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Gentry-Torfer D, Murillo E, Barrington CL, Nie S, Leeming MG, Suwanchaikasem P, Williamson NA, Roessner U, Boughton BA, Kopka J, Martinez-Seidel F. Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome. Bio Protoc 2024; 14:e4981. [PMID: 38737506 PMCID: PMC11082790 DOI: 10.21769/bioprotoc.4981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features. Thus, characterizing the state of riboproteomes provides insights to uncover the context-dependent functionality of r-protein rearrangements, as they relate to what has been termed the ribosomal code, a concept that parallels that of the histone code, in which chromatin rearrangements influence gene expression. Compared to high-resolution ribosomal structures, omics methods lag when it comes to offering customized solutions to close the knowledge gap between structure and function that currently exists in riboproteomes. Purifying the riboproteome and subsequent shot-gun proteomics typically involves protein denaturation and digestion with proteases. The results are relative abundances of r-proteins at the ribosome population level. We have previously shown that, to gain insight into the stoichiometry of individual proteins, it is necessary to measure by proteomics bound r-proteins and normalize their intensities by the sum of r-protein abundances per ribosomal complex, i.e., 40S or 60S subunits. These calculations ensure that individual r-protein stoichiometries represent the fraction of each family/paralog relative to the complex, effectively revealing which r-proteins become substoichiometric in specific physiological scenarios. Here, we present an optimized method to profile the riboproteome of any organism as well as the synthesis rates of r-proteins determined by stable isotope-assisted mass spectrometry. Our method purifies the r-proteins in a reversibly denatured state, which offers the possibility for combined top-down and bottom-up proteomics. Our method offers a milder native denaturation of the r-proteome via a chaotropic GuHCl solution as compared with previous studies that use irreversible denaturation under highly acidic conditions to dissociate rRNA and r-proteins. As such, our method is better suited to conserve post-translational modifications (PTMs). Subsequently, our method carefully considers the amino acid composition of r-proteins to select an appropriate protease for digestion. We avoid non-specific protease cleavage by increasing the pH of our standardized r-proteome dilutions that enter the digestion pipeline and by using a digestion buffer that ensures an optimal pH for a reliable protease digestion process. Finally, we provide the R package ProtSynthesis to study the fractional synthesis rates of r-proteins. The package uses physiological parameters as input to determine peptide or protein fractional synthesis rates. Once the physiological parameters are measured, our equations allow a fair comparison between treatments that alter the biological equilibrium state of the system under study. Our equations correct peptide enrichment using enrichments in soluble amino acids, growth rates, and total protein accumulation. As a means of validation, our pipeline fails to find "false" enrichments in non-labeled samples while also filtering out proteins with multiple unique peptides that have different enrichment values, which are rare in our datasets. These two aspects reflect the accuracy of our tool. Our method offers the possibility of elucidating individual r-protein family/paralog abundances, PTM status, fractional synthesis rates, and dynamic assembly into ribosomal complexes if top-down and bottom-up proteomic approaches are used concomitantly, taking one step further into mapping the native and dynamic status of the r-proteome onto high-resolution ribosome structures. In addition, our method can be used to study the proteomes of all macromolecular assemblies that can be purified, although purification is the limiting step, and the efficacy and accuracy of the proteases may be limited depending on the digestion requirements. Key features • Efficient purification of the ribosomal proteome: streamlined procedure for the specific purification of the ribosomal proteome or complex Ome. • Accurate calculation of fractional synthesis rates: robust method for calculating fractional protein synthesis rates in macromolecular complexes under different physiological steady states. • Holistic ribosome methodology focused on plants: comprehensive approach that provides insights into the ribosomes and translational control of plants, demonstrated using cold acclimation [1]. • Tailored strategies for stable isotope labeling in plants: methodology focusing on materials and labeling considerations specific to free and proteinogenic amino acid analysis [2].
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Affiliation(s)
- Dione Gentry-Torfer
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Ester Murillo
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Chloe L. Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- School of Chemistry, The University of Melbourne, Parkville, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Australia
| | - Ute Roessner
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Research School of Biology, The Australian National University, Acton, Australia
| | - Berin A. Boughton
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Joachim Kopka
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Federico Martinez-Seidel
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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Siodmak A, Martinez-Seidel F, Rayapuram N, Bazin J, Alhoraibi H, Gentry-Torfer D, Tabassum N, Sheikh AH, Kise J, Blilou I, Crespi M, Kopka J, Hirt H. Dynamics of ribosome composition and ribosomal protein phosphorylation in immune signaling in Arabidopsis thaliana. Nucleic Acids Res 2023; 51:11876-11892. [PMID: 37823590 PMCID: PMC10681734 DOI: 10.1093/nar/gkad827] [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: 06/24/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
In plants, the detection of microbe-associated molecular patterns (MAMPs) induces primary innate immunity by the activation of mitogen-activated protein kinases (MAPKs). We show here that the MAMP-activated MAPK MPK6 not only modulates defense through transcriptional regulation but also via the ribosomal protein translation machinery. To understand the effects of MPK6 on ribosomes and their constituent ribosomal proteins (RPs), polysomes, monosomes and the phosphorylation status of the RPs, MAMP-treated WT and mpk6 mutant plants were analysed. MAMP-activation induced rapid changes in RP composition of monosomes, polysomes and in the 60S ribosomal subunit in an MPK6-specific manner. Phosphoproteome analysis showed that MAMP-activation of MPK6 regulates the phosphorylation status of the P-stalk ribosomal proteins by phosphorylation of RPP0 and the concomitant dephosphorylation of RPP1 and RPP2. These events coincide with a significant decrease in the abundance of ribosome-bound RPP0s, RPP1s and RPP3s in polysomes. The P-stalk is essential in regulating protein translation by recruiting elongation factors. Accordingly, we found that RPP0C mutant plants are compromised in basal resistance to Pseudomonas syringae infection. These data suggest that MAMP-induced defense also involves MPK6-induced regulation of P-stalk proteins, highlighting a new role of ribosomal regulation in plant innate immunity.
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Affiliation(s)
- Anna Siodmak
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Naganand Rayapuram
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Hanna Alhoraibi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21551 Jeddah, Saudi Arabia
| | - Dione Gentry-Torfer
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Naheed Tabassum
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Arsheed H Sheikh
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - José Kenyi González Kise
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ikram Blilou
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Heribert Hirt
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
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3
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Bleckmann A, Spitzlberger N, Denninger P, Ehrnsberger HF, Wang L, Bruckmann A, Reich S, Holzinger P, Medenbach J, Grasser KD, Dresselhaus T. Cytosolic RGG RNA-binding proteins are temperature sensitive flowering time regulators in Arabidopsis. Biol Chem 2023; 404:1069-1084. [PMID: 37674329 DOI: 10.1515/hsz-2023-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
mRNA translation is tightly regulated by various classes of RNA-binding proteins (RBPs) during development and in response to changing environmental conditions. In this study, we characterize the arginine-glycine-glycine (RGG) motif containing RBP family of Arabidopsis thaliana representing homologues of the multifunctional translation regulators and ribosomal preservation factors Stm1 from yeast (ScStm1) and human SERBP1 (HsSERBP1). The Arabidopsis genome encodes three RGG proteins named AtRGGA, AtRGGB and AtRGGC. While AtRGGA is ubiquitously expressed, AtRGGB and AtRGGC are enriched in dividing cells. All AtRGGs localize almost exclusively to the cytoplasm and bind with high affinity to ssRNA, while being capable to interact with most nucleic acids, except dsRNA. A protein-interactome study shows that AtRGGs interact with ribosomal proteins and proteins involved in RNA processing and transport. In contrast to ScStm1, AtRGGs are enriched in ribosome-free fractions in polysome profiles, suggesting additional plant-specific functions. Mutant studies show that AtRGG proteins differentially regulate flowering time, with a distinct and complex temperature dependency for each AtRGG protein. In conclusion, we suggest that AtRGGs function in fine-tuning translation efficiency to control flowering time and potentially other developmental processes in response to environmental changes.
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Affiliation(s)
- Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Nicole Spitzlberger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Denninger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Hans F Ehrnsberger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Lele Wang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Stefan Reich
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Holzinger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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Cai M, Wu X, Liang X, Hu H, Liu Y, Yong T, Li X, Xiao C, Gao X, Chen S, Xie Y, Wu Q. Comparative proteomic analysis of two divergent strains provides insights into thermotolerance mechanisms of Ganoderma lingzhi. Fungal Genet Biol 2023; 167:103796. [PMID: 37146899 DOI: 10.1016/j.fgb.2023.103796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/18/2023] [Accepted: 04/03/2023] [Indexed: 05/07/2023]
Abstract
Heat stress (HS) is a major abiotic factor influencing fungal growth and metabolism. However, the genetic basis of thermotolerance in Ganoderma lingzhi (G. lingzhi) remains largely unknown. In this study, we investigated the thermotolerance capacities of 21 G. lingzhi strains and screened the thermo-tolerant (S566) and heat-sensitive (Z381) strains. The mycelia of S566 and Z381 were collected and subjected to a tandem mass tag (TMT)-based proteome assay. We identified 1493 differentially expressed proteins (DEPs), with 376 and 395 DEPs specific to the heat-tolerant and heat-susceptible genotypes, respectively. In the heat-tolerant genotype, upregulated proteins were linked to stimulus regulation and response. Proteins related to oxidative phosphorylation, glycosylphosphatidylinositol-anchor biosynthesis, and cell wall macromolecule metabolism were downregulated in susceptible genotypes. After HS, the mycelial growth of the heat-sensitive Z381 strain was inhibited, and mitochondrial cristae and cell wall integrity of this strain were severely impaired, suggesting that HS may inhibit mycelial growth of Z381 by damaging the cell wall and mitochondrial structure. Furthermore, thermotolerance-related regulatory pathways were explored by analyzing the protein-protein interaction network of DEPs considered to participate in the controlling the thermotolerance capacity. This study provides insights into G. lingzhi thermotolerance mechanisms and a basis for breeding a thermotolerant germplasm bank for G. lingzhi and other fungi.
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Affiliation(s)
- Manjun Cai
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaoxian Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaowei Liang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Huiping Hu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yuanchao Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Tianqiao Yong
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiangmin Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Chun Xiao
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiong Gao
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shaodan Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yizhen Xie
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Yuewei Edible Fungi Technology Co. Ltd., Guangzhou 510663, China.
| | - Qingping Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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5
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Kosová K, Vítámvás P, Skuhrovec J, Vítámvás J, Planchon S, Renaut J, Saska P. Proteomic responses of two spring wheat cultivars to the combined water deficit and aphid ( Metopolophium dirhodum) treatments. FRONTIERS IN PLANT SCIENCE 2022; 13:1005755. [PMID: 36452089 PMCID: PMC9704420 DOI: 10.3389/fpls.2022.1005755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
In the field, plants usually have to face the combined effects of abiotic and biotic stresses. In our study, two spring wheat cultivars-Septima and Quintus-were subjected to three water regimes [70%, 50%, and 40% soil water capacity (SWC)], aphid (Metopolophium dirhodum) infestation, or the combination of both stresses, i.e., water deficit (50%, 40% SWC) and aphids. The study has a 2 × 3 × 2 factorial design with three biological replicates. In the present study, the results of proteomic analysis using 2D-DIGE followed by MALDI-TOF/TOF protein identification are presented. Water deficit but also aphid infestation led to alterations in 113 protein spots including proteins assigned to a variety of biological processes ranging from signaling via energy metabolism, redox regulation, and stress and defense responses to secondary metabolism indicating a long-term adaptation to adverse conditions. The absence of specific proteins involved in plant response to herbivorous insects indicates a loss of resistance to aphids in modern wheat cultivars during the breeding process and is in accordance with the "plant vigor hypothesis." Septima revealed enhanced tolerance with respect to Quintus as indicated by higher values of morphophysiological characteristics (fresh aboveground biomass, leaf length, osmotic potential per full water saturation) and relative abundance of proteins involved in mitochondrial respiration and ATP biosynthesis.
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Affiliation(s)
- Klára Kosová
- Plant Stress Biology and Biotechnology Group, Department of Plant Genetics and Breeding, Crop Research Institute, Prague, Czechia
| | - Pavel Vítámvás
- Plant Stress Biology and Biotechnology Group, Department of Plant Genetics and Breeding, Crop Research Institute, Prague, Czechia
| | - Jiří Skuhrovec
- Functional Diversity Group, Department of Plant Protection, Crop Research Institute, Prague, Czechia
| | - Jan Vítámvás
- Plant Stress Biology and Biotechnology Group, Department of Plant Genetics and Breeding, Crop Research Institute, Prague, Czechia
- Faculty of Forestry and Wood Science, Czech University of Life Sciences, Prague, Czechia
| | - Sébastien Planchon
- Biotechnologies and Environmental Analytics Platform (BEAP), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch-sur-Alzette, Luxembourg
| | - Jenny Renaut
- Biotechnologies and Environmental Analytics Platform (BEAP), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch-sur-Alzette, Luxembourg
| | - Pavel Saska
- Functional Diversity Group, Department of Plant Protection, Crop Research Institute, Prague, Czechia
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Zhang Z, Zhang Y, Yuan L, Zhou F, Gao Y, Kang Z, Li T, Hu X. Exogenous 5-aminolevulinic acid alleviates low-temperature injury by regulating glutathione metabolism and β-alanine metabolism in tomato seedling roots. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 245:114112. [PMID: 36155340 DOI: 10.1016/j.ecoenv.2022.114112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Food availability represents a major worldwide concern due to climate change and population growth. Low-temperature stress (LTS) severely restricts the growth of tomato seedlings. Exogenous 5-aminolevulinic acid (ALA) can alleviate the harm of abiotic stress including LTS; however, data on its protective mechanism on tomato seedling roots, the effects of organelle structure, and the regulation of metabolic pathways under LTS are lacking. In this study, we hope to fill the above gaps by exploring the effects of exogenous ALA on morphology, mitochondrial ultrastructure, reactive oxygen species (ROS) enrichment, physiological indicators, related gene expression, and metabolic pathway in tomato seedlings root under LTS. Results showed that ALA pretreatment could increase the activity of antioxidant enzymes and the content of antioxidant substances in tomato seedlings roots under LTS to scavenge the massively accumulated ROS, thereby protecting the mitochondrial structure of roots and promoting root development under LTS. Combined transcriptomic and metabolomic analysis showed that exogenous ALA pretreatment activated the glutathione metabolism and β-alanine metabolism of tomato seedling roots under LTS, further enhanced the scavenging ability of tomato seedling roots to ROS, and improved the low-temperature tolerance of tomato seedlings. The findings provide a new insight into the regulation of the low-temperature tolerance of tomato by exogenous ALA.
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Affiliation(s)
- Zhengda Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Yuhui Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Luqiao Yuan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Fan Zhou
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Kang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
| | - Xiaohui Hu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China.
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Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lisón P, Taoka M, Amunts A. Cryo-EM structure and rRNA modification sites of a plant ribosome. PLANT COMMUNICATIONS 2022; 3:100342. [PMID: 35643637 PMCID: PMC9483110 DOI: 10.1016/j.xplc.2022.100342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/07/2022] [Accepted: 05/25/2022] [Indexed: 05/25/2023]
Abstract
Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.
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Affiliation(s)
- Patrick Cottilli
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València (UPV) - Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Valencia 46022, Spain
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden.
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8
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Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A Perspective. PLANTS 2022; 11:plants11162097. [PMID: 36015400 PMCID: PMC9415564 DOI: 10.3390/plants11162097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
As the centerpiece of the biomass production process, ribosome activity is highly coordinated with environmental cues. Findings revealing ribosome subgroups responsive to adverse conditions suggest this tight coordination may be grounded in the induction of variant ribosome compositions and the differential translation outcomes they might produce. In this perspective, we go through the literature linking ribosome heterogeneity to plants’ abiotic stress response. Once unraveled, this crosstalk may serve as the foundation of novel strategies to custom cultivars tolerant to challenging environments without the yield penalty.
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Martinez-Seidel F, Hsieh YC, Walther D, Kopka J, Pereira Firmino AA. [Formula: see text]: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes. BMC Bioinformatics 2021; 22:605. [PMID: 34930116 PMCID: PMC8686616 DOI: 10.1186/s12859-021-04510-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 12/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter ([Formula: see text]), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit abundance changes under specific conditions are spatially confined to particular regions within the large ribosomal complex. RESULTS [Formula: see text] translates experimentally determined structures into graphs, with nodes representing proteins and edges the spatial proximity between them. In its first implementation, [Formula: see text] considers rProteins and ignores rRNA and other objects. Spatial regions are defined using a random walk with restart methodology, followed by a procedure to obtain a minimum set of regions that cover all proteins in the complex. Structural coherence is achieved by applying weights to the edges reflecting the physical proximity between purportedly contacting proteins. The weighting probabilistically guides the random-walk path trajectory. Parameter tuning during region selection provides the option to tailor the method to specific biological questions by yielding regions of different sizes with minimum overlaps. In addition, other graph community detection algorithms may be used for the [Formula: see text] workflow, considering that they yield different sized, non-overlapping regions. All tested algorithms result in the same node kernels under equivalent regions. Based on the defined regions, available abundance change information of proteins is mapped onto the graph and subsequently tested for enrichment in any of the defined spatial regions. We applied [Formula: see text] to the cytosolic ribosome structures of Saccharomyces cerevisiae, Oryctolagus cuniculus, and Triticum aestivum using datasets with available quantitative protein abundance change information. We found that in yeast, substoichiometric rProteins depleted from translating polysomes are significantly constrained to a ribosomal region close to the tRNA entry and exit sites. CONCLUSIONS [Formula: see text] offers a computational method to partition multi-protein complexes into structural regions and a statistical approach to test for spatial enrichments of any given subsets of proteins. [Formula: see text] is applicable to any multi-protein complex given appropriate structural and abundance-change data. [Formula: see text] is publicly available as a GitHub repository https://github.com/MSeidelFed/COSNet_i and can be installed using the python installer pip.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- School of BioSciences, University of Melbourne, Parkville, VC 3010 Australia
| | - Yin-Chen Hsieh
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Institute for Arctic and Marine Biology, UiT Arctic University of Norway, 9037 Tromsø, Norway
| | - Dirk Walther
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Kosová K, Vítámvás P, Prášil IT, Klíma M, Renaut J. Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene. FRONTIERS IN PLANT SCIENCE 2021; 12:793113. [PMID: 34970290 PMCID: PMC8712444 DOI: 10.3389/fpls.2021.793113] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2021] [Indexed: 05/30/2023]
Abstract
Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.
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Affiliation(s)
- Klára Kosová
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Pavel Vítámvás
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Ilja Tom Prášil
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Miroslav Klíma
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Jenny Renaut
- Biotechnologies and Environmental Analytics Platform (BEAP), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch-Sur-Alzette, Luxembourg
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Dorion S, Ouellet JC, Rivoal J. Glutathione Metabolism in Plants under Stress: Beyond Reactive Oxygen Species Detoxification. Metabolites 2021; 11:metabo11090641. [PMID: 34564457 PMCID: PMC8464934 DOI: 10.3390/metabo11090641] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 01/16/2023] Open
Abstract
Glutathione is an essential metabolite for plant life best known for its role in the control of reactive oxygen species (ROS). Glutathione is also involved in the detoxification of methylglyoxal (MG) which, much like ROS, is produced at low levels by aerobic metabolism under normal conditions. While several physiological processes depend on ROS and MG, a variety of stresses can dramatically increase their concentration leading to potentially deleterious effects. In this review, we examine the structure and the stress regulation of the pathways involved in glutathione synthesis and degradation. We provide a synthesis of the current knowledge on the glutathione-dependent glyoxalase pathway responsible for MG detoxification. We present recent developments on the organization of the glyoxalase pathway in which alternative splicing generate a number of isoforms targeted to various subcellular compartments. Stress regulation of enzymes involved in MG detoxification occurs at multiple levels. A growing number of studies show that oxidative stress promotes the covalent modification of proteins by glutathione. This post-translational modification is called S-glutathionylation. It affects the function of several target proteins and is relevant to stress adaptation. We address this regulatory function in an analysis of the enzymes and pathways targeted by S-glutathionylation.
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Eshraky KE, Gorka M, Cheong BE, Jimenez-Posada EV, Walther D, Skirycz A, Roessner U, Kopka J, Pereira Firmino AA. Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis. Int J Mol Sci 2021; 22:6160. [PMID: 34200446 PMCID: PMC8201131 DOI: 10.3390/ijms22116160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ribosomal centers such as the polypeptide exit tunnel and the P-Stalk, respectively. In consequence, these ribosomal substructures and their assembly, especially during low temperatures, might be changed and provoke the need for dedicated quality controls. To test this, we blocked ribosome maturation during cold acclimation using two independent reil double mutant genotypes and tested changes in their ribosomal proteomes. Additionally, we normalized our mutant datasets using as a blank the cold responsiveness of a wild-type Arabidopsis genotype. This allowed us to neglect any reil-specific effects that may happen due to the presence or absence of the factor during LSU cytosolic maturation, thus allowing us to test for cold-induced changes that happen in the early nucleolar biogenesis. As a result, we report that cold acclimation triggers a reprogramming in the structural ribosomal proteome. The reprogramming alters the abundance of specific RP families and/or paralogs in non-translational LSU and translational polysome fractions, a phenomenon known as substoichiometry. Next, we tested whether the cold-substoichiometry was spatially confined to specific regions of the complex. In terms of RP proteoforms, we report that remodeling of ribosomes after a cold stimulus is significantly constrained to the polypeptide exit tunnel (PET), i.e., REIL factor binding and functional site. In terms of RP transcripts, cold acclimation induces changes in RP families or paralogs that are significantly constrained to the P-Stalk and the ribosomal head. The three modulated substructures represent possible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. We propose that non-random ribosome heterogeneity controlled by specialized biogenesis mechanisms may contribute to a preferential or ultimately even rigorous selection of transcripts needed for rapid proteome shifts and successful acclimation.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Olga Beine-Golovchuk
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- Heidelberg University, Biochemie-Zentrum, Nuclear Pore Complex and Ribosome Assembly, 69120 Heidelberg, Germany
| | - Yin-Chen Hsieh
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- Institute for Arctic and Marine Biology, UiT Arctic University of Norway, 9037 Tromsø, Norway
| | - Kheloud El Eshraky
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Michal Gorka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Bo-Eng Cheong
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Malaysia
| | - Erika V. Jimenez-Posada
- Grupo de Biotecnología-Productos Naturales, Universidad Tecnológica de Pereira, Pereira 660003, Colombia;
- Emerging Infectious Diseases and Tropical Medicine Research Group—Sci-Help, Pereira 660009, Colombia
| | - Dirk Walther
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Aleksandra Skirycz
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Alexandre Augusto Pereira Firmino
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
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