1
|
Xue M, Han X, Zhang L, Chen S. Heat-Resistant Inbred Lines Coordinate the Heat Response Gene Expression Remarkably in Maize ( Zea mays L.). Genes (Basel) 2024; 15:289. [PMID: 38540348 PMCID: PMC10970198 DOI: 10.3390/genes15030289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/10/2024] [Accepted: 02/18/2024] [Indexed: 06/14/2024] Open
Abstract
High temperatures are increasingly becoming a prominent environmental factor accelerating the adverse influence on the growth and development of maize (Zea mays L.). Therefore, it is critical to identify the key genes and pathways related to heat stress (HS) tolerance in maize. Great challenges have been faced in dissecting genetic mechanisms and uncovering master genes for HS tolerance. Here, Z58D showed more thermotolerance than AF171 at the seedling stage with a lower wilted leaf rate and H2O2 accumulation under HS conditions. Transcriptomic analysis identified 3006 differentially expressed genes (DEGs) in AF171 and 4273 DEGs in Z58D under HS treatments, respectively. Subsequently, GO enrichment analysis showed that commonly upregulated genes in AF171 and Z58D were significantly enriched in the following biological processes, including protein folding, response to heat, response to temperature stimulus and response to hydrogen peroxide. Moreover, the comparison between the two inbred lines under HS showed that response to heat and response to temperature stimulus were significantly over-represented for the 1234 upregulated genes in Z58D. Furthermore, more commonly upregulated genes exhibited higher expression levels in Z58D than AF171. In addition, maize inbred CIMBL55 was verified to be more tolerant than B73, and more commonly upregulated genes also showed higher expression levels in CIMBL55 than B73 under HS. These consistent results indicate that heat-resistant inbred lines may coordinate the remarkable expression of genes in order to recover from HS. Additionally, 35 DEGs were conserved among five inbred lines via comparative transcriptomic analysis. Most of them were more pronounced in Z58D than AF171 at the expression levels. These candidate genes may confer thermotolerance in maize.
Collapse
Affiliation(s)
- Ming Xue
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China (L.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyue Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China (L.Z.)
| | - Luyao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China (L.Z.)
| | - Saihua Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China (L.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
2
|
Dong-Chen X, Yong C, Yang X, Chen-Yu S, Li-Hua P. Signaling pathways in Parkinson's disease: molecular mechanisms and therapeutic interventions. Signal Transduct Target Ther 2023; 8:73. [PMID: 36810524 PMCID: PMC9944326 DOI: 10.1038/s41392-023-01353-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 01/16/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide, and its treatment remains a big challenge. The pathogenesis of PD may be related to environmental and genetic factors, and exposure to toxins and gene mutations may be the beginning of brain lesions. The identified mechanisms of PD include α-synuclein aggregation, oxidative stress, ferroptosis, mitochondrial dysfunction, neuroinflammation, and gut dysbiosis. The interactions among these molecular mechanisms complicate the pathogenesis of PD and pose great challenges to drug development. At the same time, the diagnosis and detection of PD are also one of obstacles to the treatment of PD due to its long latency and complex mechanism. Most conventional therapeutic interventions for PD possess limited effects and have serious side effects, heightening the need to develop novel treatments for this disease. In this review, we systematically summarized the pathogenesis, especially the molecular mechanisms of PD, the classical research models, clinical diagnostic criteria, and the reported drug therapy strategies, as well as the newly reported drug candidates in clinical trials. We also shed light on the components derived from medicinal plants that are newly identified for their effects in PD treatment, with the expectation to provide the summary and outlook for developing the next generation of drugs and preparations for PD therapy.
Collapse
Affiliation(s)
- Xu Dong-Chen
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, P. R. China
| | - Chen Yong
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, P. R. China
| | - Xu Yang
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, P. R. China
| | - ShenTu Chen-Yu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, P. R. China
| | - Peng Li-Hua
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, P. R. China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, P. R. China.
| |
Collapse
|
3
|
Zhang L, Zhu X, Zhao Y, Guo J, Zhang T, Huang W, Huang J, Hu Y, Huang CH, Ma H. Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution. Mol Biol Evol 2022; 39:6521033. [PMID: 35134207 PMCID: PMC8844509 DOI: 10.1093/molbev/msac026] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.
Collapse
Affiliation(s)
- Lin Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xinxin Zhu
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Weichen Huang
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Jie Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
4
|
Han SH, Kim JY, Lee JH, Park CM. Safeguarding genome integrity under heat stress in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab355. [PMID: 34343307 DOI: 10.1093/jxb/erab355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Heat stress adversely affects an array of molecular and cellular events in plant cells, such as denaturation of protein and lipid molecules and malformation of cellular membranes and cytoskeleton networks. Genome organization and DNA integrity are also disturbed under heat stress, and accordingly, plants have evolved sophisticated adaptive mechanisms that either protect their genomes from deleterious heat-induced damages or stimulate genome restoration responses. In particular, it is emerging that DNA damage responses are a critical defense process that underlies the acquirement of thermotolerance in plants, during which molecular players constituting the DNA repair machinery are rapidly activated. In recent years, thermotolerance genes that mediate the maintenance of genome integrity or trigger DNA repair responses have been functionally characterized in various plant species. Furthermore, accumulating evidence supports that genome integrity is safeguarded through multiple layers of thermoinduced protection routes in plant cells, including transcriptome adjustment, orchestration of RNA metabolism, protein homeostasis, and chromatin reorganization. In this review, we summarize topical progresses and research trends in understanding how plants cope with heat stress to secure genome intactness. We focus on molecular regulatory mechanisms by which plant genomes are secured against the DNA-damaging effects of heat stress and DNA damages are effectively repaired. We will also explore the practical interface between heat stress response and securing genome integrity in view of developing biotechnological ways of improving thermotolerance in crop species under global climate changes, a worldwide ecological concern in agriculture.
Collapse
Affiliation(s)
- Shin-Hee Han
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Jae Young Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - June-Hee Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| |
Collapse
|
5
|
Sun JL, Li JY, Wang MJ, Song ZT, Liu JX. Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives. MOLECULAR PLANT 2021; 14:95-114. [PMID: 33137518 DOI: 10.1016/j.molp.2020.10.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/09/2020] [Accepted: 10/28/2020] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein homeostasis in these organelles, maintained by a balance between protein synthesis and degradation, is essential for cell functions during plant growth, development, and stress resistance. Nucleus-encoded chloroplast- and mitochondrion-targeted proteins and ER-resident proteins are imported from the cytosol and undergo modification and maturation within their respective organelles. Protein folding is an error-prone process that is influenced by both developmental signals and environmental cues; a number of mechanisms have evolved to ensure efficient import and proper folding and maturation of proteins in plant organelles. Misfolded or damaged proteins with nonnative conformations are subject to degradation via complementary or competing pathways: intraorganelle proteases, the organelle-associated ubiquitin-proteasome system, and the selective autophagy of partial or entire organelles. When proteins in nonnative conformations accumulate, the organelle-specific unfolded protein response operates to restore protein homeostasis by reducing protein folding demand, increasing protein folding capacity, and enhancing components involved in proteasome-associated protein degradation and autophagy. This review summarizes recent progress on the understanding of protein quality control in the ER, chloroplasts, and mitochondria in plants, with a focus on common mechanisms shared by these organelles during protein homeostasis.
Collapse
Affiliation(s)
- Jing-Liang Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Mei-Jing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Ze-Ting Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
| |
Collapse
|
6
|
Walden N, Lucek K, Willi Y. Lineage‐specific adaptation to climate involves flowering time in North American
Arabidopsis lyrata. Mol Ecol 2020; 29:1436-1451. [DOI: 10.1111/mec.15338] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/16/2019] [Accepted: 12/10/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Nora Walden
- Department of Environmental Sciences University of Basel Basel Switzerland
- Centre for Organismal Studies Heidelberg University of Heidelberg Heidelberg Germany
| | - Kay Lucek
- Department of Environmental Sciences University of Basel Basel Switzerland
| | - Yvonne Willi
- Department of Environmental Sciences University of Basel Basel Switzerland
| |
Collapse
|
7
|
Huber CV, Jakobs BD, Mishra LS, Niedermaier S, Stift M, Winter G, Adamska I, Funk C, Huesgen PF, Funck D. DEG10 contributes to mitochondrial proteostasis, root growth, and seed yield in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5423-5436. [PMID: 31225599 PMCID: PMC6793672 DOI: 10.1093/jxb/erz294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 06/11/2019] [Indexed: 05/04/2023]
Abstract
Maintaining mitochondrial proteome integrity is especially important under stress conditions to ensure a continued ATP supply for protection and adaptation responses in plants. Deg/HtrA proteases are important factors in the cellular protein quality control system, but little is known about their function in mitochondria. Here we analyzed the expression pattern and physiological function of Arabidopsis thaliana DEG10, which has homologs in all photosynthetic eukaryotes. Both expression of DEG10:GFP fusion proteins and immunoblotting after cell fractionation showed an unambiguous subcellular localization exclusively in mitochondria. DEG10 promoter:GUS fusion constructs showed that DEG10 is expressed in trichomes but also in the vascular tissue of roots and aboveground organs. DEG10 loss-of-function mutants were impaired in root elongation, especially at elevated temperature. Quantitative proteome analysis revealed concomitant changes in the abundance of mitochondrial respiratory chain components and assembly factors, which partially appeared to depend on altered mitochondrial retrograde signaling. Under field conditions, lack of DEG10 caused a decrease in seed production. Taken together, our findings demonstrate that DEG10 affects mitochondrial proteostasis, is required for optimal root development and seed set under challenging environmental conditions, and thus contributes to stress tolerance of plants.
Collapse
Affiliation(s)
- Catharina V Huber
- Department of Biology, University of Konstanz, Universitätsstraße, Konstanz, Germany
| | - Barbara D Jakobs
- Department of Biology, University of Konstanz, Universitätsstraße, Konstanz, Germany
| | - Laxmi S Mishra
- Department of Chemistry, Umeå University, Linnaeus väg, Umeå, Sweden
| | - Stefan Niedermaier
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Marc Stift
- Department of Biology, University of Konstanz, Universitätsstraße, Konstanz, Germany
| | - Gudrun Winter
- Department of Biology, University of Konstanz, Universitätsstraße, Konstanz, Germany
| | - Iwona Adamska
- Department of Biology, University of Konstanz, Universitätsstraße, Konstanz, Germany
| | - Christiane Funk
- Department of Chemistry, Umeå University, Linnaeus väg, Umeå, Sweden
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
- Medical Faculty and University Hospital, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Dietmar Funck
- Department of Biology, University of Konstanz, Universitätsstraße, Konstanz, Germany
| |
Collapse
|
8
|
Broda M, Millar AH, Van Aken O. Mitophagy: A Mechanism for Plant Growth and Survival. TRENDS IN PLANT SCIENCE 2018; 23:434-450. [PMID: 29576328 DOI: 10.1016/j.tplants.2018.02.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/13/2018] [Accepted: 02/23/2018] [Indexed: 05/17/2023]
Abstract
Mitophagy is a conserved cellular process that is important for autophagic removal of damaged mitochondria to maintain a healthy mitochondrial population. Mitophagy also appears to occur in plants and has roles in development, stress response, senescence, and programmed cell death. However, many of the genes that control mitophagy in yeast and animal cells are absent from plants, and no plant proteins marking defunct mitochondria for autophagic degradation are yet known. New insights implicate general autophagy-related proteins in mitophagy, affecting the senescence of plant tissues. Mitophagy control and its importance for energy metabolism, survival, signaling, and cell death in plants are discussed. Furthermore, we suggest mitochondrial membrane proteins containing ATG8-interacting motifs, which might serve as mitophagy receptor proteins in plant mitochondria.
Collapse
Affiliation(s)
- Martyna Broda
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - A Harvey Millar
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - Olivier Van Aken
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden.
| |
Collapse
|
9
|
The genetics of Parkinson disease. Ageing Res Rev 2018; 42:72-85. [PMID: 29288112 DOI: 10.1016/j.arr.2017.12.007] [Citation(s) in RCA: 330] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 12/21/2022]
Abstract
About 15% of patients with Parkinson disease (PD) have family history and 5-10% have a monogenic form of the disease with Mendelian inheritance. To date, at least 23 loci and 19 disease-causing genes for parkinsonism have been found, but many more genetic risk loci and variants for sporadic PD phenotype have been identified in various association studies. Investigating the mutated protein products has uncovered potential pathogenic pathways that provide insights into mechanisms of neurodegeneration in familial and sporadic PD. To commemorate the 200th anniversary of Parkinson's publication of An Essay on the Shaking Palsy, we provide a comprehensive and critical overview of the current clinical, neuropathological, and genetic understanding of genetic forms of PD. We also discuss advances in screening for genetic PD-related risk factors and how they impact genetic counseling and contribute to the development of potential disease-modifying therapies.
Collapse
|
10
|
Majsec K, Bhuiyan NH, Sun Q, Kumari S, Kumar V, Ware D, van Wijk KJ. The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. THE PLANT CELL 2017; 29:2687-2710. [PMID: 28947489 PMCID: PMC5728138 DOI: 10.1105/tpc.17.00481] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/29/2017] [Accepted: 09/21/2017] [Indexed: 05/17/2023]
Abstract
Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.
Collapse
Affiliation(s)
- Kristina Majsec
- Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Nazmul H Bhuiyan
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853
| | - Sunita Kumari
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Vivek Kumar
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Doreen Ware
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Klaas J van Wijk
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
| |
Collapse
|
11
|
Kissen R, Øverby A, Winge P, Bones AM. Allyl-isothiocyanate treatment induces a complex transcriptional reprogramming including heat stress, oxidative stress and plant defence responses in Arabidopsis thaliana. BMC Genomics 2016; 17:740. [PMID: 27639974 PMCID: PMC5027104 DOI: 10.1186/s12864-016-3039-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/24/2016] [Indexed: 01/30/2023] Open
Abstract
Background Isothiocyanates (ITCs) are degradation products of the plant secondary metabolites glucosinolates (GSLs) and are known to affect human health as well as plant herbivores and pathogens. To investigate the processes engaged in plants upon exposure to isothiocyanate we performed a genome scale transcriptional profiling of Arabidopsis thaliana at different time points in response to an exogenous treatment with allyl-isothiocyanate. Results The treatment triggered a substantial response with the expression of 431 genes affected (P < 0.05 and log2 ≥ 1 or ≤ -1) already after 30 min and that of 3915 genes affected after 9 h of exposure, most of the affected genes being upregulated. These are involved in a considerable number of different biological processes, some of which are described in detail: glucosinolate metabolism, sulphate uptake and assimilation, heat stress response, oxidative stress response, elicitor perception, plant defence and cell death mechanisms. Conclusion Exposure of Arabidopsis thaliana to vapours of allyl-isothiocyanate triggered a rapid and substantial transcriptional response affecting numerous biological processes. These include multiple stress stimuli such as heat stress response and oxidative stress response, cell death and sulphur secondary defence metabolism. Hence, effects of isothiocyanates on plants previously reported in the literature were found to be regulated at the gene expression level. This opens some avenues for further investigations to decipher the molecular mechanisms underlying the effects of isothiocyanates on plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3039-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ralph Kissen
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Anders Øverby
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.,Present address: Center for Clinical Pharmacy and Clinical Sciences, School of Pharmaceutical Sciences, Kitasato University, Minato-ku, Tokyo, Japan
| | - Per Winge
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Atle M Bones
- Department of Biology, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
| |
Collapse
|
12
|
Fernandez-Caggiano M, Schröder E, Cho HJ, Burgoyne J, Barallobre-Barreiro J, Mayr M, Eaton P. Oxidant-induced Interprotein Disulfide Formation in Cardiac Protein DJ-1 Occurs via an Interaction with Peroxiredoxin 2. J Biol Chem 2016; 291:10399-410. [PMID: 26945066 DOI: 10.1074/jbc.m115.699850] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 12/24/2022] Open
Abstract
The role and responses of the dimeric DJ-1 protein to cardiac oxidative stress is incompletely understood. H2O2 induces a 50-kDa DJ-1 interprotein homodimer disulfide, known to form between Cys-53 on each subunit. A trimeric 75-kDa DJ-1 complex that mass spectrometry shows contained 2-Cys peroxiredoxin also formed and precedes the appearance of the disulfide dimer. These observations may represent peroxiredoxin sensing and transducing the oxidant signal to DJ-1. The dimeric disulfide DJ-1 complex was stabilized by auranofin, suggesting that thioredoxin recycles it in cells. Higher concentrations of H2O2 concomitantly induce DJ-1 Cys-106 hyperoxidation (sulfination or sulfonation) in myocytes, perfused heart, or HEK cells. An oxidation-resistant C53A DJ-1 shows potentiated H2O2-induced Cys-106 hyperoxidation. DJ-1 also forms multiple disulfides with unknown target proteins during H2O2 treatment, the formation of which is also potentiated in cells expressing the C53A mutant. This suggests that the intersubunit disulfide induces a conformational change that limits Cys-106 forming heterodisulfide protein complexes or from hyperoxidizing. High concentrations of H2O2 also induce cell death, with DJ-1 Cys-106 sulfonation appearing causal in these events, as expressionof C53A DJ-1 enhanced both Cys-106 sulfonation and cell death. Nonetheless, expression of the DJ-1 C106A mutant, which fully prevents hyperoxidation, also showed exacerbated cell death responses to H2O2 A rational explanation for these findings is that DJ-1 Cys-106 forms disulfides with target proteins to limit oxidant-induced cell death. However, when Cys-106 is hyperoxidized, formation of these potentially protective heterodimeric disulfide complexes is limited, and so cell death is exacerbated.
Collapse
Affiliation(s)
- Mariana Fernandez-Caggiano
- From the King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom and
| | - Ewald Schröder
- From the King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom and
| | - Hyun-Ju Cho
- From the King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom and
| | - Joseph Burgoyne
- From the King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom and
| | - Javier Barallobre-Barreiro
- King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The James Black Centre, King's College Hospital, London SE5 9NU, United Kingdom
| | - Manuel Mayr
- King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The James Black Centre, King's College Hospital, London SE5 9NU, United Kingdom
| | - Philip Eaton
- From the King's College London, Cardiovascular Division, The British Heart Foundation Centre of Excellence, The Rayne Institute, St. Thomas' Hospital, London SE1 7EH, United Kingdom and
| |
Collapse
|
13
|
A Proteomics Approach to Investigate miR-153-3p and miR-205-5p Targets in Neuroblastoma Cells. PLoS One 2015; 10:e0143969. [PMID: 26633009 PMCID: PMC4669106 DOI: 10.1371/journal.pone.0143969] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/11/2015] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are key regulators associated with numerous diseases. In HEK293 cells, miR-153-3p and miR-205-5p down-regulate alpha-synuclein (SNCA) and Leucine-rich repeat kinase 2 (LRRK2), two key proteins involved in Parkinson’s disease (PD). We have used two-dimensional gel electrophoresis (2D-PAGE) coupled to mass spectrometry (MS) to identify a spectrum of miR-153-3p and miR-205-5p targets in neuronal SH-SY5Y cells. We overexpressed and inhibited both microRNAs in SH-SY5Y cells and through comparative proteomics profiling we quantified ~240 protein spots from each analysis. Combined, thirty-three protein spots were identified showing significant (p-value < 0.05) changes in abundance. Modulation of miR-153-3p resulted in seven up-regulated proteins and eight down-regulated proteins. miR-205 modulation resulted in twelve up-regulated proteins and six down-regulated proteins. Several of the proteins are associated with neuronal processes, including peroxiredoxin-2 and -4, cofilin-1, prefoldin 2, alpha-enolase, human nucleoside diphosphate kinase B (Nm23) and 14-3-3 protein epsilon. Many of the differentially expressed proteins are involved in diverse pathways including metabolism, neurotrophin signaling, actin cytoskeletal regulation, HIF-1 signaling and the proteasome indicating that miR-153-3p and miR-205-5p are involved in the regulation of a wide variety of biological processes in neuroblastoma cells.
Collapse
|
14
|
|
15
|
van Wijk KJ. Protein maturation and proteolysis in plant plastids, mitochondria, and peroxisomes. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:75-111. [PMID: 25580835 DOI: 10.1146/annurev-arplant-043014-115547] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plastids, mitochondria, and peroxisomes are key organelles with dynamic proteomes in photosynthetic eukaryotes. Their biogenesis and activity must be coordinated and require intraorganellar protein maturation, degradation, and recycling. The three organelles together are predicted to contain ∼200 presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar proteins, such as N-end degrons and tagging systems, have not been identified, but the substrate recognition mechanisms likely share similarities between organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome. This review summarizes (putative) plant organellar protease functions and substrate-protease relationships. Examples illustrate key proteolytic events.
Collapse
Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14853;
| |
Collapse
|