritreyee Datta
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India
| | - Chacko Jobichen
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dileep Vasudevan
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India
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Watson-Lazowski A, Papanicolaou A, Koller F, Ghannoum O. The transcriptomic responses of C 4 grasses to subambient CO 2 and low light are largely species specific and only refined by photosynthetic subtype. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1170-1184. [PMID: 31651067 DOI: 10.1111/tpj.14583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 09/23/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
Three subtypes of C4 photosynthesis exist (NADP-ME, NAD-ME and PEPCK), each known to be beneficial under specific environmental conditions. However, the influence of photosynthetic subtype on transcriptomic plasticity, as well as the genes underpinning this variability, remain largely unknown. Here, we comprehensively investigate the responses of six C4 grass species, spanning all three C4 subtypes, to two controlled environmental stresses: low light (200 µmol m-2 sec-1 ) and glacial CO2 (subambient; 180 ppm). We identify a susceptibility within NADP-ME species to glacial CO2 . Notably, although glacial CO2 phenotypes could be tied to C4 subtype, biochemical and transcriptomic responses to glacial CO2 were largely species specific. Nevertheless, we were able to identify subtype specific subsets of significantly differentially expressed transcripts which link resource acquisition and allocation to NADP-ME species susceptibility to glacial CO2 . Here, low light phenotypes were comparable across species with no clear subtype response, while again, transcriptomic responses to low light were largely species specific. However, numerous functional similarities were noted within the transcriptomic responses to low light, suggesting these responses are functionally relatively conserved. Additionally, PEPCK species exhibited heightened regulation of transcripts related to metabolism in response to both stresses, likely tied to their C4 metabolic pathway. These results highlight the influence that both species and subtype can have on plant responses to abiotic stress, building on our mechanistic understanding of acclimation within C4 grasses and highlighting avenues for future crop improvements.
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Affiliation(s)
- Alexander Watson-Lazowski
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
| | - Fiona Koller
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
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15
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Serrano-Bueno G, Said FE, de Los Reyes P, Lucas-Reina EI, Ortiz-Marchena MI, Romero JM, Valverde F. CONSTANS-FKBP12 interaction contributes to modulation of photoperiodic flowering in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1287-1302. [PMID: 31661582 DOI: 10.1111/tpj.14590] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/21/2019] [Indexed: 05/22/2023]
Abstract
Flowering time is a key process in plant development. Photoperiodic signals play a crucial role in the floral transition in Arabidopsis thaliana, and the protein CONSTANS (CO) has a central regulatory function that is tightly regulated at the transcriptional and post-translational levels. The stability of CO protein depends on a light-driven proteasome process that optimizes its accumulation in the evening to promote the production of the florigen FLOWERING LOCUS T (FT) and induce seasonal flowering. To further investigate the post-translational regulation of CO protein we have dissected its interactome network employing in vivo and in vitro assays and molecular genetics approaches. The immunophilin FKBP12 has been identified in Arabidopsis as a CO interactor that regulates its accumulation and activity. FKBP12 and CO interact through the CCT domain, affecting the stability and function of CO. fkbp12 insertion mutants show a delay in flowering time, while FKBP12 overexpression accelerates flowering, and these phenotypes can be directly related to a change in accumulation of FT protein. The interaction is conserved between the Chlamydomonas algal orthologs CrCO-CrFKBP12, revealing an ancient regulatory step in photoperiod regulation of plant development.
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Affiliation(s)
- Gloria Serrano-Bueno
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 49 Americo Vespucio, 41092, Sevilla, Spain
| | - Fatima E Said
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 49 Americo Vespucio, 41092, Sevilla, Spain
| | - Pedro de Los Reyes
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 49 Americo Vespucio, 41092, Sevilla, Spain
| | - Eva I Lucas-Reina
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 49 Americo Vespucio, 41092, Sevilla, Spain
| | - M Isabel Ortiz-Marchena
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 49 Americo Vespucio, 41092, Sevilla, Spain
| | - José M Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 49 Americo Vespucio, 41092, Sevilla, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Reina Mercedes, 41012, Sevilla, Spain
| | - Federico Valverde
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 49 Americo Vespucio, 41092, Sevilla, Spain
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16
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López-Hernández F, Cortés AJ. Last-Generation Genome-Environment Associations Reveal the Genetic Basis of Heat Tolerance in Common Bean ( Phaseolus vulgaris L.). Front Genet 2019; 10:954. [PMID: 31824551 PMCID: PMC6883007 DOI: 10.3389/fgene.2019.00954] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/06/2019] [Indexed: 01/10/2023] Open
Abstract
Genome-environment associations (GEAs) are a powerful strategy for the study of adaptive traits in wild plant populations, yet they still lack behind in the use of modern statistical methods as the ones suggested for genome-wide association studies (GWASs). In order to bridge this gap, we couple GEA with last-generation GWAS algorithms in common bean to identify novel sources of heat tolerance across naturally heterogeneous ecosystems. Common bean (Phaseolus vulgaris L.) is the most important legume for human consumption, and breeding it for resistance to heat stress is key because annual increases in atmospheric temperature are causing decreases in yield of up to 9% for every 1°C. A total of 78 geo-referenced wild accessions, spanning the two gene pools of common bean, were genotyped by sequencing (GBS), leading to the discovery of 23,373 single-nucleotide polymorphism (SNP) markers. Three indices of heat stress were developed for each accession and inputted in last-generation algorithms (i.e. SUPER, FarmCPU, and BLINK) to identify putative associated loci with the environmental heterogeneity in heat stress. Best-fit models revealed 120 significantly associated alleles distributed in all 11 common bean chromosomes. Flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Some of these genes were directly linked to heat-responsive pathways, such as the activation of heat shock proteins (MED23, MED25, HSFB1, HSP40, and HSP20). We also found protein domains related to thermostability in plants such as S1 and Zinc finger A20 and AN1. Other genes were related to biological processes that may correlate with plant tolerance to high temperature, such as time to flowering (MED25, MBD9, and PAP), germination and seedling development (Pkinase_Tyr, Ankyrin-B, and Family Glicosil-hydrolase), cell wall stability (GAE6), and signaling pathway of abiotic stress via abscisic acid (histone-like transcription factors NFYB and phospholipase C) and auxin (Auxin response factor and AUX_IAA). This work offers putative associated loci for marker-assisted and genomic selection for heat tolerance in common bean. It also demonstrates that it is feasible to identify genome-wide environmental associations with modest sample sizes by using a combination of various carefully chosen environmental indices and last-generation GWAS algorithms.
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Affiliation(s)
- Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia) - CI La Selva, Rionegro, Colombia
- Facultad de Ciencias – Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia - Sede Medellín, Medellín, Colombia
| | - Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia) - CI La Selva, Rionegro, Colombia
- Facultad de Ciencias Agrarias - Departamento de Ciencias Forestales, Universidad Nacional de Colombia - Sede Medellín, Medellín, Colombia
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Bulgakov VP, Wu HC, Jinn TL. Coordination of ABA and Chaperone Signaling in Plant Stress Responses. TRENDS IN PLANT SCIENCE 2019; 24:636-651. [PMID: 31085125 DOI: 10.1016/j.tplants.2019.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/09/2019] [Accepted: 04/13/2019] [Indexed: 05/14/2023]
Abstract
The abscisic acid (ABA) and chaperone signaling pathways are the central regulators of plant stress defense. Despite their significance and potential overlap, these systems have been described separately. In this review, we summarize information about mechanisms by which the ABA and chaperone signaling pathways might be coregulated. The central factors that join the ABA and chaperone signaling systems are the SWI/SNF chromatin-remodeling proteins, which are involved in stress memory. A benefit from coordination is that the signals sensed through both the ABA and chaperone signaling systems are perceived and stored via chromatin-remodeling factors. For improving plant stress resistance, we propose new bioengineering strategies, which we term 'bioengineering memory'.
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Affiliation(s)
- Victor P Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity (Institute of Biology and Soil Science), Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., Vladivostok, 690022, Russia; Far Eastern Federal University, Sukhanova Str. 8, 690950, Vladivostok, Russia.
| | - Hui-Chen Wu
- Department of Biological Sciences and Technology, National University of Tainan, Tainan 70005, Taiwan
| | - Tsung-Luo Jinn
- Department of Life Science and Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
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18
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Joseph A, Nagaraja V, Natesh R. Mycobacterial transcript cleavage factor Gre, exhibits chaperone-like activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:757-764. [PMID: 31125617 DOI: 10.1016/j.bbapap.2019.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 05/13/2019] [Accepted: 05/18/2019] [Indexed: 02/05/2023]
Abstract
Gre factors reactivate stalled elongation complexes by enhancing the intrinsic transcript cleavage activity of RNA polymerase. Previous work by us has shown that unlike in Escherichia coli (E.coli), Mycobacterium tuberculosis Gre factor is essential for its survival. Apart from their role in transcription regulation Gre factors have been implicated in stress response. A recent study has shown the role of E.coli GreA as a cellular chaperone, which inhibits aggregation of substrate proteins under heat stress condition. Moreover it was shown that GreA enables E.coli to survive heat shock and oxidative stress. In the current work, we have characterized the moonlighting chaperone activity and its plausible mechanism in Mycobacterium smegmatis Gre (MsGre) factor. We show here that MsGre prevents heat-induced aggregation of the substrate protein and also protects enzymatic activity. Interestingly Gre factor exists as a dimer in solution and does not undergo heat induced oligomerization. From the 8-anilino-1-naphthalene sulfonate (ANS) binding studies MsGre was shown to expose hydrophobic surface upon heat stress that would allow binding to unfolded or partially folded substrate protein. From Circular Dichroism (CD) studies, we also show that MsGre has a stable secondary structure under thermal stress. We propose that the presence of C-terminal FKBP-like fold in MsGre factor that might contribute to its chaperone-like function.
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Affiliation(s)
- Abyson Joseph
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Trivandrum, Kerala 695551, India
| | - Valakunja Nagaraja
- Microbiology and Cell Biology Unit, Indian Institute of Science, Bangalore, Karnataka, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Ramanathan Natesh
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Trivandrum, Kerala 695551, India.
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19
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Bernal-Bayard P, Álvarez C, Calvo P, Castell C, Roncel M, Hervás M, Navarro JA. The singular properties of photosynthetic cytochrome c 550 from the diatom Phaeodactylum tricornutum suggest new alternative functions. PHYSIOLOGIA PLANTARUM 2019; 166:199-210. [PMID: 30499233 DOI: 10.1111/ppl.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
Cytochrome c550 is an extrinsic component in the luminal side of photosystem II (PSII) in cyanobacteria, as well as in eukaryotic algae from the red photosynthetic lineage including, among others, diatoms. We have established that cytochrome c550 from the diatom Phaeodactylum tricornutum can be obtained as a complete protein from the membrane fraction of the alga, although a C-terminal truncated form is purified from the soluble fractions of this diatom as well as from other eukaryotic algae. Eukaryotic cytochromes c550 show distinctive electrostatic features as compared with cyanobacterial cytochrome c550 . In addition, co-immunoseparation and mass spectrometry experiments, as well as immunoelectron microscopy analyses, indicate that although cytochrome c550 from P. tricornutum is mainly located in the thylakoid domain of the chloroplast - where it interacts with PSII - , it can also be found in the chloroplast pyrenoid, related with proteins linked to the CO2 concentrating mechanism and assimilation. These results thus suggest new alternative functions of this heme protein in eukaryotes.
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Affiliation(s)
- Pilar Bernal-Bayard
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Purificación Calvo
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Carmen Castell
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Mercedes Roncel
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - José A Navarro
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
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20
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Mohanta TK, Yadav D, Khan AL, Hashem A, Abd Allah EF, Al-Harrasi A. Molecular Players of EF-hand Containing Calcium Signaling Event in Plants. Int J Mol Sci 2019; 20:E1476. [PMID: 30909616 PMCID: PMC6471108 DOI: 10.3390/ijms20061476] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 11/28/2022] Open
Abstract
Ca2+ is a universal second messenger that plays a pivotal role in diverse signaling mechanisms in almost all life forms. Since the evolution of life from an aquatic to a terrestrial environment, Ca2+ signaling systems have expanded and diversified enormously. Although there are several Ca2+ sensing molecules found in a cell, EF-hand containing proteins play a principal role in calcium signaling event in plants. The major EF-hand containing proteins are calmodulins (CaMs), calmodulin like proteins (CMLs), calcineurin B-like (CBL) and calcium dependent protein kinases (CDPKs/CPKs). CaMs and CPKs contain calcium binding conserved D-x-D motifs in their EF-hands (one motif in each EF-hand) whereas CMLs contain a D-x₃-D motif in the first and second EF-hands that bind the calcium ion. Calcium signaling proteins form a complex interactome network with their target proteins. The CMLs are the most primitive calcium binding proteins. During the course of evolution, CMLs are evolved into CaMs and subsequently the CaMs appear to have merged with protein kinase molecules to give rise to calcium dependent protein kinases with distinct and multiple new functions. Ca2+ signaling molecules have evolved in a lineage specific manner with several of the calcium signaling genes being lost in the monocot lineage.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman.
| | - Dhananjay Yadav
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman.
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
- Mycology and Plant Survey Department, Plant Pathology Research Institute, ARC, Giza 12511, Egypt.
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman.
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Dong Q, Mao K, Duan D, Zhao S, Wang Y, Wang Q, Huang D, Li C, Liu C, Gong X, Ma F. Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple. BMC Genomics 2018; 19:707. [PMID: 30253753 PMCID: PMC6156878 DOI: 10.1186/s12864-018-5097-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 09/20/2018] [Indexed: 12/30/2022] Open
Abstract
Background The FK506-binding proteins (FKBPs) play diverse roles in numerous critical processes for plant growth, development, and abiotic stress responses. However, the FKBP gene family in the important fruit crop apple (Malus × domestica Borkh.) has not been studied as thoroughly as in other species. Our research objective was to investigate the mechanisms by which apple FKBPs enable apple plants to tolerate the effects of abiotic stresses. Results Using bioinformatics-based methods, RT-PCR, and qRT-PCR technologies, we identified 38 FKBP genes and cloned 16 of them in the apple genome. The phylogenetic analysis revealed three major groups within that family. The results from sequence alignments, 3-D structures, phylogenetics, and analyses of conserved domains indicated that apple FKBPs are highly and structurally conserved. Furthermore, genomics structure analysis showed that those genes are also highly and structurally conserved in several other species. Comprehensive qRT-PCR analysis found various expression patterns for MdFKBPs in different tissues and in plant responses to water-deficit and salt stresses. Based on the results from interaction network and co-expression analyses, we determined that the pairing in the MdFKBP62a/MdFKBP65a/b-mediated network is involved in water-deficit and salt-stress signaling, both of which are uniformly up-regulated through interactions with heat shock proteins in apple. Conclusions These results provide new insight for further study of FKBP genes and their functions in abiotic stress response and multiple metabolic and physiological processes in apple. Electronic supplementary material The online version of this article (10.1186/s12864-018-5097-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qinglong Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Dingyue Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yanpeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Qian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Dong Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Changhai Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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Alavilli H, Lee H, Park M, Yun DJ, Lee BH. Enhanced multiple stress tolerance in Arabidopsis by overexpression of the polar moss peptidyl prolyl isomerase FKBP12 gene. PLANT CELL REPORTS 2018; 37:453-465. [PMID: 29247292 DOI: 10.1007/s00299-017-2242-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
PaFKBP12 overexpression in Arabidopsis resulted in stress tolerance to heat, ABA, drought, and salt stress, in addition to growth promotion under normal conditions. Polytrichastrum alpinum (alpine haircap moss) is one of polar organisms that can withstand the severe conditions of the Antarctic. In this study, we report the isolation of a peptidyl prolyl isomerase FKBP12 gene (PaFKBP12) from P. alpinum collected in the Antarctic and its functional implications in development and stress responses in plants. In P. alpinum, PaFKBP12 expression was induced by heat and ABA. Overexpression of PaFKBP12 in Arabidopsis increased the plant size, which appeared to result from increased rates of cell cycle. Under heat stress conditions, PaFKBP12-overexpressing lines (PaFKBP12-OE) showed better growth and survival than the wild type. PaFKBP12-OE also showed higher root elongation rates, better shoot growth and enhanced survival at higher concentrations of ABA in comparison to the wild type. In addition, PaFKBP12-OE were more tolerant to drought and salt stress than the wild type. All these phenotypes were accompanied with higher induction of the stress responsive genes in PaFKBP12-OE than in the wild type. Taken together, our findings revealed important functions of PaFKBP12 in plant development and abiotic stress responses.
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Affiliation(s)
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Mira Park
- Department of Life Science, Sogang University, Seoul, 04107, South Korea
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul, 04107, South Korea.
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Geisler M, Aryal B, di Donato M, Hao P. A Critical View on ABC Transporters and Their Interacting Partners in Auxin Transport. PLANT & CELL PHYSIOLOGY 2017; 58:1601-1614. [PMID: 29016918 DOI: 10.1093/pcp/pcx104] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/18/2017] [Indexed: 05/24/2023]
Abstract
Different subclasses of ATP-binding cassette (ABC) transporters have been implicated in the transport of native variants of the phytohormone auxin. Here, the putative, individual roles of key members belonging to the ABCB, ABCD and ABCG families, respectively, are highlighted and the knowledge of their assumed expression and transport routes is reviewed and compared with their mutant phenotypes. Protein-protein interactions between ABC transporters and regulatory components during auxin transport are summarized and their importance is critically discussed. There is a focus on the functional interaction between members of the ABCB family and the FKBP42, TWISTED DWARF1, acting as a chaperone during plasma membrane trafficking of ABCBs. Further, the mode and relevance of functional ABCB-PIN interactions is diagnostically re-evaluated. A new nomenclature describing precisely the most likely ABCB-PIN interaction scenarios is suggested. Finally, available tools for the detection and prediction of ABC transporter interactomes are summarized and the potential of future ABC transporter interactome maps is highlighted.
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Affiliation(s)
- Markus Geisler
- University of Fribourg, Department of Biology, CH-1700 Fribourg, Switzerland
| | - Bibek Aryal
- University of Fribourg, Department of Biology, CH-1700 Fribourg, Switzerland
| | - Martin di Donato
- University of Fribourg, Department of Biology, CH-1700 Fribourg, Switzerland
| | - Pengchao Hao
- University of Fribourg, Department of Biology, CH-1700 Fribourg, Switzerland
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Bündig C, Jozefowicz AM, Mock HP, Winkelmann T. Proteomic analysis of two divergently responding potato genotypes ( Solanum tuberosum L.) following osmotic stress treatment in vitro. J Proteomics 2016; 143:227-241. [DOI: 10.1016/j.jprot.2016.04.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/20/2016] [Accepted: 04/28/2016] [Indexed: 11/17/2022]
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Zhao B, Lv M, Feng Z, Campbell T, Liscum E, Li J. TWISTED DWARF 1 Associates with BRASSINOSTEROID-INSENSITIVE 1 to Regulate Early Events of the Brassinosteroid Signaling Pathway. MOLECULAR PLANT 2016; 9:582-92. [PMID: 26802250 DOI: 10.1016/j.molp.2016.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 12/10/2015] [Accepted: 01/02/2016] [Indexed: 05/13/2023]
Abstract
A genome-wide screen for mutants showing altered brassinosteroid (BR) sensitivity or bri1-like phenotypes resulted in the identification of two new mutant alleles of TWISTED DWARF 1 (TWD1), twd1-4, and twd1-5. Previous studies indicated that TWD1, also named as ULTRACURVATA 2 or FKBP42, associates with auxin efflux transporters and is essential for their biological functions. Although earlier reports showed that BR signaling is downregulated in twd1, how TWD1 is integrated in BR signaling has not been elucidated. Here, we provide genetic and biochemical evidence demonstrating that TWD1 interacts with the BR receptor BRI1 in vivo in a BR-independent manner. Further analyses indicated that TWD1 modulates the BR signal transduction not by altering ER quality control or protein abundance of BRI1; instead, TWD1 appears to be critical in BR-induced interaction of BRI1 and its co-receptor BAK1, as well as BR-induced phosphorylation of these two proteins. These results provide better understanding of the early events of the BR signaling pathway.
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Affiliation(s)
- Baolin Zhao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Minghui Lv
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zengxiu Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Thomas Campbell
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Emmanuel Liscum
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA; C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Tomašić Paić A, Fulgosi H. Chloroplast immunophilins. PROTOPLASMA 2016; 253:249-258. [PMID: 25963286 DOI: 10.1007/s00709-015-0828-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/30/2015] [Indexed: 06/04/2023]
Abstract
Immunophilins occur in almost all living organisms. They are ubiquitously expressed proteins including cyclophilins, FK506/rapamycin-binding proteins, and parvulins. Their functional significance in vascular plants is mostly related to plant developmental processes, signalling, and regulation of photosynthesis. Enzymatically active immunophilins catalyse isomerization of proline imidic peptide bonds and assist in rapid folding of nascent proline-containing polypeptides. They also participate in protein trafficking and assembly of supramolecular protein complexes. Complex immunophilins possess various additional functional domains associated with a multitude of molecular interactions. A considerable number of immunophilins act as auxiliary and/or regulatory proteins in highly specialized cellular compartments, such as lumen of thylakoids. In this review, we present a comprehensive overview of so far identified chloroplast immunophilins that assist in specific assembly/repair processes necessary for the maintenance of efficient photosynthetic energy conversion.
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Affiliation(s)
- Ana Tomašić Paić
- Division of Molecular Biology, Rudjer Bošković Institute, Bijenička cesta 54, HR-10002, Zagreb, Croatia
| | - Hrvoje Fulgosi
- Division of Molecular Biology, Rudjer Bošković Institute, Bijenička cesta 54, HR-10002, Zagreb, Croatia.
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Cregeen S, Radisek S, Mandelc S, Turk B, Stajner N, Jakse J, Javornik B. Different Gene Expressions of Resistant and Susceptible Hop Cultivars in Response to Infection with a Highly Aggressive Strain of Verticillium albo-atrum. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:689-704. [PMID: 25999664 PMCID: PMC4432018 DOI: 10.1007/s11105-014-0767-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Verticillium wilt has become a serious threat to hop production in Europe due to outbreaks of lethal wilt caused by a highly virulent strain of Verticillium albo-atrum. In order to enhance our understanding of resistance mechanisms, the fungal colonization patterns and interactions of resistant and susceptible hop cultivars infected with V. albo-atrum were analysed in time course experiments. Quantification of fungal DNA showed marked differences in spatial and temporal fungal colonization patterns in the two cultivars. Two differential display methods obtained 217 transcripts with altered expression, of which 84 showed similarity to plant proteins and 8 to fungal proteins. Gene ontology categorised them into cellular and metabolic processes, response to stimuli, biological regulation, biogenesis and localization. The expression patterns of 17 transcripts with possible implication in plant immunity were examined by real-time PCR (RT-qPCR). Our results showed strong expression of genes encoding pathogenesis-related (PR) proteins in susceptible plants and strong upregulation of genes implicated in ubiquitination and vesicle trafficking in the incompatible interaction and their downregulation in susceptible plants, suggesting the involvement of these processes in the hop resistance reaction. In the resistant cultivar, the RT-qPCR expression patterns of most genes showed their peak at 20 dpi and declined towards 30 dpi, comparable to the gene expression pattern of in planta detected fungal protein and coinciding with the highest fungal biomass in plants at 15 dpi. These expression patterns suggest that the defence response in the resistant cultivar is strong enough at 20 dpi to restrict further fungus colonization.
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Affiliation(s)
- Sara Cregeen
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sebastjan Radisek
- Slovenian Institute for Hop Research and Brewing, Cesta ŽalskegaTabora 2, SI-3320 Žalec, Slovenia
| | - Stanislav Mandelc
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Natasa Stajner
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Jernej Jakse
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Branka Javornik
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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Plant immunophilins: a review of their structure-function relationship. Biochim Biophys Acta Gen Subj 2014; 1850:2145-58. [PMID: 25529299 DOI: 10.1016/j.bbagen.2014.12.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 01/02/2023]
Abstract
BACKGROUND Originally discovered as receptors for immunosuppressive drugs, immunophilins consist of two major groups, FK506 binding proteins (FKBPs) and cyclosporin A binding proteins (cyclophilins, CYPs). Many members in both FKBP and CYP families are peptidyl prolyl isomerases that are involved in protein folding processes, though they share little sequence homology. It is not surprising to find immunophilins in all organisms examined so far, including viruses, bacteria, fungi, plants and animals, as protein folding represents a common process in all living systems. SCOPE OF REVIEW Studies on plant immunophilins have revealed new functions beyond protein folding and new structural properties beyond that of typical PPIases. This review focuses on the structural and functional diversity of plant FKBPs and CYPs. MAJOR CONCLUSIONS The differences in sequence, structure as well as subcellular localization, have added on to the diversity of this family of molecular chaperones. In particular, the large number of immunophilins present in the thylakoid lumen of the photosynthetic organelle, promises to deliver insights into the regulation of photosynthesis, a unique feature of plant systems. However, very little structural information and functional data are available for plant immunophilins. GENERAL SIGNIFICANCE Studies on the structure and function of plant immunophilins are important in understanding their role in plant biology. By reviewing the structural and functional properties of some immunophilins that represent the emerging area of research in plant biology, we hope to increase the interest of researchers in pursuing further research in this area. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Hanes SD. Prolyl isomerases in gene transcription. Biochim Biophys Acta Gen Subj 2014; 1850:2017-34. [PMID: 25450176 DOI: 10.1016/j.bbagen.2014.10.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Peptidyl-prolyl isomerases (PPIases) are enzymes that assist in the folding of newly-synthesized proteins and regulate the stability, localization, and activity of mature proteins. They do so by catalyzing reversible (cis-trans) rotation about the peptide bond that precedes proline, inducing conformational changes in target proteins. SCOPE OF REVIEW This review will discuss how PPIases regulate gene transcription by controlling the activity of (1) DNA-binding transcription regulatory proteins, (2) RNA polymerase II, and (3) chromatin and histone modifying enzymes. MAJOR CONCLUSIONS Members of each family of PPIase (cyclophilins, FKBPs, and parvulins) regulate gene transcription at multiple levels. In all but a few cases, the exact mechanisms remain elusive. Structure studies, development of specific inhibitors, and new methodologies for studying cis/trans isomerization in vivo represent some of the challenges in this new frontier that merges two important fields. GENERAL SIGNIFICANCE Prolyl isomerases have been found to play key regulatory roles in all phases of the transcription process. Moreover, PPIases control upstream signaling pathways that regulate gene-specific transcription during development, hormone response and environmental stress. Although transcription is often rate-limiting in the production of enzymes and structural proteins, post-transcriptional modifications are also critical, and PPIases play key roles here as well (see other reviews in this issue). This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Steven D Hanes
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E Adams St., Syracuse, NY 13210 USA.
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Ifuku K. The PsbP and PsbQ family proteins in the photosynthetic machinery of chloroplasts. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 81:108-14. [PMID: 24477118 DOI: 10.1016/j.plaphy.2014.01.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/03/2014] [Indexed: 05/06/2023]
Abstract
The PsbP and PsbQ proteins are extrinsic subunits of the photosystem II in eukaryotic photosynthetic organisms including higher plants, green algae and euglena. It has been suggested that PsbP and PsbQ have evolved from their cyanobacterial homologs, while considerable genetic and functional modifications have occurred to generate the eukaryote-type proteins. In addition, number of PsbP and PsbQ homologs exist in the thylakoid lumen of chloroplasts. These homologs are nuclear-encoded and likely diverged by gene duplication, and recent studies have elucidated their various functions in the photosynthetic machinery. In this short review, recent findings and new idea about these components will be discussed.
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Affiliation(s)
- Kentaro Ifuku
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.
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31
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Lu YB, Yang LT, Qi YP, Li Y, Li Z, Chen YB, Huang ZR, Chen LS. Identification of boron-deficiency-responsive microRNAs in Citrus sinensis roots by Illumina sequencing. BMC PLANT BIOLOGY 2014; 14:123. [PMID: 24885979 PMCID: PMC4041134 DOI: 10.1186/1471-2229-14-123] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/30/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Boron (B)-deficiency is a widespread problem in many crops, including Citrus. MicroRNAs (miRNAs) play important roles in nutrient deficiencies. However, little is known on B-deficiency-responsive miRNAs in plants. In this study, we first identified miRNAs and their expression pattern in B-deficient Citrus sinensis roots by Illumina sequencing in order to identify miRNAs that might be involved in the tolerance of plants to B-deficiency. RESULTS We isolated 52 (40 known and 12 novel) up-regulated and 82 (72 known and 10 novel) down-regulated miRNAs from B-deficient roots, demonstrating remarkable metabolic flexibility of roots, which might contribute to the tolerance of plants to B-deficiency. A model for the possible roles of miRNAs in the tolerance of roots to B-deficiency was proposed. miRNAs might regulate the adaptations of roots to B-deficiency through following several aspects: (a) inactivating reactive oxygen species (ROS) signaling and scavenging through up-regulating miR474 and down-regulating miR782 and miR843; (b) increasing lateral root number by lowering miR5023 expression and maintaining a certain phenotype favorable for B-deficiency-tolerance by increasing miR394 expression; (c) enhancing cell transport by decreasing the transcripts of miR830, miR5266 and miR3465; (d) improving osmoprotection (miR474) and regulating other metabolic reactions (miR5023 and miR821). Other miRNAs such as miR472 and miR2118 in roots increased in response to B-deficiency, thus decreasing the expression of their target genes, which are involved in disease resistance, and hence, the disease resistance of roots. CONCLUSIONS Our work demonstrates the possible roles of miRNAs and related mechanisms in the response of plant roots to B-deficiency.
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Affiliation(s)
- Yi-Bin Lu
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin-Tong Yang
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China
| | - Yan Li
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong Li
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan-Bin Chen
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeng-Rong Huang
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Phukan UJ, Mishra S, Timbre K, Luqman S, Shukla RK. Mentha arvensis exhibit better adaptive characters in contrast to Mentha piperita when subjugated to sustained waterlogging stress. PROTOPLASMA 2014; 251:603-614. [PMID: 24154494 DOI: 10.1007/s00709-013-0561-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/02/2013] [Indexed: 05/29/2023]
Abstract
Waterlogging is becoming a critical threat to plants growing in areas prone to flooding. Some plants adapt various morphological and biochemical alterations which are regulated transcriptionally to cope with the situation. A comparative study of waterlogging response in two different varieties of Mentha namely Mentha piperita and Mentha arvensis was performed. M. arvensis showed better response towards waterlogging in comparison to M. piperita. M. arvensis maintained a healthy posture by utilizing its carbohydrate content; also, it showed a flourished vegetative growth under waterlogged condition. Soluble protein, chlorophyll content, relative water content, and nitric oxide scavenging activity were comparatively more salient in M. arvensis during this hypoxia treatment. Lipid peroxidation was less in M. arvensis. M. arvensis also showed vigorous outgrowth of adventitious roots to assist waterlogging tolerance. To further investigate the possible gene transcripts involved in this response, we did cDNA subtraction of waterlogging treated M. piperita and M. arvensis seedlings. cDNA subtraction has identified thirty seven novel putative Expressed Sequence Tags which were further classified functionally. Functional classification revealed that maximum percentage of proteins belonged to hypothetical proteins followed by proteins involved in biosynthesis. Some of the identified ESTs were further quantified for their induced expression in M. arvensis in comparison to M. piperita through quantitative real-time PCR.
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Affiliation(s)
- Ujjal J Phukan
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
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Järvi S, Gollan PJ, Aro EM. Understanding the roles of the thylakoid lumen in photosynthesis regulation. FRONTIERS IN PLANT SCIENCE 2013; 4:434. [PMID: 24198822 PMCID: PMC3813922 DOI: 10.3389/fpls.2013.00434] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/12/2013] [Indexed: 05/20/2023]
Abstract
It has been known for a long time that the thylakoid lumen provides the environment for oxygen evolution, plastocyanin-mediated electron transfer, and photoprotection. More recently lumenal proteins have been revealed to play roles in numerous processes, most often linked with regulating thylakoid biogenesis and the activity and turnover of photosynthetic protein complexes, especially the photosystem II and NAD(P)H dehydrogenase-like complexes. Still, the functions of the majority of lumenal proteins in Arabidopsis thaliana are unknown. Interestingly, while the thylakoid lumen proteome of at least 80 proteins contains several large protein families, individual members of many protein families have highly divergent roles. This is indicative of evolutionary pressure leading to neofunctionalization of lumenal proteins, emphasizing the important role of the thylakoid lumen for photosynthetic electron transfer and ultimately for plant fitness. Furthermore, the involvement of anterograde and retrograde signaling networks that regulate the expression and activity of lumen proteins is increasingly pertinent. Recent studies have also highlighted the importance of thiol/disulfide modulation in controlling the functions of many lumenal proteins and photosynthetic regulation pathways.
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Affiliation(s)
| | | | - Eva-Mari Aro
- *Correspondence: Eva-Mari Aro, Molecular Plant Biology, Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland e-mail:
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Miernyk JA, Johnston ML. Proteomic analysis of the testa from developing soybean seeds. J Proteomics 2013; 89:265-72. [PMID: 23707235 DOI: 10.1016/j.jprot.2013.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 01/20/2023]
Abstract
Soybean (Glycine max (L.) Merr. cv Jack) seed development was separated into nine defined stages (S1 to S9). Testa (seed coats) were removed from developing seeds at stages S2, 4, 6, 8, and 9, and subjected to shotgun proteomic profiling. For each stage "total proteins" were isolated from 150 mg dry weight of seed coat using a phenol-based method, then reduced, alkylated, and digested with trypsin. The tryptic peptides were separated using a C18-reversed phase matrix, then analyzed using an LTQ Orbitrap Mass Spectrometer. Spectra were searched against the Phytozome G. max DB using the Sorcerer 2 IDA Sequest-based search algorithm. Identities were verified using Scaffold 3. A total of 306 (S2), 328 (S4), 273 (S6), 193 (S8), and 272 (S9) proteins were identified in three out of three biological replicates, and sorted into 11 functional groups: Primary Metabolism, Secondary Metabolism, Cellular Structure, Stress Responses, Nucleic Acid metabolism, Protein Synthesis, Protein Folding, Protein Targeting, Hormones and Signaling, Seed Storage Proteins, and Proteins of Unknown Function. In selected instances, individual seed coat proteins were quantified by spectral counting. The number of proteins involved in intermediary metabolism, flavonoid biosynthesis, protein folding and degradation are discussed as they relate to seed coat function. BIOLOGICAL SIGNIFICANCE Most previous analyses of seed coats have either targeted individual enzymes or used the results from high-throughput transcript profiling to infer biological function. Because there is seldom a linear correlation between transcript and protein levels, we have undertaken a shotgun proteomics-based description of soybean (G. max (L.) Merr. cv Jack) seed coats, as a function of development, in order to bridge this gap and to establish the baseline for a more comprehensive understanding of seed biology.
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Affiliation(s)
- Ján A Miernyk
- USDA, Agricultural Research Service, Plant Genetics Research Unit, USA.
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Delic M, Valli M, Graf AB, Pfeffer M, Mattanovich D, Gasser B. The secretory pathway: exploring yeast diversity. FEMS Microbiol Rev 2013; 37:872-914. [PMID: 23480475 DOI: 10.1111/1574-6976.12020] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 02/14/2013] [Accepted: 02/17/2013] [Indexed: 12/11/2022] Open
Abstract
Protein secretion is an essential process for living organisms. In eukaryotes, this encompasses numerous steps mediated by several hundred cellular proteins. The core functions of translocation through the endoplasmic reticulum membrane, primary glycosylation, folding and quality control, and vesicle-mediated secretion are similar from yeasts to higher eukaryotes. However, recent research has revealed significant functional differences between yeasts and mammalian cells, and even among diverse yeast species. This review provides a current overview of the canonical protein secretion pathway in the model yeast Saccharomyces cerevisiae, highlighting differences to mammalian cells as well as currently unresolved questions, and provides a genomic comparison of the S. cerevisiae pathway to seven other yeast species where secretion has been investigated due to their attraction as protein production platforms, or for their relevance as pathogens. The analysis of Candida albicans, Candida glabrata, Kluyveromyces lactis, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, and Schizosaccharomyces pombe reveals that many - but not all - secretion steps are more redundant in S. cerevisiae due to duplicated genes, while some processes are even absent in this model yeast. Recent research obviates that even where homologous genes are present, small differences in protein sequence and/or differences in the regulation of gene expression may lead to quite different protein secretion phenotypes.
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Affiliation(s)
- Marizela Delic
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
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