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Kato Y, Kuroda H, Ozawa SI, Saito K, Dogra V, Scholz M, Zhang G, de Vitry C, Ishikita H, Kim C, Hippler M, Takahashi Y, Sakamoto W. Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts. eLife 2023; 12:RP88822. [PMID: 37986577 PMCID: PMC10665015 DOI: 10.7554/elife.88822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH.
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Affiliation(s)
- Yusuke Kato
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Faculty of Agriculture, Setsunan UniversityOsakaJapan
| | - Hiroshi Kuroda
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Shin-Ichiro Ozawa
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Vivek Dogra
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesShanghaiChina
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampurIndia
| | - Martin Scholz
- Institute of Plant Biology and Biotechnology, University of MünsterMünsterGermany
| | - Guoxian Zhang
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
| | - Catherine de Vitry
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université Pierre et Marie CurieParisFrance
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesShanghaiChina
| | - Michael Hippler
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Institute of Plant Biology and Biotechnology, University of MünsterMünsterGermany
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
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Giese J, Eirich J, Walther D, Zhang Y, Lassowskat I, Fernie AR, Elsässer M, Maurino VG, Schwarzländer M, Finkemeier I. The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1172-1193. [PMID: 37522418 DOI: 10.1111/tpj.16406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Diurnal dark to light transition causes profound physiological changes in plant metabolism. These changes require distinct modes of regulation as a unique feature of photosynthetic lifestyle. The activities of several key metabolic enzymes are regulated by light-dependent post-translational modifications (PTM) and have been studied at depth at the level of individual proteins. In contrast, a global picture of the light-dependent PTMome dynamics is lacking, leaving the response of a large proportion of cellular function undefined. Here, we investigated the light-dependent metabolome and proteome changes in Arabidopsis rosettes in a time resolved manner to dissect their kinetic interplay, focusing on phosphorylation, lysine acetylation, and cysteine-based redox switches. Of over 24 000 PTM sites that were detected, more than 1700 were changed during the transition from dark to light. While the first changes, as measured 5 min after onset of illumination, occurred mainly in the chloroplasts, PTM changes at proteins in other compartments coincided with the full activation of the Calvin-Benson cycle and the synthesis of sugars at later timepoints. Our data reveal connections between metabolism and PTM-based regulation throughout the cell. The comprehensive multiome profiling analysis provides unique insight into the extent by which photosynthesis reprograms global cell function and adds a powerful resource for the dissection of diverse cellular processes in the context of photosynthetic function.
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Affiliation(s)
- Jonas Giese
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Dirk Walther
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Ines Lassowskat
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Marlene Elsässer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Veronica G Maurino
- Institute of Cellular and Molecular Botany (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
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Martí-Guillén JM, Pardo-Hernández M, Martínez-Lorente SE, Almagro L, Rivero RM. Redox post-translational modifications and their interplay in plant abiotic stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1027730. [PMID: 36388514 PMCID: PMC9644032 DOI: 10.3389/fpls.2022.1027730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/10/2022] [Indexed: 05/27/2023]
Abstract
The impact of climate change entails a progressive and inexorable modification of the Earth's climate and events such as salinity, drought, extreme temperatures, high luminous intensity and ultraviolet radiation tend to be more numerous and prolonged in time. Plants face their exposure to these abiotic stresses or their combination through multiple physiological, metabolic and molecular mechanisms, to achieve the long-awaited acclimatization to these extreme conditions, and to thereby increase their survival rate. In recent decades, the increase in the intensity and duration of these climatological events have intensified research into the mechanisms behind plant tolerance to them, with great advances in this field. Among these mechanisms, the overproduction of molecular reactive species stands out, mainly reactive oxygen, nitrogen and sulfur species. These molecules have a dual activity, as they participate in signaling processes under physiological conditions, but, under stress conditions, their production increases, interacting with each other and modifying and-or damaging the main cellular components: lipids, carbohydrates, nucleic acids and proteins. The latter have amino acids in their sequence that are susceptible to post-translational modifications, both reversible and irreversible, through the different reactive species generated by abiotic stresses (redox-based PTMs). Some research suggests that this process does not occur randomly, but that the modification of critical residues in enzymes modulates their biological activity, being able to enhance or inhibit complete metabolic pathways in the process of acclimatization and tolerance to the exposure to the different abiotic stresses. Given the importance of these PTMs-based regulation mechanisms in the acclimatization processes of plants, the present review gathers the knowledge generated in recent years on this subject, delving into the PTMs of the redox-regulated enzymes of plant metabolism, and those that participate in the main stress-related pathways, such as oxidative metabolism, primary metabolism, cell signaling events, and photosynthetic metabolism. The aim is to unify the existing information thus far obtained to shed light on possible fields of future research in the search for the resilience of plants to climate change.
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Affiliation(s)
- José M. Martí-Guillén
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
- Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Miriam Pardo-Hernández
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - Sara E. Martínez-Lorente
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - Lorena Almagro
- Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Rosa M. Rivero
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
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4
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Dogra V, Singh RM, Li M, Li M, Singh S, Kim C. EXECUTER2 modulates the EXECUTER1 signalosome through its singlet oxygen-dependent oxidation. MOLECULAR PLANT 2022; 15:438-453. [PMID: 34968736 DOI: 10.1016/j.molp.2021.12.016] [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: 02/11/2021] [Revised: 11/29/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Oxidative post-translational modifications of specific chloroplast proteins contribute to the initiation of retrograde signaling. The Arabidopsis thaliana EXECUTER1 (EX1) protein, a chloroplast-localized singlet oxygen (1O2) sensor, undergoes tryptophan (Trp) 643 oxidation by 1O2, a chloroplast-derived and light-dependent reactive oxygen species. The indole side chain of Trp is vulnerable to 1O2, leading to the generation of oxidized Trp variants and priming EX1 for degradation by a membrane-bound FtsH protease. The perception of 1O2 via Trp643 oxidation and subsequent EX1 proteolysis facilitate chloroplast-to-nucleus retrograde signaling. In this study, we discovered that the EX1-like protein EX2 also undergoes 1O2-dependent Trp530 oxidation and FtsH-dependent turnover, which attenuates 1O2 signaling by decelerating EX1-Trp643 oxidation and subsequent EX1 degradation. Consistent with this finding, the loss of EX2 function reinforces EX1-dependent retrograde signaling by accelerating EX1-Trp643 oxidation and subsequent EX1 proteolysis, whereas overexpression of EX2 produces molecular phenotypes opposite to those observed in the loss-of- function mutants of EX2. Intriguingly, phylogenetic analysis suggests that EX2 may have emerged evolutionarily to attenuate the sensitivity of EX1 toward 1O2. Collectively, these results suggest that EX2 functions as a negative regulator of the EX1 signalosome through its own 1O2-dependent oxidation, providing a new mechanistic insight into the regulation of EX1-mediated 1O2 signaling.
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Affiliation(s)
- Vivek Dogra
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rahul Mohan Singh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mengping Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyue Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Somesh Singh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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5
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Zhan H, Song L, Kamran A, Han F, Li B, Zhou Z, Liu T, Shen L, Li Y, Wang F, Yang J. Comprehensive Proteomic Analysis of Lysine Ubiquitination in Seedling Leaves of Nicotiana tabacum. ACS OMEGA 2020; 5:20122-20133. [PMID: 32832766 PMCID: PMC7439365 DOI: 10.1021/acsomega.0c01741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/23/2020] [Indexed: 05/04/2023]
Abstract
Lysine ubiquitination, a widely studied posttranslational modification, plays vital roles in various biological processes in eukaryotic cells. Although several studies have examined the plant ubiquitylome, no such research has been performed in tobacco, a model plant for molecular biology. Here, we comprehensively analyzed lysine ubiquitination in tobacco (Nicotiana tabacum) using LC-MS/MS along with highly sensitive immune-affinity purification. In total, 964 lysine-ubiquitinated (Kub) sites were identified in 572 proteins. Extensive bioinformatics studies revealed the distribution of these proteins in various cellular locations, including the cytoplasm, chloroplast, nucleus, and plasma membrane. Notably, 25% of the Kub proteins were located in the chloroplast of which 21 were enzymatically involved in important pathways, that is, photosynthesis and carbon fixation. Western blot analysis indicated that TMV infection can cause changes in ubiquitination levels. This is the first comprehensive proteomic analysis of lysine ubiquitination in tobacco, illustrating the vital role of ubiquitination in various physiological and biochemical processes and representing a valuable addition to the existing landscape of lysine ubiquitination.
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Affiliation(s)
- Huaixu Zhan
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Graduate
School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liyun Song
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ali Kamran
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fei Han
- State
Tobacco Monopoly Administration, Beijing 100045, China
| | - Bin Li
- Sichuan
Tobacco Company, Chengdu 610017, China
| | - Zhicheng Zhou
- Hunan
Tobacco Science Institute, Changsha 410004, China
| | - Tianbo Liu
- Hunan
Tobacco Science Institute, Changsha 410004, China
| | - Lili Shen
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ying Li
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fenglong Wang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- wangfenglong@ caas.cn
| | - Jinguang Yang
- Key
Laboratory of Tobacco Pest Monitoring, Controlling & Integrated
Management, Tobacco Research Institute of
Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- . Tel.: +86-532-88703236
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6
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Metatranscriptomics and Metaproteomics for Microbial Communities Profiling. UNRAVELLING THE SOIL MICROBIOME 2020. [DOI: 10.1007/978-3-030-15516-2_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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7
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Duan J, Lee KP, Dogra V, Zhang S, Liu K, Caceres-Moreno C, Lv S, Xing W, Kato Y, Sakamoto W, Liu R, Macho AP, Kim C. Impaired PSII Proteostasis Promotes Retrograde Signaling via Salicylic Acid. PLANT PHYSIOLOGY 2019; 180:2182-2197. [PMID: 31160506 PMCID: PMC6670100 DOI: 10.1104/pp.19.00483] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/21/2019] [Indexed: 05/18/2023]
Abstract
Photodamage of the PSII reaction center (RC) is an inevitable process in an oxygen-rich environment. The damaged PSII RC proteins (Dam-PSII) undergo degradation via the thylakoid membrane-bound FtsH metalloprotease, followed by posttranslational assembly of PSII. While the effect of Dam-PSII on gene regulation is described for cyanobacteria, its role in land plants is largely unknown. In this study, we reveal an intriguing retrograde signaling pathway by using the Arabidopsis (Arabidopsis thaliana) yellow variegated2-9 mutant, which expresses a mutated FtsH2 (FtsH2G267D) metalloprotease, specifically impairing its substrate-unfolding activity. This lesion leads to the perturbation of PSII protein homeostasis (proteostasis) and the accumulation of Dam-PSII. Subsequently, this results in an up-regulation of salicylic acid (SA)-responsive genes, which is abrogated by inactivation of either an SA transporter in the chloroplast envelope membrane or extraplastidic SA signaling components as well as by removal of SA. These results suggest that the stress hormone SA, which is mainly synthesized via the chloroplast isochorismate pathway in response to the impaired PSII proteostasis, mediates the retrograde signaling. These findings reinforce the emerging view of chloroplast function toward plant stress responses and suggest SA as a potential plastid factor mediating retrograde signaling.
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Affiliation(s)
- Jianli Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Keun Pyo Lee
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Vivek Dogra
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Siyuan Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiwei Liu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Carlos Caceres-Moreno
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Lv
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Weiman Xing
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yusuke Kato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Renyi Liu
- College of Horticulture and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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8
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Dogra V, Li M, Singh S, Li M, Kim C. Oxidative post-translational modification of EXECUTER1 is required for singlet oxygen sensing in plastids. Nat Commun 2019; 10:2834. [PMID: 31249292 PMCID: PMC6597547 DOI: 10.1038/s41467-019-10760-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/29/2019] [Indexed: 12/26/2022] Open
Abstract
Environmental information perceived by chloroplasts can be translated into retrograde signals that alter the expression of nuclear genes. Singlet oxygen (1O2) generated by photosystem II (PSII) can cause photo-oxidative damage of PSII but has also been implicated in retrograde signaling. We previously reported that a nuclear-encoded chloroplast FtsH2 metalloprotease coordinates 1O2-triggered retrograde signaling by promoting the degradation of the EXECUTER1 (EX1) protein, a putative 1O2 sensor. Here, we show that a 1O2-mediated oxidative post-translational modification of EX1 is essential for initiating 1O2-derived signaling. Specifically, the Trp643 residue in DUF3506 domain of EX1 is prone to oxidation by 1O2. Both the substitution of Trp643 with 1O2-insensitive amino acids and the deletion of the DUF3506 domain abolish the EX1-mediated 1O2 signaling. We thus provide mechanistic insight into how EX1 senses 1O2 via Trp643 located in the DUF3506 domain.
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Affiliation(s)
- Vivek Dogra
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Mingyue Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.,University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Somesh Singh
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Mengping Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.,University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China. .,University of the Chinese Academy of Sciences, 100049, Beijing, China.
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9
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Kim C. ROS-Driven Oxidative Modification: Its Impact on Chloroplasts-Nucleus Communication. FRONTIERS IN PLANT SCIENCE 2019; 10:1729. [PMID: 32038693 PMCID: PMC6990121 DOI: 10.3389/fpls.2019.01729] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/09/2019] [Indexed: 05/20/2023]
Abstract
As a light-harvesting organelle, the chloroplast inevitably produces a substantial amount of reactive oxygen species (ROS) primarily through the photosystems. These ROS, such as superoxide anion, hydrogen peroxide, hydroxyl radical, and singlet oxygen, are potent oxidizing agents, thereby damaging the photosynthetic apparatus. On the other hand, it became increasingly clear that ROS act as beneficial tools under photo-oxidative stress conditions by stimulating chloroplast-nucleus communication, a process called retrograde signaling (RS). These ROS-mediated RS cascades appear to participate in a broad spectrum of plant physiology, such as acclimation, resistance, programmed cell death (PCD), and growth. Recent reports imply that ROS-driven oxidation of RS-associated components is essential in sensing and responding to an increase in ROS contents. ROS appear to activate RS pathways via reversible or irreversible oxidation of sensor molecules. This review provides an overview of the emerging perspective on the topic of "oxidative modification-associated retrograde signaling."
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10
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Ramarathinam SH, Gras S, Alcantara S, Yeung AWS, Mifsud NA, Sonza S, Illing PT, Glaros EN, Center RJ, Thomas SR, Kent SJ, Ternette N, Purcell DFJ, Rossjohn J, Purcell AW. Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics. Proteomics 2018; 18:e1700253. [PMID: 29437277 DOI: 10.1002/pmic.201700253] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/29/2018] [Indexed: 12/20/2022]
Abstract
The recognition of pathogen-derived peptides by T lymphocytes is the cornerstone of adaptive immunity, whereby intracellular antigens are degraded in the cytosol and short peptides assemble with class I human leukocyte antigen (HLA) molecules in the ER. These peptide-HLA complexes egress to the cell surface and are scrutinized by cytotoxic CD8+ T-cells leading to the eradication of the infected cell. Here, naturally presented HLA-B*57:01 bound peptides derived from the envelope protein of the human immunodeficiency virus (HIVenv) are identified. HIVenv peptides are present at a very small percentage of the overall HLA-B*57:01 peptidome (<0.1%) and both native and posttranslationally modified forms of two distinct HIV peptides are identified. Notably, a peptide bearing a natively encoded C-terminal tryptophan residue is also present in a modified form containing a kynurenine residue. Kynurenine is a major product of tryptophan catabolism and is abundant during inflammation and infection. Binding of these peptides at a molecular level and their immunogenicity in preliminary functional studies are examined. Modest immune responses are observed to the modified HIVenv peptide, highlighting a potential role for kynurenine-modified peptides in the immune response to HIV and other viral infections.
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Affiliation(s)
- Sri H Ramarathinam
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Stephanie Gras
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Amanda W S Yeung
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Secondo Sonza
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Patricia T Illing
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Elias N Glaros
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Robert J Center
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.,Burnet Institute, Melbourne, Australia
| | - Shane R Thomas
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.,Melbourne Sexual Health Centre, Central Clinical School, Monash University, Melbourne, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Australia
| | - Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, UK
| | - Damian F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Anthony W Purcell
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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11
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Weisz DA, Gross ML, Pakrasi HB. Reactive oxygen species leave a damage trail that reveals water channels in Photosystem II. SCIENCE ADVANCES 2017; 3:eaao3013. [PMID: 29159285 PMCID: PMC5693562 DOI: 10.1126/sciadv.aao3013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/19/2017] [Indexed: 05/30/2023]
Abstract
Photosystem II (PSII), a unique membrane-bound oxidoreductase, catalyzes light-driven oxidation of water to molecular oxygen. Although high-resolution structures of PSII are known, the exact path of the substrate water molecules to the catalytic Mn4CaO5 center within the PSII complex remains poorly understood. PSII produces reactive oxygen species (ROS), responsible for the frequent damage and turnover of this megacomplex that occur under physiological conditions. Such ROS are known to specifically modify PSII proteins. Using high-resolution tandem mass spectrometry, we identified oxidative modifications on 36 amino acid residues on the lumenal side of PSII, in the core PSII proteins D1, D2, and CP43 of the cyanobacterium Synechocystis sp. PCC 6803. Remarkably, these oxidized residues clustered into three nearly continuous formations, tracking the pathways of ROS diffusion from the manganese center all the way out to the surface of PSII. We suggest that these profiles of oxidized residues reveal the locations of water channels within PSII. Our results provide the most comprehensive experimental evidence to date of physiologically relevant oxidized residues in PSII and illuminate three possible channels for water between the catalytic Mn cluster in the PSII complex and the bulk medium around it.
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Affiliation(s)
- Daniel A. Weisz
- Department of Biology, Washington University, St. Louis, MO 63130, USA
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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12
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Yamazaki S, Diaz MA, Carlino TM, Gotluru C, Mazza MMA, Scott AM. Ultrafast Spectroscopic Dynamics of Quinacrine-Riboflavin Binding Protein Interactions. J Phys Chem B 2017; 121:8291-8299. [PMID: 28762739 DOI: 10.1021/acs.jpcb.7b05304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Redox active cofactors play a dynamic role inside protein binding active sites because the amino acids responsible for binding participate in electron transfer (ET) reactions. Here, we use femtosecond transient absorption (FsTA) spectroscopy to examine the ultrafast ET between quinacrine (Qc), an antimalarial drug with potential anticancer activity, and riboflavin binding protein (RfBP) with a known Kd = 264 nM. Steady-state absorption reveals a ∼ 10 nm red-shift in the ground state when QcH32+ is titrated with RfBP, and a Stern-Volmer analysis shows ∼84% quenching and a blue-shift of the QcH32+ photoluminescence to form a 1:1 binding ratio of the QcH32+-RfBP complex. Upon selective photoexcitation of QcH32+ in the QcH32+-RfBP complex, we observe charge separation in 7 ps to form 1[QcH3_red•+-RfBP•+], which persists for 138 ps. The FsTA spectra show the spectroscopic identification of QcH3_red•+, determined from spectroelectrochemical measurements in DMSO. We correlate our results to literature and report lifetimes that are 10-20× slower than the natural riboflavin, Rf-RfBP, complex and are oxygen independent. Driving force (ΔG) calculations, corrected for estimated dielectric constants for protein hydrophobic pockets, and Marcus theory depict a favorable one-electron ET process between QcH32+ and nearby redox active tyrosine (Tyr) or tryptophan (Trp) residues.
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Affiliation(s)
- Shiori Yamazaki
- University of Miami , Department of Chemistry, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Matthew A Diaz
- University of Miami , Department of Chemistry, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Thomas M Carlino
- University of Miami , Department of Chemistry, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Chitra Gotluru
- University of Miami , Department of Chemistry, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Mercedes M A Mazza
- University of Miami , Department of Chemistry, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Amy M Scott
- University of Miami , Department of Chemistry, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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13
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Weisz DA, Gross ML, Pakrasi HB. The Use of Advanced Mass Spectrometry to Dissect the Life-Cycle of Photosystem II. FRONTIERS IN PLANT SCIENCE 2016; 7:617. [PMID: 27242823 PMCID: PMC4862242 DOI: 10.3389/fpls.2016.00617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/22/2016] [Indexed: 05/23/2023]
Abstract
Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has been gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. We conclude with an outlook for the opportunity of future MS contributions to PSII research.
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Affiliation(s)
- Daniel A. Weisz
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
| | - Himadri B. Pakrasi
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
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14
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Xiao QJ, Li ZG, Yang J, He Q, Xi L, Du LF. Heat-induced unfolding of apo-CP43 studied by fluorescence spectroscopy and CD spectroscopy. PHOTOSYNTHESIS RESEARCH 2015; 126:427-435. [PMID: 26071019 DOI: 10.1007/s11120-015-0166-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
CP43 is a chlorophyll-binding protein, which acts as a conduit for the excitation energy transfer. The thermal stability of apo-CP43 was studied by intrinsic fluorescence, exogenous ANS fluorescence, and circular dichroism spectroscopy. Under heat treatment, the structure of apo-CP43 changed and existed transition state occurred between 56 and 62 °C by the intrinsic, exogenous ANS fluorescence and the analysis of hydrophobicity. Besides, the isosbestic point of the sigmoidal curve was 58.10 ± 1.02 °C by calculating α-helix transition and the Tm was 56.45 ± 0.52 and 55.59 ± 0.68 °C by calculating the unfolded fraction of tryptophan and tyrosine fluorescence, respectively. During the process of unfolding, the hydrophobic structure of C-terminal segment firstly started to expose at 40 °C, and then the hydrophobic cluster adjacent to the N-terminal segment also gradually exposed to hydrophilic environment with increasing temperature. Our results indicated that heat treatment, especially above 40 °C, has an important impact on the structural stability of apo-CP43.
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Affiliation(s)
- Qing-Jie Xiao
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Zai-Geng Li
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jiao Yang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Qing He
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Lei Xi
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Lin-Fang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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15
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Bricker TM, Mummadisetti MP, Frankel LK. Recent advances in the use of mass spectrometry to examine structure/function relationships in photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:227-46. [PMID: 26390944 DOI: 10.1016/j.jphotobiol.2015.08.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 01/24/2023]
Abstract
Tandem mass spectrometry often coupled with chemical modification techniques, is developing into increasingly important tool in structural biology. These methods can provide important supplementary information concerning the structural organization and subunit make-up of membrane protein complexes, identification of conformational changes occurring during enzymatic reactions, identification of the location of posttranslational modifications, and elucidation of the structure of assembly and repair complexes. In this review, we will present a brief introduction to Photosystem II, tandem mass spectrometry and protein modification techniques that have been used to examine the photosystem. We will then discuss a number of recent case studies that have used these techniques to address open questions concerning PS II. These include the nature of subunit-subunit interactions within the phycobilisome, the interaction of phycobilisomes with Photosystem I and the Orange Carotenoid Protein, the location of CyanoQ, PsbQ and PsbP within Photosystem II, and the identification of phosphorylation and oxidative modification sites within the photosystem. Finally, we will discuss some of the future prospects for the use of these methods in examining other open questions in PS II structural biochemistry.
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Affiliation(s)
- Terry M Bricker
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Manjula P Mummadisetti
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Laurie K Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States
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16
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Fiore CL, Longnecker K, Kido Soule MC, Kujawinski EB. Release of ecologically relevant metabolites by the cyanobacterium Synechococcus elongates CCMP 1631. Environ Microbiol 2015; 17:3949-63. [PMID: 25970745 DOI: 10.1111/1462-2920.12899] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/04/2015] [Accepted: 05/04/2015] [Indexed: 01/08/2023]
Abstract
Photoautotrophic plankton in the surface ocean release organic compounds that fuel secondary production by heterotrophic bacteria. Here we show that an abundant marine cyanobacterium, Synechococcus elongatus, contributes a variety of nitrogen-rich and sulfur-containing compounds to dissolved organic matter. A combination of targeted and untargeted metabolomics and genomic tools was used to characterize the intracellular and extracellular metabolites of S. elongatus. Aromatic compounds, such as 4-hydroxybenzoic acid and phenylalanine, as well as nucleosides (e.g. thymidine, 5'-methylthioadenosine, xanthosine), the organosulfur compound 3-mercaptopropionate, and the plant auxin indole 3-acetic acid, were released by S. elongatus at multiple time points during its growth. Further, the amino acid kynurenine was found to accumulate in the media even though it was not present in the predicted metabolome of S. elongatus. This indicates that some metabolites, including those not predicted by an organism's genome, are likely excreted into the environment as waste; however, these molecules may have broader ecological relevance if they are labile to nearby microbes. The compounds described herein provide excellent targets for quantitative analysis in field settings to assess the source and lability of dissolved organic matter in situ.
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Affiliation(s)
- Cara L Fiore
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
| | - Krista Longnecker
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
| | - Melissa C Kido Soule
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
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17
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Pagliano C, Saracco G, Barber J. Structural, functional and auxiliary proteins of photosystem II. PHOTOSYNTHESIS RESEARCH 2013; 116:167-88. [PMID: 23417641 DOI: 10.1007/s11120-013-9803-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/07/2013] [Indexed: 05/06/2023]
Abstract
Photosystem II (PSII) is the water-splitting enzyme complex of photosynthesis and consists of a large number of protein subunits. Most of these proteins have been structurally and functionally characterized, although there are differences between PSII of plants, algae and cyanobacteria. Here we catalogue all known PSII proteins giving a brief description, where possible of their genetic origin, physical properties, structural relationships and functions. We have also included details of auxiliary proteins known at present to be involved in the in vivo assembly, maintenance and turnover of PSII and which transiently bind to the reaction centre core complex. Finally, we briefly give details of the proteins which form the outer light-harvesting systems of PSII in different types of organisms.
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Affiliation(s)
- Cristina Pagliano
- Applied Science and Technology Department-BioSolar Lab, Politecnico di Torino, Viale T. Michel 5, 15121, Torino, Alessandria, Italy,
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18
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Torosantucci R, Sharov VS, van Beers M, Brinks V, Schöneich C, Jiskoot W. Identification of oxidation sites and covalent cross-links in metal catalyzed oxidized interferon Beta-1a: potential implications for protein aggregation and immunogenicity. Mol Pharm 2013; 10:2311-22. [PMID: 23534382 DOI: 10.1021/mp300665u] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oxidation via Cu(2+)/ascorbate of recombinant human interferon beta-1a (IFNβ1a) leads to highly immunogenic aggregates, however it is unknown which amino acids are modified and how covalent aggregates are formed. In the present work we mapped oxidized and cross-linked amino acid residues in aggregated IFNβ1a, formed via Cu(2+)/ascorbate catalyzed oxidation. Size exclusion chromatography (SEC) was used to confirm extensive aggregation of oxidized IFNβ1a. Circular dichroism and intrinsic fluorescence spectroscopy indicated substantial loss of secondary and tertiary structure, respectively. Derivatization with 4-(aminomethyl)benzenesulfonic acid was used to demonstrate, by fluorescence in combination with SEC, the presence of tyrosine (Tyr) oxidation products. High performance liquid chromatography coupled to electrospray ionization mass spectrometry of reduced, alkylated, and digested protein was employed to localize chemical degradation products. Oxidation products of methionine, histidine, phenylalanine (Phe), tryptophan, and Tyr residues were identified throughout the primary sequence. Covalent cross-links via 1,4- or 1,6-type addition between primary amines and DOCH (2-amino-3-(3,4-dioxocyclohexa-1,5-dien-1-yl)propanoic acid, an oxidation product of Phe and Tyr) were detected. There was no evidence of disulfide bridge, Schiff base, or dityrosine formation. The chemical cross-links identified in this work are most likely responsible for the formation of covalent aggregates of IFNβ1a induced by oxidation, which have previously been shown to be highly immunogenic.
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Affiliation(s)
- Riccardo Torosantucci
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
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19
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Frankel LK, Sallans L, Limbach PA, Bricker TM. Oxidized amino acid residues in the vicinity of Q(A) and Pheo(D1) of the photosystem II reaction center: putative generation sites of reducing-side reactive oxygen species. PLoS One 2013; 8:e58042. [PMID: 23469138 PMCID: PMC3585169 DOI: 10.1371/journal.pone.0058042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/30/2013] [Indexed: 02/04/2023] Open
Abstract
Under a variety of stress conditions, Photosystem II produces reactive oxygen species on both the reducing and oxidizing sides of the photosystem. A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem. In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues 239F, 241Q, 242E and the D2 residues 238P, 239T, 242E and 247M) and PheoD1 (D1 residues 130E, 133L and 135F). These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.
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Affiliation(s)
- Laurie K. Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Larry Sallans
- The Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Patrick A. Limbach
- The Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Terry M. Bricker
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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20
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Meierhoff K, Westhoff P. The Biogenesis of the Thylakoid Membrane: Photosystem II, a Case Study. PLASTID DEVELOPMENT IN LEAVES DURING GROWTH AND SENESCENCE 2013. [DOI: 10.1007/978-94-007-5724-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Kasson TMD, Barry BA. Reactive oxygen and oxidative stress: N-formyl kynurenine in photosystem II and non-photosynthetic proteins. PHOTOSYNTHESIS RESEARCH 2012; 114:97-110. [PMID: 23161228 DOI: 10.1007/s11120-012-9784-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 10/31/2012] [Indexed: 06/01/2023]
Abstract
While light is the essential driving force for photosynthetic carbon fixation, high light intensities are toxic to photosynthetic organisms. Prolonged exposure to high light results in damage to the photosynthetic membrane proteins and suboptimal activity, a phenomenon called photoinhibition. The primary target for inactivation is the photosystem II (PSII) reaction center. PSII catalyzes the light-induced oxidation of water at the oxygen-evolving complex. Reactive oxygen species (ROS) are generated under photoinhibitory conditions and induce oxidative post translational modifications of amino acid side chains. Specific modification of tryptophan residues to N-formylkynurenine (NFK) occurs in the CP43 and D1 core polypeptides of PSII. The NFK modification has also been detected in other proteins, such as mitochondrial respiratory enzymes, and is formed by a non-random, ROS-targeted mechanism. NFK has been shown to accumulate in PSII during conditions of high light stress in vitro. This review provides a summary of what is known about the generation and function of NFK in PSII and other proteins. Currently, the role of ROS in photoinhibition is under debate. Furthermore, the triggers for the degradation and accelerated turnover of PSII subunits, which occur under high light, are not yet identified. Owing to its unique optical and Raman signal, NFK provides a new marker to use in the identification of ROS generation sites in PSII and other proteins. Also, the speculative hypothesis that NFK, and other oxidative modifications of tryptophan, play a role in the PSII damage and repair cycle is discussed. NFK may have a similar function during oxidative stress in other biologic systems.
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Affiliation(s)
- Tina M Dreaden Kasson
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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22
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Bachi A, Dalle-Donne I, Scaloni A. Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises. Chem Rev 2012. [DOI: 10.1021/cr300073p] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Angela Bachi
- Biological Mass Spectrometry Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
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23
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Frankel LK, Sallans L, Limbach PA, Bricker TM. Identification of oxidized amino acid residues in the vicinity of the Mn(4)CaO(5) cluster of Photosystem II: implications for the identification of oxygen channels within the Photosystem. Biochemistry 2012; 51:6371-7. [PMID: 22827410 DOI: 10.1021/bi300650n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As a light-driven water-plastoquinone oxidoreductase, Photosystem II produces molecular oxygen as an enzymatic product. Additionally, under a variety of stress conditions, reactive oxygen species are produced at or near the active site for oxygen evolution. In this study, Fourier-transform ion cyclotron resonance mass spectrometry was used to identify oxidized amino acid residues located in several core Photosystem II proteins (D1, D2, CP43, and CP47) isolated from spinach Photosystem II membranes. While the majority of these oxidized residues (81%) are located on the oxygenated solvent-exposed surface of the complex, several residues on the CP43 protein ((354)E, (355)T, (356)M, and (357)R) which are in close proximity (<15 Å) to the Mn(4)CaO(5) active site are also modified. These residues appear to be associated with putative oxygen/reactive oxygen species exit channel(s) in the photosystem. These results are discussed within the context of a number of computational studies which have identified putative oxygen channels within the photosystem.
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Affiliation(s)
- Laurie K Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, USA
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24
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Dreaden Kasson TM, Rexroth S, Barry BA. Light-induced oxidative stress, N-formylkynurenine, and oxygenic photosynthesis. PLoS One 2012; 7:e42220. [PMID: 22860088 PMCID: PMC3409137 DOI: 10.1371/journal.pone.0042220] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 07/02/2012] [Indexed: 01/30/2023] Open
Abstract
Light stress in plants results in damage to the water oxidizing reaction center, photosystem II (PSII). Redox signaling, through oxidative modification of amino acid side chains, has been proposed to participate in this process, but the oxidative signals have not yet been identified. Previously, we described an oxidative modification, N-formylkynurenine (NFK), of W365 in the CP43 subunit. The yield of this modification increases under light stress conditions, in parallel with the decrease in oxygen evolving activity. In this work, we show that this modification, NFK365-CP43, is present in thylakoid membranes and may be formed by reactive oxygen species produced at the Mn(4)CaO(5) cluster in the oxygen-evolving complex. NFK accumulation correlates with the extent of photoinhibition in PSII and thylakoid membranes. A modest increase in ionic strength inhibits NFK365-CP43 formation, and leads to accumulation of a new, light-induced NFK modification (NFK317) in the D1 polypeptide. Western analysis shows that D1 degradation and oligomerization occur under both sets of conditions. The NFK modifications in CP43 and D1 are found 17 and 14 Angstrom from the Mn(4)CaO(5) cluster, respectively. Based on these results, we propose that NFK is an oxidative modification that signals for damage and repair in PSII. The data suggest a two pathway model for light stress responses. These pathways involve differential, specific, oxidative modification of the CP43 or D1 polypeptides.
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Affiliation(s)
- Tina M. Dreaden Kasson
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Sascha Rexroth
- Department of Biology, Ruhr-Universität, Bochum, Germany
| | - Bridgette A. Barry
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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25
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From colorimetric chemosensors to metal nanoparticles using two new tyrosine Schiff-base ligands for Cu2+ detection. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2011.08.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Ellis-Steinborner ST, Scanlon D, Musgrave IF, Tran TTN, Hack S, Wang T, Abell AD, Tyler MJ, Bowie JH. An unusual kynurenine-containing opioid tetrapeptide from the skin gland secretion of the Australian red tree frog Litoria rubella. Sequence determination by electrospray mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1735-1740. [PMID: 21598333 DOI: 10.1002/rcm.5041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Kyn-containing peptide FP-Kyn-L(NH(2)) is an unusual minor component of the skin peptide profile of the Australian red tree frog Litoria rubella collected from an area within a 20 kilometre radius of Alice Springs in central Australia. The structure was determined by electrospray mass spectrometry and synthesis. The major component of the skin secretion is the analogous tryptophyllin peptide FPWL(NH(2)). Both peptides show opioid activity at 10(-7) M, and are likely to act via the μ opioid receptor.
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27
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Dreaden TM, Chen J, Rexroth S, Barry BA. N-formylkynurenine as a marker of high light stress in photosynthesis. J Biol Chem 2011; 286:22632-41. [PMID: 21527632 PMCID: PMC3121407 DOI: 10.1074/jbc.m110.212928] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/28/2011] [Indexed: 11/06/2022] Open
Abstract
Photosystem II (PSII) is the membrane protein complex that catalyzes the photo-induced oxidation of water at a manganese-calcium active site. Light-dependent damage and repair occur in PSII under conditions of high light stress. The core reaction center complex is composed of the D1, D2, CP43, and CP47 intrinsic polypeptides. In this study, a new chromophore formed from the oxidative post-translational modification of tryptophan is identified in the CP43 subunit. Tandem mass spectrometry peptide sequencing is consistent with the oxidation of the CP43 tryptophan side chain, Trp-365, to produce N-formylkynurenine (NFK). Characterization with ultraviolet visible absorption and ultraviolet resonance Raman spectroscopy supports this assignment. An optical assay suggests that the yield of NFK increases 2-fold (2.2 ± 0.5) under high light illumination. A concomitant 2.4 ± 0.5-fold decrease is observed in the steady-state rate of oxygen evolution under the high light conditions. NFK is the product formed from reaction of tryptophan with singlet oxygen, which can be produced under high light stress in PSII. Reactive oxygen species reactions lead to oxidative damage of the reaction center, D1 protein turnover, and inhibition of electron transfer. Our results are consistent with a role for the CP43 NFK modification in photoinhibition.
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Affiliation(s)
- Tina M. Dreaden
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Jun Chen
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Sascha Rexroth
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Bridgette A. Barry
- From the School of Chemistry and Biochemistry and the Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
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Galetskiy D, Lohscheider JN, Kononikhin AS, Popov IA, Nikolaev EN, Adamska I. Mass spectrometric characterization of photooxidative protein modifications in Arabidopsis thaliana thylakoid membranes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:184-90. [PMID: 21154902 DOI: 10.1002/rcm.4855] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Oxidative and nitrosative stress leaves footprints in the plant chloroplast in the form of oxidatively modified proteins. Using a mass spectrometric approach, we identified 126 tyrosine and 12 tryptophan nitration sites in 164 nitrated proteolytic peptides, mainly from photosystem I (PSI), photosystem II (PSII), cytochrome b(6) /f and ATP-synthase complexes and 140 oxidation products of tyrosine, tryptophan, proline, phenylalanine and histidine residues. While a high number of nitration sites were found in proteins from four photosynthetic complexes indicating that the nitration belongs to one of the prominent posttranslational protein modifications in photosynthetic apparatus, amino acid oxidation products were determined mostly in PSII and to a lower extent in PSI. Exposure of plants to light stress resulted in an increased level of tyrosine and tryptophan nitration and tryptophan oxidation in proteins of PSII reaction center and the oxygen-evolving complex, as compared to low light conditions. In contrast, the level of nitration and oxidation of these amino acid residues strongly decreased for all light-harvesting proteins of PSII under the same conditions. Based on these data, we propose that oxidative modifications of proteins by reactive oxygen and nitrogen species might represent an important regulatory mechanism of protein turnover under light stress conditions, especially for PSII and its antenna proteins.
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Affiliation(s)
- Dmitry Galetskiy
- Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation
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29
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Yang M, Ge W, Chowdhury R, Claridge TDW, Kramer HB, Schmierer B, McDonough MA, Gong L, Kessler BM, Ratcliffe PJ, Coleman ML, Schofield CJ. Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor. J Biol Chem 2010; 286:7648-60. [PMID: 21177872 PMCID: PMC3045019 DOI: 10.1074/jbc.m110.193540] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Factor-inhibiting hypoxia-inducible factor (FIH) catalyzes the β-hydroxylation of an asparagine residue in the C-terminal transcriptional activation domain of the hypoxia inducible factor (HIF), a modification that negatively regulates HIF transcriptional activity. FIH also catalyzes the hydroxylation of highly conserved Asn residues within the ubiquitous ankyrin repeat domain (ARD)-containing proteins. Hydroxylation has been shown to stabilize localized regions of the ARD fold in the case of a three-repeat consensus ankyrin protein, but this phenomenon has not been demonstrated for the extensive naturally occurring ARDs. Here we report that the cytoskeletal ankyrin family are substrates for FIH-catalyzed hydroxylations. We show that the ARD of ankyrinR is multiply hydroxylated by FIH both in vitro and in endogenous proteins purified from human and mouse erythrocytes. Hydroxylation of the D34 region of ankyrinR ARD (ankyrin repeats 13–24) increases its conformational stability and leads to a reduction in its interaction with the cytoplasmic domain of band 3 (CDB3), demonstrating the potential for FIH-catalyzed hydroxylation to modulate protein-protein interactions. Unexpectedly we found that aspartate residues in ankyrinR and ankyrinB are hydroxylated and that FIH-catalyzed aspartate hydroxylation also occurs in other naturally occurring AR sequences. The crystal structure of an FIH variant in complex with an Asp-substrate peptide together with NMR analyses of the hydroxylation product identifies the 3S regio- and stereoselectivity of the FIH-catalyzed Asp hydroxylation, revealing a previously unprecedented posttranslational modification.
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Affiliation(s)
- Ming Yang
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom
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30
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Goswami N, Makhal A, Pal SK. Toward an Alternative Intrinsic Probe for Spectroscopic Characterization of a Protein. J Phys Chem B 2010; 114:15236-43. [DOI: 10.1021/jp105943d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Nirmal Goswami
- Department of Chemical, Biological and Macromolecular Sciences, Unit for Nano Science and Technology, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Abhinandan Makhal
- Department of Chemical, Biological and Macromolecular Sciences, Unit for Nano Science and Technology, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, Unit for Nano Science and Technology, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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31
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Sirpiö S, Khrouchtchova A, Allahverdiyeva Y, Hansson M, Fristedt R, Vener AV, Scheller HV, Jensen PE, Haldrup A, Aro EM. AtCYP38 ensures early biogenesis, correct assembly and sustenance of photosystem II. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:639-51. [PMID: 18445132 DOI: 10.1111/j.1365-313x.2008.03532.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
AtCYP38 is a thylakoid lumen protein comprising the immunophilin domain and the phosphatase inhibitor module. Here we show the association of AtCYP38 with the photosystem II (PSII) monomer complex and address its functional role using AtCYP38-deficient mutants. The dynamic greening process of etiolated leaves failed in the absence of AtCYP38, due to specific problems in the biogenesis of PSII complexes. Also the development of leaves under short-day conditions was severely disturbed. Detailed biophysical and biochemical analysis of mature AtCYP38-deficient plants from favorable growth conditions (long photoperiod) revealed: (i) intrinsic malfunction of PSII, which (ii) occurred on the donor side of PSII and (iii) was dependent on growing light intensity. AtCYP38 mutant plants also showed decreased accumulation of PSII, which was shown not to originate from impaired D1 synthesis or assembly of PSII monomers, dimers and supercomplexes as such but rather from the incorrect fine-tuning of the oxygen-evolving side of PSII. This, in turn, rendered PSII centers extremely susceptible to photoinhibition. AtCYP38 deficiency also drastically decreased the in vivo phosphorylation of PSII core proteins, probably related to the absence of the AtCYP38 phosphatase inhibitor domain. It is proposed that during PSII assembly AtCYP38 protein guides the proper folding of D1 (and CP43) into PSII, thereby enabling the correct assembly of the water-splitting Mn(4)-Ca cluster even with high turnover of PSII.
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Affiliation(s)
- Sari Sirpiö
- Department of Biology, Plant Physiology and Molecular Biology, University of Turku, FI-20014 Turku, Finland
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32
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Yamauchi Y, Furutera A, Seki K, Toyoda Y, Tanaka K, Sugimoto Y. Malondialdehyde generated from peroxidized linolenic acid causes protein modification in heat-stressed plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:786-93. [PMID: 18538576 DOI: 10.1016/j.plaphy.2008.04.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Indexed: 05/19/2023]
Abstract
When polyunsaturated fatty acids (PUFAs) in biomembrane are peroxidized, a great diversity of aldehydes is formed, and some of which are highly reactive. Thus they are thought to have biological impacts in stressed plants; however, the detailed mechanism of generation and biochemical effects are unknown. In this study, we show that chloroplasts are major organelles in which malondialdehyde (MDA) generated from peroxidized linolenic acid modifies proteins in heat-stressed plants. First, to clarify the biochemical process of MDA generation from PUFAs and its attachment to proteins, we carried out in vitro experiments using model proteins (BSA and Rubisco) and methylesters of C18 PUFAs that are major components of plant biomembrane. Protein modification was detected by Western blotting using monoclonal antibodies that recognize MDA binding to proteins. Results showed that peroxidation of linolenic acid methylester by reactive oxygen species was essential for protein modification by MDA, and the MDA modification was highly dependent on temperature, leading to a loss of Rubisco activity. When isolated spinach thylakoid membrane was peroxidized at 37 degrees C, oxygen-evolving complex 33kDa protein (OEC33) was modified by MDA. These model experiments suggest that protein modification by MDA preferentially occurs under higher temperatures and oxidative conditions, thus we examined protein modification in heat-stressed plants. Spinach plants were heat-stressed at 40 degrees C under illumination, and modification of OEC33 protein by MDA was detected. In heat-stressed Arabidopsis plants, light-harvesting complex protein was modified by MDA under illumination. This modification was not observed in linolenic acid-deficient mutants (fad3fad7fad8 triple mutant), suggesting that linolenic acid is a major source of protein modification by MDA in heat-stressed plants.
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Affiliation(s)
- Yasuo Yamauchi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
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33
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Helland R, Fjellbirkeland A, Karlsen OA, Ve T, Lillehaug JR, Jensen HB. An oxidized tryptophan facilitates copper binding in Methylococcus capsulatus-secreted protein MopE. J Biol Chem 2008; 283:13897-904. [PMID: 18348978 DOI: 10.1074/jbc.m800340200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins can coordinate metal ions with endogenous nitrogen and oxygen ligands through backbone amino and carbonyl groups, but the amino acid side chains coordinating metals do not include tryptophan. Here we show for the first time the involvement of the tryptophan metabolite kynurenine in a protein metal-binding site. The crystal structure to 1.35 angstroms of MopE* from the methane-oxidizing Methylococcus capsulatus (Bath) provided detailed information about its structure and mononuclear copper-binding site. MopE* contains a novel protein fold of which only one-third of the structure displays similarities to other known folds. The geometry around the copper ion is distorted tetrahedral with one oxygen ligand from a water molecule, two histidine imidazoles (His-132 and His-203), and at the fourth distorted tetrahedral position, the N1 atom of the kynurenine, an oxidation product of Trp-130. Trp-130 was not oxidized to kynurenine in MopE* heterologously expressed in Escherichia coli, nor did this protein bind copper. Our findings indicate that the modification of tryptophan to kynurenine and its involvement in copper binding is an innate property of M. capsulatus MopE*.
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Affiliation(s)
- Ronny Helland
- Norwegian Structural Biology Centre, Faculty of Science, University of Tromso, N-9073 Tromso, Norway
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34
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Rinalducci S, Murgiano L, Zolla L. Redox proteomics: basic principles and future perspectives for the detection of protein oxidation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:3781-801. [PMID: 18977746 DOI: 10.1093/jxb/ern252] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The production and scavenging of chemically reactive species, such as ROS/RNS, are central to a broad range of biotic and abiotic stress and physiological responses in plants. Among the techniques developed for the identification of oxidative stress-induced modifications on proteins, the so-called 'redox proteome', proteomics appears to be the best-suited approach. Oxidative or nitrosative stress leaves different footprints in the cell in the form of different oxidatively modified components and, using the redox proteome, it will be possible to decipher the potential roles played by ROS/RNS-induced modifications in stressed cells. The purpose of this review is to present an overview of the latest research endeavours in the field of plant redox proteomics to identify the role of post-translational modifications of proteins in developmental cell stress. All the strategies set up to analyse the different oxidized/nitrosated amino acids, as well as the different reactivities of ROS and RNS for different amino acids are revised and discussed. A growing body of evidence indicates that ROS/RNS-induced protein modifications may be of physiological significance, and that in some cellular stresses they may act causatively and not arise as a secondary consequence of cell damage. Thus, although previously the oxidative modification of proteins was thought to represent a detrimental process in which the modified proteins were irreversibly inactivated, it is now clear that, in plants, oxidatively/nitrosatively modified proteins can be specific and reversible, playing a key role in normal cell physiology. In this sense, redox proteomics will have a central role in the definition of redox molecular mechanisms associated with cellular stresses.
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Affiliation(s)
- Sara Rinalducci
- Department of Environmental Sciences, University of Tuscia, Largo dell'Università snc, I-01100, Viterbo, Italy
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35
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Rexroth S, Wong CCL, Park JH, Yates JR, Barry BA. An Activated Glutamate Residue Identified in Photosystem II at the Interface between the Manganese-stabilizing Subunit and the D2 Polypeptide. J Biol Chem 2007; 282:27802-9. [PMID: 17666402 DOI: 10.1074/jbc.m704394200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Photosystem II (PSII) catalyzes the oxidation of water during oxygenic photosynthesis. PSII is composed both of intrinsic subunits, such as D1, D2, and CP47, and extrinsic subunits, such as the manganese-stabilizing subunit (MSP). Previous work has shown that amines covalently bind to amino acid residues in the CP47, D1, and D2 subunits of plant and cyanobacterial PSII, and that these covalent reactions are prevented by the addition of chloride in plant preparations depleted of the 18- and 24-kDa extrinsic subunits. It has been proposed that these reactive groups are carbonyl-containing, post-translationally modified amino acid side chains (Ouellette, A. J. A., Anderson, L. B., and Barry, B. A. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 2204-2209 and Anderson, L. B., Ouellette, A. J. A., and Barry, B. A. (2000) J. Biol. Chem. 275, 4920-4927). To identify the amino acid binding site in the spinach D2 subunit, we have employed a biotin-amine labeling reagent, which can be used in conjunction with avidin affinity chromatography to purify biotinylated peptides from the PSII complex. Multidimensional chromato-graphic separation and multistage mass spectrometry localizes a novel post-translational modification in the D2 subunit to glutamate 303. We propose that this glutamate is activated for amine reaction by post-translational modification. Because the modified glutamate is located at a contact site between the D2 and manganese-stabilizing subunits, we suggest that the modification is important in vivo in stabilizing the interaction between these two PSII subunits. Consistent with this conclusion, mutations at the modified glutamate alter the steady-state rate of photosynthetic oxygen evolution.
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Affiliation(s)
- Sascha Rexroth
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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36
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Si S, Mandal TK. Tryptophan-based peptides to synthesize gold and silver nanoparticles: a mechanistic and kinetic study. Chemistry 2007; 13:3160-8. [PMID: 17245786 DOI: 10.1002/chem.200601492] [Citation(s) in RCA: 227] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Synthetic oligopeptides with a tryptophan residue at the C-terminus have been used for the synthesis of gold and silver nanoparticles at pH 11. The tryptophan residue in the peptides is responsible for the reduction of metal ions to the respective metals, possibly through electron transfer. A mechanistic pathway has been proposed to explain the reductive properties of the tryptophan moiety of the peptide based on some spectroscopic techniques, such as UV-visible and fluorescence spectroscopy. This study reveals that some of the peptide molecules are converted to its corresponding ditryptophan, kynurenine form and some cross-linked products, all of which are highly fluorescent species. The resultant peptide-functionalized metal nanoparticles have also been characterized by UV-visible spectroscopy, transmission electron microscopy, and Fourier transform IR spectroscopy and thermogravimatric analysis.
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Affiliation(s)
- Satyabrata Si
- Polymer Science Unit & Centre for Advanced Materials, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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37
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Maron PA, Ranjard L, Mougel C, Lemanceau P. Metaproteomics: a new approach for studying functional microbial ecology. MICROBIAL ECOLOGY 2007; 53:486-93. [PMID: 17431707 DOI: 10.1007/s00248-006-9196-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 11/17/2006] [Accepted: 11/26/2006] [Indexed: 05/14/2023]
Abstract
In the postgenomic era, there is a clear recognition of the limitations of nucleic acid-based methods for getting information on functions expressed by microbial communities in situ. In this context, the large-scale study of proteins expressed by indigenous microbial communities (metaproteome) should provide information to gain insights into the functioning of the microbial component in ecosystems. Characterization of the metaproteome is expected to provide data linking genetic and functional diversity of microbial communities. Studies on the metaproteome together with those on the metagenome and the metatranscriptome will contribute to progress in our knowledge of microbial communities and their contribution in ecosystem functioning. Effectiveness of the metaproteomic approach will be improved as increasing metagenomic information is made available thanks to the environmental sequencing projects currently running. More specifically, analysis of metaproteome in contrasted environmental situations should allow (1) tracking new functional genes and metabolic pathways and (2) identifying proteins preferentially associated with specific stresses. These proteins considered as functional bioindicators should contribute, in the future, to help policy makers in defining strategies for sustainable management of our environment.
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Affiliation(s)
- Pierre-Alain Maron
- UMR Microbiologie et Géochimie des Sols, INRA/Université de Bourgogne, CMSE, BP 86510, 17 rue de Sully, 21065, Dijon Cedex, France
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38
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Okada M, Sato I, Jeong Cho S, Dubnau D, Sakagami Y. Chemical synthesis of ComX pheromone and related peptides containing isoprenoidal tryptophan residues. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.06.074] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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39
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Song H, Bao S, Ramanadham S, Turk J. Effects of biological oxidants on the catalytic activity and structure of group VIA phospholipase A2. Biochemistry 2006; 45:6392-406. [PMID: 16700550 PMCID: PMC2044503 DOI: 10.1021/bi060502a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Group VIA phospholipase A(2) (iPLA(2)beta) is expressed in phagocytes, vascular cells, pancreatic islet beta-cells, neurons, and other cells and plays roles in transcriptional regulation, cell proliferation, apoptosis, secretion, and other events. A bromoenol lactone (BEL) suicide substrate used to study iPLA(2)beta functions inactivates iPLA(2)beta by alkylating Cys thiols. Because thiol redox reactions are important in signaling and some cells that express iPLA(2)beta produce biological oxidants, iPLA(2)beta might be subject to redox regulation. We report that biological concentrations of H(2)O(2), NO, and HOCl inactivate iPLA(2)beta, and this can be partially reversed by dithiothreitol (DTT). Oxidant-treated iPLA(2)beta modifications were studied by LC-MS/MS analyses of tryptic digests and included DTT-reversible events, e.g., formation of disulfide bonds and sulfenic acids, and others not so reversed, e.g., formation of sulfonic acids, Trp oxides, and Met sulfoxides. W(460) oxidation could cause irreversible inactivation because it is near the lipase consensus sequence ((463)GTSTG(467)), and site-directed mutagenesis of W(460) yields active mutant enzymes that exhibit no DTT-irreversible oxidative inactivation. Cys651-sulfenic acid formation could be one DTT-reversible inactivation event because Cys651 modification correlates closely with activity loss and its mutagenesis reduces sensitivity to inhibition. Intermolecular disulfide bond formation might also cause reversible inactivation because oxidant-treated iPLA(2)beta contains DTT-reducible oligomers, and oligomerization occurs with time- and temperature-dependent iPLA(2)beta inactivation that is attenuated by DTT or ATP. Subjecting insulinoma cells to oxidative stress induces iPLA(2)beta oligomerization, loss of activity, and subcellular redistribution and reduces the rate of release of arachidonate from phospholipids. These findings raise the possibility that redox reactions affect iPLA(2)beta functions.
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Affiliation(s)
- Haowei Song
- Medicine Department Mass Spectrometry Facility, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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40
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Dalle-Donne I, Scaloni A, Giustarini D, Cavarra E, Tell G, Lungarella G, Colombo R, Rossi R, Milzani A. Proteins as biomarkers of oxidative/nitrosative stress in diseases: the contribution of redox proteomics. MASS SPECTROMETRY REVIEWS 2005; 24:55-99. [PMID: 15389864 DOI: 10.1002/mas.20006] [Citation(s) in RCA: 306] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Reactive oxygen species (ROS) and reactive nitrogen species (RNS) contribute to the pathogenesis and/or progression of several human diseases. Proteins are important molecular signposts of oxidative/nitrosative damage. However, it is generally unresolved whether the presence of oxidatively/nitrosatively modified proteins has a causal role or simply reflects secondary epiphenomena. Only direct identification and characterization of the modified protein(s) in a given pathophysiological condition can decipher the potential roles played by ROS/RNS-induced protein modifications. During the last few years, mass spectrometry (MS)-based technologies have contributed in a significant way to foster a better understanding of disease processes. The study of oxidative/nitrosative modifications, investigated by redox proteomics, is contributing to establish a relationship between pathological hallmarks of disease and protein structural and functional abnormalities. MS-based technologies promise a contribution in a new era of molecular medicine, especially in the discovery of diagnostic biomarkers of oxidative/nitrosative stress, enabling early detection of diseases. Indeed, identification and characterization of oxidatively/nitrosatively modified proteins in human diseases has just begun.
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Affiliation(s)
- Isabella Dalle-Donne
- Department of Biology, University of Milan, via Celoria 26, I-20133, Milan, Italy.
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41
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Zhang H, Joseph J, Crow J, Kalyanaraman B. Mass spectral evidence for carbonate-anion-radical-induced posttranslational modification of tryptophan to kynurenine in human Cu, Zn superoxide dismutase. Free Radic Biol Med 2004; 37:2018-26. [PMID: 15544920 DOI: 10.1016/j.freeradbiomed.2004.08.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 08/27/2004] [Accepted: 08/30/2004] [Indexed: 11/25/2022]
Abstract
Previously, we showed that oxidation of tryptophan-32 (Trp-32) residue was crucial for H(2)O(2)/bicarbonate (HCO(3)(-))-dependent covalent aggregation of human Cu,Zn SOD1 (hSOD1). The carbonate anion radical (CO(3)(-))-induced oxidation of Trp-32 to kynurenine-type oxidation products was proposed to cause the aggregation of hSOD1. Here we used the matrix-assisted laser desorption ionization-time of flight mass spectroscopy, high-performance liquid chromatography-electrospray ionization mass spectroscopy, and liquid chromatography mass spectroscopy methods to characterize products. Results show that a peptide region (31-36) of hSOD1 containing the Trp-32 residue (VWGSIK) is oxidatively modified to the N-formylkynurenine (NFK)- and kynurenine (Kyn)-containing peptides (V(NFK)GSIK) and (V(Kyn)GSIK) during HCO(-)-dependent peroxidase activity of hSOD1. Also, UV photolysis of a cobalt complex that generates authentic CO(3)(-) radical induced a similar product profile from hSOD1. Similar products were obtained using a synthetic peptide with the same amino acid sequence (i.e., VWGSIK). We propose a mechanism involving a tryptophanyl radical for CO(3)(-)-induced oxidation of Trp-32 residue (VWGSIK) in hSOD1 to V(NFK)GSIK and V(Kyn)GSIK.
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Affiliation(s)
- Hao Zhang
- Department of Biophysics and Free Radical Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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42
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Grotjohann I, Jolley C, Fromme P. Evolution of photosynthesis and oxygen evolution: Implications from the structural comparison of Photosystems I and II. Phys Chem Chem Phys 2004. [DOI: 10.1039/b408980d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Zhang H, Andrekopoulos C, Joseph J, Chandran K, Karoui H, Crow JP, Kalyanaraman B. Bicarbonate-dependent peroxidase activity of human Cu,Zn-superoxide dismutase induces covalent aggregation of protein: intermediacy of tryptophan-derived oxidation products. J Biol Chem 2003; 278:24078-89. [PMID: 12686560 DOI: 10.1074/jbc.m302051200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study addresses the mechanism of covalent aggregation of human Cu,Zn-superoxide dismutase (hSOD1WT) induced by bicarbonate (HCO3-)-mediated peroxidase activity. Higher molecular weight species (apparent dimers and trimers) of hSOD1WT were formed from incubation mixtures containing hSOD1WT, H2O2, and HCO3-. HCO3--dependent peroxidase activity and covalent aggregation of hSOD1WT were mimicked by UV photolysis of hSOD1-WT in the presence of a [Co(NH3)5CO3]+ complex that generates the carbonate radical anion (CO3.). Human SOD1WT has but one aromatic residue, a tryptophan residue (Trp-32) on the surface of the protein. Substitution of Trp-32 with phenylalanine produced a mutant (hSOD1W32F) that exhibits HCO3--dependent peroxidase activity similar to wild-type enzyme. However, unlike hSOD1WT, incubations containing hSOD1W32F,H2O2, and HCO3-did not result in covalent aggregation of SOD1. These findings indicate that Trp-32 is crucial for CO3.-induced covalent aggregation of hSOD1WT. Spin-trapping results revealed the formation of the Trp-32 radical from hSOD1WT, but not from hSOD1W32F. Spin traps also inhibited the covalent aggregation of hSOD1WT. Fluorescence experiments revealed that Trp-32 was further oxidized by CO3., forming kynurenine-type products in the presence of oxygen. Molecular oxygen was needed for HCO3-/H2O2-dependent aggregation of hSOD1WT, implicating a role for a Trp-32-dependent peroxidative reaction in the covalent aggregation of hSOD1WT. Taken together, these results indicate that Trp-32 oxidation is crucial for covalent aggregation of hSOD1. Implications of HCO3--dependent SOD1 peroxidase activity in amyotrophic lateral sclerosis disease are discussed.
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Affiliation(s)
- Hao Zhang
- Biophysics Research Institute and Free Radical Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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Taylor SW, Fahy E, Murray J, Capaldi RA, Ghosh SS. Oxidative post-translational modification of tryptophan residues in cardiac mitochondrial proteins. J Biol Chem 2003; 278:19587-90. [PMID: 12679331 DOI: 10.1074/jbc.c300135200] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We examined the distribution of N-formylkynurenine, a product of the dioxidation of tryptophan residues in proteins, throughout the human heart mitochondrial proteome. This oxidized amino acid is associated with a distinct subset of proteins, including an over-representation of complex I subunits as well as complex V subunits and enzymes involved in redox metabolism. No relationship was observed between the tryptophan modification and methionine oxidation, a known artifact of sample handling. As the mitochondria were isolated from normal human heart tissue and not subject to any artificially induced oxidative stress, we suggest that the susceptible tryptophan residues in this group of proteins are "hot spots" for oxidation in close proximity to a source of reactive oxygen species in respiring mitochondria.
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Abstract
Proteomics seeks to monitor the global complement of proteins within a cell or organism and accompanying plasticity with respect to development and environment. The proteome is dynamic, the product of current and past gene expression, countless protein-protein interactions and selective proteolytic systems. Consequently the snapshot that a proteomic measurement yields must be integrated into proteome flux; the flow of nutrients and energy through the protein pathways that catalyze and drive life. The thylakoid membrane proteome poses many technical challenges for proteomics. Integral membrane proteins present awkward physico-chemical properties and the abundant photosynthetic machinery conceals much less abundant and no less important proteins such as channels and transporters that control the interaction of stroma and lumen. Discussed here are contrasting approaches to thylakoid proteomics; 'shotgun' techniques that provide throughput benefits by cleaving proteins into smaller more-manageable peptide chunks versus intact protein techniques that provide more detailed and accurate pictures. A two-dimensional chromatography system directly interfaced to electrospray-ionization mass spectrometry has allowed the direct visualization of large reaction-center proteins (up to 83 kDa) from both Photosystems 1 and 2 providing an attractive avenue for characterization of thylakoid membrane proteomes under different conditions because of the ability to resolve molecular heterogeneity resulting from post-translational modifications such as phosphorylation and oxidation. A high-resolution spectrum of Bacteriorhodopsin recorded to an accuracy of 8 ppm using Fourier-transform mass spectrometry demonstrates the first application of this technique to intact polytopic integral membrane proteins.
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Affiliation(s)
- Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, Departments of Psychiatry and Biobehavioral Sciences, Chemistry and Biochemistry, and the Neuropsychiatric Institute, University of California, Los Angeles, CA, 90095, USA,
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