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Srivastava R, Singh N, Kanda T, Yadav S, Yadav S, Atri N. Cyanobacterial Proteomics: Diversity and Dynamics. J Proteome Res 2024; 23:2680-2699. [PMID: 38470568 DOI: 10.1021/acs.jproteome.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.
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Affiliation(s)
| | - Nidhi Singh
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Tripti Kanda
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Sadhana Yadav
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Neelam Atri
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
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Hishida A, Shirai R, Higo A, Matsutani M, Nimura-Matsune K, Takahashi T, Watanabe S, Ehira S, Hihara Y. CRISPRi knockdown of the cyabrB1 gene induces the divergently transcribed icfG and sll1783 operons related to carbon metabolism in the cyanobacterium Synechocystis sp. PCC 6803. J GEN APPL MICROBIOL 2024; 70:n/a. [PMID: 38267064 DOI: 10.2323/jgam.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Most cyanobacterial genomes possess more than two copies of genes encoding cyAbrBs (cyanobacterial AbrB-like proteins) having an AbrB-like DNA-binding domain at their C-terminal region. Accumulating data suggest that a wide variety of metabolic and physiologic processes are regulated by cyAbrBs. In this study, we investigated the function of the essential gene cyabrB1 (sll0359) in Synechocystis sp. PCC 6803 by using CRISPR interference technology. The conditional knockdown of cyabrB1 caused increases of cyAbrB2 transcript and protein levels. However, the effect of cyabrB1 knockdown on global gene expression profile was quite limited compared to the previously reported profound effect of knockout of cyabrB2. Among 24 up-regulated genes, 16 genes were members of the divergently transcribed icfG and sll1783 operons related to carbon metabolism. The results of this and previous studies indicate the different contributions of two cyAbrBs to transcriptional regulation of genes related to carbon, hydrogen and nitrogen metabolism. Possession of a pair of cyAbrBs has been highly conserved during the course of evolution of the cyanobacterial phylum, suggesting physiological significance of transcriptional regulation attained by their interaction.
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Affiliation(s)
- Atsuko Hishida
- Graduate School of Science and Engineering, Saitama University
| | - Ryo Shirai
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University
| | - Akiyoshi Higo
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | | | | | | | | | - Shigeki Ehira
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University
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Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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Minagawa J, Dann M. Extracellular CahB1 from Sodalinema gerasimenkoae IPPAS B-353 Acts as a Functional Carboxysomal β-Carbonic Anhydrase in Synechocystis sp. PCC6803. PLANTS (BASEL, SWITZERLAND) 2023; 12:265. [PMID: 36678979 PMCID: PMC9865033 DOI: 10.3390/plants12020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Cyanobacteria mostly rely on the active uptake of hydrated CO2 (i.e., bicarbonate ions) from the surrounding media to fuel their inorganic carbon assimilation. The dehydration of bicarbonate in close vicinity of RuBisCO is achieved through the activity of carboxysomal carbonic anhydrase (CA) enzymes. Simultaneously, many cyanobacterial genomes encode extracellular α- and β-class CAs (EcaA, EcaB) whose exact physiological role remains largely unknown. To date, the CahB1 enzyme of Sodalinema gerasimenkoae (formerly Microcoleus/Coleofasciculus chthonoplastes) remains the sole described active extracellular β-CA in cyanobacteria, but its molecular features strongly suggest it to be a carboxysomal rather than a secreted protein. Upon expression of CahB1 in Synechocystis sp. PCC6803, we found that its expression complemented the loss of endogenous CcaA. Moreover, CahB1 was found to localize to a carboxysome-harboring and CA-active cell fraction. Our data suggest that CahB1 retains all crucial properties of a cellular carboxysomal CA and that the secretion mechanism and/or the machinations of the Sodalinema gerasimenkoae carboxysome are different from those of Synechocystis.
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Affiliation(s)
- Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology (NIBB), Aichi, Okazaki 444-8585, Japan
| | - Marcel Dann
- Division of Environmental Photobiology, National Institute for Basic Biology (NIBB), Aichi, Okazaki 444-8585, Japan
- Plant Molecular Biology, Ludwig-Maximilian University (LMU) Munich, 82152 Planegg, Germany
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Mechanisms of Stress Tolerance in Cyanobacteria under Extreme Conditions. STRESSES 2022. [DOI: 10.3390/stresses2040036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyanobacteria are oxygen-evolving photoautotrophs with worldwide distribution in every possible habitat, and they account for half of the global primary productivity. Because of their ability to thrive in a hostile environment, cyanobacteria are categorized as “extremophiles”. They have evolved a fascinating repository of distinct secondary metabolites and biomolecules to promote their development and survival in various habitats, including severe conditions. However, developing new proteins/enzymes and metabolites is mostly directed by an appropriate gene regulation system that results in stress adaptations. However, only few proteins have been characterized to date that have the potential to improve resistance against abiotic stresses. As a result, studying environmental stress responses to post-genomic analysis, such as proteome changes using latest structural proteomics and synthetic biology techniques, is critical. In this regard, scientists working on these topics will benefit greatly from the stress of proteomics research. Progress in these disciplines will aid in understanding cyanobacteria’s physiology, biochemical, and metabolic systems. This review summarizes the most recent key findings of cyanobacterial proteome study under various abiotic stresses and the application of secondary metabolites formed during different abiotic conditions.
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Proximity Labeling Facilitates Defining the Proteome Neighborhood of Photosystem II Oxygen Evolution Complex in a Model Cyanobacterium. Mol Cell Proteomics 2022; 21:100440. [PMID: 36356940 PMCID: PMC9764255 DOI: 10.1016/j.mcpro.2022.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Ascorbate peroxidase (APEX)-based proximity labeling coupled with mass spectrometry has a great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO. In total, 38 integral membrane proteins (IMPs) and 93 luminal proteins were identified as proximal to the OEC. A significant portion of these proteins are involved in PS II assembly, maturation, and repair, while the majority of the rest were not previously implicated with PS II. The IMPs include subunits of PS II and cytochrome b6/f, but not of photosystem I (except for PsaL) and ATP synthases, suggesting that the latter two complexes are spatially separated from the OEC with a distance longer than the APEX2 labeling radius. Besides, the topologies of six IMPs were successfully predicted because their lumen-facing regions exclusively contain potential APEX2 labeling sites. The luminal proteins include 66 proteins with a predicted signal peptide and 57 proteins localized also in periplasm, providing important targets to study the regulation and selectivity of protein translocation. Together, we not only developed a robust workflow for the application of APEX2-based proximity labeling in Synechocystis and showcased the feasibility to define the neighborhood proteome of an important protein complex with a short radius but also discovered a set of the proteins that potentially interact with and regulate PS II structure and function.
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Selão TT. Exploring cyanobacterial diversity for sustainable biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3057-3071. [PMID: 35467729 DOI: 10.1093/jxb/erac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an evolutionarily ancient and diverse group of microorganisms. Their genetic diversity has
allowed them to occupy and play vital roles in a wide range of ecological niches, from desert soil crusts to tropical oceans. Owing to bioprospecting efforts and the development of new platform technologies enabling their study and manipulation, our knowledge of cyanobacterial metabolism is rapidly expanding. This review explores our current understanding of the genetic and metabolic features of cyanobacteria, from the more established cyanobacterial model strains to the newly isolated/described species, particularly the fast-growing, highly productive, and genetically amenable strains, as promising chassis for renewable biotechnology. It also discusses emerging technologies for their study and manipulation, enabling researchers to harness the astounding diversity of the cyanobacterial genomic and metabolic treasure trove towards the establishment of a sustainable bioeconomy.
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Affiliation(s)
- Tiago Toscano Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
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Meixner K, Daffert C, Dalnodar D, Mrázová K, Hrubanová K, Krzyzanek V, Nebesarova J, Samek O, Šedrlová Z, Slaninova E, Sedláček P, Obruča S, Fritz I. Glycogen, poly(3-hydroxybutyrate) and pigment accumulation in three Synechocystis strains when exposed to a stepwise increasing salt stress. JOURNAL OF APPLIED PHYCOLOGY 2022; 34:1227-1241. [PMID: 35673609 PMCID: PMC9165259 DOI: 10.1007/s10811-022-02693-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/07/2022] [Accepted: 01/07/2022] [Indexed: 06/15/2023]
Abstract
The cyanobacterial genus Synechocystis is of particular interest to science and industry because of its efficient phototrophic metabolism, its accumulation of the polymer poly(3-hydroxybutyrate) (PHB) and its ability to withstand or adapt to adverse growing conditions. One such condition is the increased salinity that can be caused by recycled or brackish water used in cultivation. While overall reduced growth is expected in response to salt stress, other metabolic responses relevant to the efficiency of phototrophic production of biomass or PHB (or both) have been experimentally observed in three Synechocystis strains at stepwise increasing salt concentrations. In response to recent reports on metabolic strategies to increase stress tolerance of heterotrophic and phototrophic bacteria, we focused particularly on the stress-induced response of Synechocystis strains in terms of PHB, glycogen and photoactive pigment dynamics. Of the three strains studied, the strain Synechocystis cf. salina CCALA192 proved to be the most tolerant to salt stress. In addition, this strain showed the highest PHB accumulation. All the three strains accumulated more PHB with increasing salinity, to the point where their photosystems were strongly inhibited and they could no longer produce enough energy to synthesize more PHB.
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Affiliation(s)
- K. Meixner
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
- BEST Bioenergy and Sustainable Technologies GmbH, Inffeldgasse 21b, 8010 Graz, Austria
| | - C. Daffert
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - D. Dalnodar
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - K. Mrázová
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - K. Hrubanová
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - V. Krzyzanek
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - J. Nebesarova
- Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, Charles University, Vinicna 7, 128 44 Prague 2, Czech Republic
| | - O. Samek
- Institute of Scientific Instruments, The Czech Academy of Sciences, Královopolská 147, 61264 Brno, Czech Republic
| | - Z. Šedrlová
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - E. Slaninova
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - P. Sedláček
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - S. Obruča
- Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - I. Fritz
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
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Wang J, Huang X, Ge H, Wang Y, Chen W, Zheng L, Huang C, Yang H, Li L, Sui N, Wang Y, Zhang Y, Lu D, Fang L, Xu W, Jiang Y, Huang F, Wang Y. The Quantitative Proteome Atlas of a Model Cyanobacterium. J Genet Genomics 2021; 49:96-108. [PMID: 34775074 DOI: 10.1016/j.jgg.2021.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are a group of oxygenic photosynthetic bacteria with great potentials in biotechnological applications and advantages as models for photosynthesis research. The subcellular locations of the majority of proteins in any cyanobacteria remain undetermined, representing a major challenge in using cyanobacteria for both basic and industrial researches. Here, using label free quantitative proteomics we mapped 2027 proteins of Synechocystis sp. PCC6803, a model cyanobacterium, to different subcellular compartments, and generated a proteome atlas with such information. The atlas leads to numerous unexpected but important findings, including the predominant localization of the histidine kinases Hik33 and Hik27 on the thylakoid but not the plasma membrane. Such information completely changes the concept regarding how the two kinases are activated. Together, the atlas provides subcellular localization information for nearly 60% proteome of a model cyanobacterium, and will serve as an important resource for the cyanobacterial research community.
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Affiliation(s)
- Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyang Chen
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haomeng Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Lingyu Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Yu Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Yuqiang Jiang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Huang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China.
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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12
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Dahlgren KK, Gates C, Lee T, Cameron JC. Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002. PHOTOSYNTHESIS RESEARCH 2021; 147:177-195. [PMID: 33280076 PMCID: PMC7880944 DOI: 10.1007/s11120-020-00806-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.
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Affiliation(s)
- Kelsey K Dahlgren
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Colin Gates
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Thomas Lee
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA.
- National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
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14
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Russo DA, Zedler JAZ. Genomic insights into cyanobacterial protein translocation systems. Biol Chem 2020; 402:39-54. [PMID: 33544489 DOI: 10.1515/hsz-2020-0247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
Cyanobacteria are ubiquitous oxygenic photosynthetic bacteria with a versatile metabolism that is highly dependent on effective protein targeting. Protein sorting in diderm bacteria is not trivial and, in cyanobacteria, even less so due to the presence of a complex membrane system: the outer membrane, the plasma membrane and the thylakoid membrane. In cyanobacteria, protein import into the thylakoids is essential for photosynthesis, export to the periplasm fulfills a multifunctional role in maintaining cell homeostasis, and secretion mediates motility, DNA uptake and environmental interactions. Intriguingly, only one set of genes for the general secretory and the twin-arginine translocation pathways seem to be present. However, these systems have to operate in both plasma and thylakoid membranes. This raises the question of how substrates are recognized and targeted to their correct, final destination. Additional complexities arise when a protein has to be secreted across the outer membrane, where very little is known regarding the mechanisms involved. Given their ecological importance and biotechnological interest, a better understanding of protein targeting in cyanobacteria is of great value. This review will provide insights into the known knowns of protein targeting, propose hypotheses based on available genomic sequences and discuss future directions.
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Affiliation(s)
- David A Russo
- Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Julie A Z Zedler
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Dornburgerstr. 159, D-07743 Jena, Germany
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15
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Hu L, He J, Dong M, Tang X, Jiang P, Lei A, Wang J. Divergent metabolic and transcriptomic responses of Synechocystis sp. PCC 6803 to salt stress after adaptive laboratory evolution. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Tanniche I, Collakova E, Denbow C, Senger RS. Characterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopy. PeerJ 2020; 8:e8535. [PMID: 32266110 PMCID: PMC7115747 DOI: 10.7717/peerj.8535] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND During their long evolution, Synechocystis sp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (RametrixTM) were employed to investigate the phenotypic changes in response to external stressors and correlate specific Raman bands with their corresponding biomolecules determined with widely used analytical methods. METHODS Synechocystis cells were grown in the presence of (i) acetate (7.5-30 mM), (ii) NaCl (50-150 mM) and (iii) limiting levels of MgSO4 (0-62.5 mM) in BG-11 media. Principal component analysis (PCA) and discriminant analysis of PCs (DAPC) were performed with the RametrixTM LITE Toolbox for MATLABⓇ. Next, validation of these models was realized via RametrixTM PRO Toolbox where prediction of accuracy, sensitivity, and specificity for an unknown Raman spectrum was calculated. These analyses were coupled with statistical tests (ANOVA and pairwise comparison) to determine statistically significant changes in the phenotypic responses. Finally, amino acid and fatty acid levels were measured with well-established analytical methods. The obtained data were correlated with previously established Raman bands assigned to these biomolecules. RESULTS Distinguishable clusters representative of phenotypic responses were observed based on the external stimuli (i.e., acetate, NaCl, MgSO4, and controls grown on BG-11 medium) or its concentration when analyzing separately. For all these cases, RametrixTM PRO was able to predict efficiently the corresponding concentration in the culture media for an unknown Raman spectra with accuracy, sensitivity and specificity exceeding random chance. Finally, correlations (R > 0.7) were observed for all amino acids and fatty acids between well-established analytical methods and Raman bands.
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Affiliation(s)
- Imen Tanniche
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Eva Collakova
- School of Plant & Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Cynthia Denbow
- School of Plant & Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Ryan S. Senger
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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17
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Kupriyanova EV, Sinetova MA, Mironov KS, Novikova GV, Dykman LA, Rodionova MV, Gabrielyan DA, Los DA. Highly active extracellular α-class carbonic anhydrase of Cyanothece sp. ATCC 51142. Biochimie 2019; 160:200-209. [DOI: 10.1016/j.biochi.2019.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/15/2019] [Indexed: 12/31/2022]
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18
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Sun N, Han X, Xu M, Kaplan A, Espie GS, Mi H. A thylakoid-located carbonic anhydrase regulates CO 2 uptake in the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2019; 222:206-217. [PMID: 30383301 DOI: 10.1111/nph.15575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
Carbonic anhydrases (CAs) are involved in CO2 uptake and conversion, a fundamental process in photosynthetic organisms. Nevertheless, the mechanism underlying the regulation of CO2 uptake and intracellular conversion in cyanobacteria is largely unknown. We report the characterization of a previously unrecognized thylakoid-located CA Slr0051 (EcaB) from the cyanobacterium Synechocystis sp. PCC 6803, which possesses CA activity to regulate CO2 uptake. Inactivation of ecaB stimulated CO2 hydration in the thylakoids, suppressed by the classical CA inhibitor acetazolamide. Absence of ecaB increased the reduced state of the photosynthetic electron transport system, lowered the rate of photosynthetic O2 evolution at high light (HL) and pH, and decreased the cellular affinity for extracellular inorganic carbon. Furthermore, EcaB was upregulated in cells grown at limiting CO2 concentration or HL in tandem with CupA. EcaB is mainly located in the thylakoid membranes where it interacts with CupA and CupB involved in CO2 uptake by converting it to bicarbonate. We propose that modulation of the EcaB level and activity in response to CO2 changes, illumination or pH reversibly regulates its conversion to HCO3 by the two CO2 -uptake systems (CupA, CupB), dissipating the excess HCO3- and alleviating photoinhibition, and thereby optimizes photosynthesis, especially under HL and alkaline conditions.
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Affiliation(s)
- Nan Sun
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xunling Han
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
| | - Min Xu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
| | - Aaron Kaplan
- Department Plant and Environmental Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - George S Espie
- Department of Biology, University of Toronto, Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
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19
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Stebegg R, Schmetterer G, Rompel A. Transport of organic substances through the cytoplasmic membrane of cyanobacteria. PHYTOCHEMISTRY 2019; 157:206-218. [PMID: 30447471 DOI: 10.1016/j.phytochem.2018.08.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/25/2018] [Accepted: 08/17/2018] [Indexed: 06/09/2023]
Abstract
Cyanobacteria are mainly known to incorporate inorganic molecules like carbon dioxide and ammonia from the environment into organic material within the cell. Nevertheless cyanobacteria do import and export organic substances through the cytoplasmic membrane and these processes are essential for all cyanobacteria. In addition understanding the mechanisms of transport of organic molecules through the cytoplasmic membrane might become very important. Genetically modified strains of cyanobacteria could serve as producers and exporters of commercially important substances. In this review we attempt to present all data of transport of organic molecules through the cytoplasmic membrane of cyanobacteria that are currently available with the transported molecules ordered according to their chemical classes.
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Affiliation(s)
- Ronald Stebegg
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria(1).
| | - Georg Schmetterer
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria(1).
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria(1).
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20
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Polyviou D, Machelett MM, Hitchcock A, Baylay AJ, MacMillan F, Moore CM, Bibby TS, Tews I. Structural and functional characterization of IdiA/FutA (Tery_3377), an iron-binding protein from the ocean diazotroph Trichodesmium erythraeum. J Biol Chem 2018; 293:18099-18109. [PMID: 30217820 PMCID: PMC6254336 DOI: 10.1074/jbc.ra118.001929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/31/2018] [Indexed: 11/17/2022] Open
Abstract
Atmospheric nitrogen fixation by photosynthetic cyanobacteria (diazotrophs) strongly influences oceanic primary production and in turn affects global biogeochemical cycles. Species of the genus Trichodesmium are major contributors to marine diazotrophy, accounting for a significant proportion of the fixed nitrogen in tropical and subtropical oceans. However, Trichodesmium spp. are metabolically constrained by the availability of iron, an essential element for both the photosynthetic apparatus and the nitrogenase enzyme. Survival strategies in low-iron environments are typically poorly characterized at the molecular level, because these bacteria are recalcitrant to genetic manipulation. Here, we studied a homolog of the iron deficiency-induced A (IdiA)/ferric uptake transporter A (FutA) protein, Tery_3377, which has been used as an in situ iron-stress biomarker. IdiA/FutA has an ambiguous function in cyanobacteria, with its homologs hypothesized to be involved in distinct processes depending on their cellular localization. Using signal sequence fusions to GFP and heterologous expression in the model cyanobacterium Synechocystis sp. PCC 6803, we show that Tery_3377 is targeted to the periplasm by the twin-arginine translocase and can complement the deletion of the native Synechocystis ferric-iron ABC transporter periplasmic binding protein (FutA2). EPR spectroscopy revealed that purified recombinant Tery_3377 has specificity for iron in the Fe3+ state, and an X-ray crystallography–determined structure uncovered a functional iron substrate–binding domain, with Fe3+ pentacoordinated by protein and buffer ligands. Our results support assignment of Tery_3377 as a functional FutA subunit of an Fe3+ ABC transporter but do not rule out dual IdiA function.
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Affiliation(s)
- Despo Polyviou
- From the Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, United Kingdom
| | - Moritz M Machelett
- From the Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, United Kingdom,; the Department of Biological Sciences, Faculty of Natural and Environmental Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
| | - Andrew Hitchcock
- From the Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, United Kingdom
| | - Alison J Baylay
- From the Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, United Kingdom
| | - Fraser MacMillan
- the School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - C Mark Moore
- From the Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, United Kingdom
| | - Thomas S Bibby
- From the Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, United Kingdom
| | - Ivo Tews
- the Department of Biological Sciences, Faculty of Natural and Environmental Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and.
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21
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Ge H, Fang L, Huang X, Wang J, Chen W, Liu Y, Zhang Y, Wang X, Xu W, He Q, Wang Y. Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium. Mol Cell Proteomics 2018; 16:1258-1274. [PMID: 28668777 DOI: 10.1074/mcp.m116.068080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/07/2017] [Indexed: 01/18/2023] Open
Abstract
The histidine kinase Hik33 plays important roles in mediating cyanobacterial response to divergent types of abiotic stresses including cold, salt, high light (HL), and osmotic stresses. However, how these functions are regulated by Hik33 remains to be addressed. Using a hik33-deficient strain (Δhik33) of Synechocystis sp. PCC 6803 (Synechocystis) and quantitative proteomics, we found that Hik33 depletion induces differential protein expression highly like that induced by divergent types of stresses. This typically includes downregulation of proteins in photosynthesis and carbon assimilation that are necessary for cell propagation, and upregulation of heat shock proteins, chaperons, and proteases that are important for cell survival. This observation indicates that depletion of Hik33 alone mimics divergent types of abiotic stresses, and that Hik33 could be important for preventing abnormal stress response in the normal condition. Moreover, we found most proteins of plasmid origin were significantly upregulated in Δhik33, though their biological significance remains to be addressed. Together, the systematically characterized Hik33-regulated cyanobacterial proteome, which is largely involved in stress responses, builds the molecular basis for Hik33 as a general regulator of stress responses.
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Affiliation(s)
- Haitao Ge
- From the ‡State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan 250100, China
| | - Longfa Fang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiahe Huang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Jinlong Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiyang Chen
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Liu
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanya Zhang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Xiaorong Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Xu
- ‖Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504
| | - Qingfang He
- From the ‡State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan 250100, China; .,**Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas
| | - Yingchun Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China; .,¶University of Chinese Academy of Sciences, Beijing, 100049, China
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22
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Miranda H, Immerzeel P, Gerber L, Hörnaeus K, Lind SB, Pattanaik B, Lindberg P, Mamedov F, Lindblad P. Sll1783, a monooxygenase associated with polysaccharide processing in the unicellular cyanobacterium Synechocystis PCC 6803. PHYSIOLOGIA PLANTARUM 2017; 161:182-195. [PMID: 28429526 DOI: 10.1111/ppl.12582] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/25/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
Cyanobacteria play a pivotal role as the primary producer in many aquatic ecosystems. The knowledge on the interacting processes of cyanobacteria with its environment - abiotic and biotic factors - is still very limited. Many potential exocytoplasmic proteins in the model unicellular cyanobacterium Synechocystis PCC 6803 have unknown functions and their study is essential to improve our understanding of this photosynthetic organism and its potential for biotechnology use. Here we characterize a deletion mutant of Synechocystis PCC 6803, Δsll1783, a strain that showed a remarkably high light resistance which is related with its lower thylakoid membrane formation. Our results suggests Sll1783 to be involved in a mechanism of polysaccharide degradation and uptake and we hypothesize it might function as a sensor for cell density in cyanobacterial cultures.
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Affiliation(s)
- Hélder Miranda
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Peter Immerzeel
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Lorenz Gerber
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Katarina Hörnaeus
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Sara Bergström Lind
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Bagmi Pattanaik
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Pia Lindberg
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Fikret Mamedov
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Peter Lindblad
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
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Abstract
Low temperature can greatly restrict the growth and development of rice. The rice seedlings show growth retardation, lamina wrap, and part of blade even died under the condition of low temperature. In order to get more information about cold stress responses in rice, two dimensional electrophoresis and bioinformatics analysis of mass spectrometry were used to preliminary survey the cold tolerance of cold sensitive line 9311 and cold resistance variety Fujisaka 5 under cold stress. Two dimensional electrophoresis maps of 9311 and Fujisaka 5 were established under cold treatment. With analysis of bioinformation, the proteins were found involve in many aspects of rice development. The largest category of proteins is functioning on metabolism. By comparing the proteins from the two varieties, it can be found that most proteins from 9311 were down-regulated and were up-regulated in Fujisaka 5. The results showed that the membrane composition and structure were damaged, metabolism changed dramatically and rice defense system was activated under the cold stimulation. Fifty-nine proteins related to the resistance of cold stress were identified in our study, and we have investigated and classified all of their biological functions. The importance of our study are providing some conduct for the research of rice resistant to cold stress, supporting auxiliary technique for rice varieties and widening the search field of cold tolerance in plants.
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The HhoA protease from Synechocystis sp. PCC 6803 – Novel insights into structure and activity regulation. J Struct Biol 2017; 198:147-153. [DOI: 10.1016/j.jsb.2016.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 11/18/2022]
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25
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Dong W, Wang J, Niu G, Zhao S, Liu L. Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803. FEBS Lett 2016; 590:3435-3442. [PMID: 27616292 DOI: 10.1002/1873-3468.12416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/04/2016] [Accepted: 09/05/2016] [Indexed: 11/05/2022]
Abstract
The high temperature requirement A (HtrA) proteases are oligomeric serine proteases essential for protein quality control. HtrA homolog A (HhoA) from the photosynthetic cyanobacterium Synechocystis sp. PCC 6803 assembles into a proteolytically active hexamer. Herein, we present the crystal structure of the hexameric HhoA in complex with the copurified peptide. Our data indicate the presence of three methionines in close proximity to the peptide-binding site of the PDZ domain. Unexpectedly, we observed that a zinc ion is accommodated within the central channel formed by a HhoA trimer. However, neither calcium nor magnesium showed affinity for HhoA. The role of the zinc ion in HhoA was tested in an in vitro proteolytic assay against the nonspecific substrate β-casein and was found to be inhibitory. Our findings provide insights into the regulation of HhoA by a redox-related mechanism involving methionine residues and by zinc ion-binding within the central channel.
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Affiliation(s)
- Wei Dong
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Wang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoqi Niu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shun Zhao
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lin Liu
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
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26
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Yadav RK, Thagela P, Tripathi K, Abraham G. Physiological and proteomic analysis of salinity tolerance of the halotolerant cyanobacterium Anabaena sp. World J Microbiol Biotechnol 2016; 32:147. [PMID: 27430514 DOI: 10.1007/s11274-016-2098-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 06/15/2016] [Indexed: 12/12/2022]
Abstract
The halotolerant cyanobacterium Anabaena sp was grown under NaCl concentration of 0, 170 and 515 mM and physiological and proteomic analysis was performed. At 515 mM NaCl the cyanobacterium showed reduced photosynthetic activities and significant increase in soluble sugar content, proline and SOD activity. On the other hand Anabaena sp grown at 170 mM NaCl showed optimal growth, photosynthetic activities and comparatively low soluble sugar content, proline accumulation and SOD activity. The intracellular Na(+) content of the cells increased both at 170 and 515 mM NaCl. In contrast, the K(+) content of the cyanobacterium Anabaena sp remained stable in response to growth at identical concentration of NaCl. While cells grown at 170 mM NaCl showed highest intracellular K(+)/Na(+) ratio, salinity level of 515 mM NaCl resulted in reduced ratio of K(+)/Na(+). Proteomic analysis revealed 50 salt-responsive proteins in the cyanobacterium Anabaena sp under salt treatment compared with control. Ten protein spots were subjected to MALDI-TOF-MS/MS analysis and the identified proteins are involved in photosynthesis, protein folding, cell organization and energy metabolism. Differential expression of proteins related to photosynthesis, energy metabolism was observed in Anabaena sp grown at 170 mM NaCl. At 170 mM NaCl increased expression of photosynthesis related proteins and effective osmotic adjustment through increased antioxidant enzymes and modulation of intracellular ions contributed to better salinity tolerance and optimal growth. On the contrary, increased intracellular Na(+) content coupled with down regulation of photosynthetic and energy related proteins resulted in reduced growth at 515 mM NaCl. Therefore reduced growth at 515 mM NaCl could be due to accumulation of Na(+) ions and requirement to maintain higher organic osmolytes and antioxidants which is energy intensive. The results thus show that the basis of salt tolerance is different when the halotolerant cyanobacterium Anabaena sp is grown under low and high salinity levels.
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Affiliation(s)
- Ravindra Kumar Yadav
- Centre for Conservation and Utilization of BGA, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Preeti Thagela
- Centre for Conservation and Utilization of BGA, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Keshawanand Tripathi
- Centre for Conservation and Utilization of BGA, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - G Abraham
- Centre for Conservation and Utilization of BGA, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Giner-Lamia J, Pereira SB, Bovea-Marco M, Futschik ME, Tamagnini P, Oliveira P. Extracellular Proteins: Novel Key Components of Metal Resistance in Cyanobacteria? Front Microbiol 2016; 7:878. [PMID: 27375598 PMCID: PMC4894872 DOI: 10.3389/fmicb.2016.00878] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/24/2016] [Indexed: 11/13/2022] Open
Abstract
Metals are essential for all living organisms and required for fundamental biochemical processes. However, when in excess, metals can turn into highly-toxic agents able to disrupt cell membranes, alter enzymatic activities, and damage DNA. Metal concentrations are therefore tightly controlled inside cells, particularly in cyanobacteria. Cyanobacteria are ecologically relevant prokaryotes that perform oxygenic photosynthesis and can be found in many different marine and freshwater ecosystems, including environments contaminated with heavy metals. As their photosynthetic machinery imposes high demands for metals, homeostasis of these micronutrients has been widely studied in cyanobacteria. So far, most studies have focused on how cells are capable of controlling their internal metal pools, with a strong bias toward the analysis of intracellular processes. Ultrastructure, modulation of physiology, dynamic changes in transcription and protein levels have been studied, but what takes place in the extracellular environment when cells are exposed to an unbalanced metal availability remains largely unknown. The interest in studying the subset of proteins present in the extracellular space has only recently begun and the identification and functional analysis of the cyanobacterial exoproteomes are just emerging. Remarkably, metal-related proteins such as the copper-chaperone CopM or the iron-binding protein FutA2 have already been identified outside the cell. With this perspective, we aim to raise the awareness that metal-resistance mechanisms are not yet fully known and hope to motivate future studies assessing the role of extracellular proteins on bacterial metal homeostasis, with a special focus on cyanobacteria.
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Affiliation(s)
- Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, Centro de Ciências do Mar, Universidade do AlgarveFaro, Portugal; Center for Biomedical Research, Universidade do AlgarveFaro, Portugal
| | - Sara B Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do PortoPorto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do PortoPorto, Portugal
| | | | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, Centro de Ciências do Mar, Universidade do AlgarveFaro, Portugal; Center for Biomedical Research, Universidade do AlgarveFaro, Portugal
| | - Paula Tamagnini
- Instituto de Investigação e Inovação em Saúde, Universidade do PortoPorto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do PortoPorto, Portugal; Faculdade de Ciências, Departamento de Biologia, Universidade do PortoPorto, Portugal
| | - Paulo Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do PortoPorto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do PortoPorto, Portugal
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Cheregi O, Wagner R, Funk C. Insights into the Cyanobacterial Deg/HtrA Proteases. FRONTIERS IN PLANT SCIENCE 2016; 7:694. [PMID: 27252714 PMCID: PMC4877387 DOI: 10.3389/fpls.2016.00694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/05/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.
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Selão TT, Zhang L, Knoppová J, Komenda J, Norling B. Photosystem II Assembly Steps Take Place in the Thylakoid Membrane of the Cyanobacterium Synechocystis sp. PCC6803. PLANT & CELL PHYSIOLOGY 2016; 57:95-104. [PMID: 26578692 DOI: 10.1093/pcp/pcv178] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/09/2015] [Indexed: 05/09/2023]
Abstract
Thylakoid biogenesis is an intricate process requiring accurate and timely assembly of proteins, pigments and other cofactors into functional, photosynthetically competent membranes. PSII assembly is studied in particular as its core protein, D1, is very susceptible to photodamage and has a high turnover rate, particularly in high light. PSII assembly is a modular process, with assembly steps proceeding in a specific order. Using aqueous two-phase partitioning to separate plasma membranes (PM) and thylakoid membranes (TM), we studied the subcellular localization of the early assembly steps for PSII biogenesis in a Synechocystis sp. PCC6803 cyanobacterium strain lacking the CP47 antenna. This strain accumulates the early D1-D2 assembly complex which was localized in TM along with associated PSII assembly factors. We also followed insertion and processing of the D1 precursor (pD1) by radioactive pulse-chase labeling. D1 is inserted into the membrane with a C-terminal extension which requires cleavage by a specific protease, the C-terminal processing protease (CtpA), to allow subsequent assembly of the oxygen-evolving complex. pD1 insertion as well as its conversion to mature D1 under various light conditions was seen only in the TM. Epitope-tagged CtpA was also localized in the same membrane, providing further support for the thylakoid location of pD1 processing. However, Vipp1 and PratA, two proteins suggested to be part of the so-called 'thylakoid centers', were found to associate with the PM. Together, these results suggest that early PSII assembly steps occur in TM or specific areas derived from them, with interaction with PM needed for efficient PSII and thylakoid biogenesis.
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Affiliation(s)
- Tiago T Selão
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Lifang Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Jana Knoppová
- Institute of Microbiology, Center Algatech, Opatovický mlýn, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - Josef Komenda
- Institute of Microbiology, Center Algatech, Opatovický mlýn, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - Birgitta Norling
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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Gao L, Wang J, Ge H, Fang L, Zhang Y, Huang X, Wang Y. Toward the complete proteome of Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2015; 126:203-219. [PMID: 25862646 DOI: 10.1007/s11120-015-0140-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/02/2015] [Indexed: 06/04/2023]
Abstract
The proteome of the photosynthetic model organism Synechocystis sp. PCC 6803 has been extensively analyzed in the last 15 years for the purpose of identifying proteins specifically expressed in subcellular compartments or differentially expressed in different environmental or internal conditions. This review summarizes the progress achieved so far with the emphasis on the impact of different techniques, both in sample preparation and protein identification, on the increasing coverage of proteome identification. In addition, this review evaluates the current completeness of proteome identification, and provides insights on the potential factors that could affect the complete identification of the Synechocystis proteome.
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Affiliation(s)
- Liyan Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Haitao Ge
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China.
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Inactivation of the Deg protease family in the cyanobacterium Synechocystis sp. PCC 6803 has impact on the outer cell layers. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:383-94. [DOI: 10.1016/j.jphotobiol.2015.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 12/13/2022]
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Battchikova N, Angeleri M, Aro EM. Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:47-70. [PMID: 25359503 DOI: 10.1007/s11120-014-0050-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/18/2014] [Indexed: 05/03/2023]
Abstract
Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.
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Affiliation(s)
- Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland.
| | - Martina Angeleri
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
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Frain KM, Gangl D, Jones A, Zedler JAZ, Robinson C. Protein translocation and thylakoid biogenesis in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:266-73. [PMID: 26341016 DOI: 10.1016/j.bbabio.2015.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/17/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022]
Abstract
Cyanobacteria exhibit a complex form of membrane differentiation that sets them apart from most bacteria. Many processes take place in the plasma membrane, but photosynthetic light capture, electron transport and ATP synthesis take place in an abundant internal thylakoid membrane. This review considers how this system of subcellular compartmentalisation is maintained, and how proteins are directed towards the various subcompartments--specifically the plasma membrane, periplasm, thylakoid membrane and thylakoid lumen. The involvement of Sec-, Tat- and signal recognition particle- (SRP)-dependent protein targeting pathways is discussed, together with the possible involvement of a so-called 'spontaneous' pathway for the insertion of membrane proteins, previously characterised for chloroplast thylakoid membrane proteins. An intriguing aspect of cyanobacterial cell biology is that most contain only a single set of genes encoding Sec, Tat and SRP components, yet the proteomes of the plasma and thylakoid membranes are very different. The implications for protein sorting mechanisms are considered. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof Conrad Mullineaux.
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Affiliation(s)
- Kelly M Frain
- Centre for Molecular Processing, School of Biosciences, University of Kent, Ingram Building, Canterbury, CT2 7NJ, United Kingdom
| | - Doris Gangl
- Centre for Molecular Processing, School of Biosciences, University of Kent, Ingram Building, Canterbury, CT2 7NJ, United Kingdom
| | - Alexander Jones
- Centre for Molecular Processing, School of Biosciences, University of Kent, Ingram Building, Canterbury, CT2 7NJ, United Kingdom
| | - Julie A Z Zedler
- Centre for Molecular Processing, School of Biosciences, University of Kent, Ingram Building, Canterbury, CT2 7NJ, United Kingdom
| | - Colin Robinson
- Centre for Molecular Processing, School of Biosciences, University of Kent, Ingram Building, Canterbury, CT2 7NJ, United Kingdom.
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Sen S, Agrawal C, Mishra Y, Rai S, Chatterjee A, Yadav S, Singh S, Rai LC. Exploring the membrane proteome of the diazotropic cyanobacterium Anabaena PCC7120 through gel-based proteomics and in silico approaches. J Proteomics 2015. [PMID: 26210591 DOI: 10.1016/j.jprot.2015.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UNLABELLED This paper focuses on the gel-based membrane proteomics from diazotrophic cyanobacterium Anabaena PCC7120 by modifying the protocol of Hall et al. [1]. The bioinformatic analysis revealed that 59 (29 integral, 30 peripheral) of the 67 proteins identified were membrane proteins. Of the 29 integral proteins, except Alr0834, the remaining 28 contained 1-12 transmembrane helices. Sixteen integral proteins harboring signal peptides (Sec/TAT/LipoP) suggest that protein targeting in Anabaena involves both sec-dependent and sec-independent pathways. While majority of photosynthesis and respiration proteins (21 of 24) were confined to broad pH gradient the hypothetical and unknown (12 of 13), and cell envelope proteins (3 of 3) preferred the narrow pH range. Of the 5 transporters and binding proteins, Na(+)/H(+)-exchanging protein and Alr2372 were present in broad, pstS1 and cmpD in narrow and cmpA was common to both pH ranges. The distribution of proteins across pH gradient, thus clearly indicates the functional and structural diversity in membrane proteome of Anabaena. It requires mention that protochlorophyllide oxido-reductase, Na(+)/H(+)-exchanging protein, All1355, Alr2055, Alr3514, Alr2903 and Alr2751 were new entries to the 2DE membrane protein profile of Anabaena. This study demonstrates suitability of the modified protocol for the study of membrane protein from filamentous cyanobacteria. SIGNIFICANCE Anabaena sp. PCC7120 is used as a model organism due to its agriculture significance as biofertilizer, close resemblance with higher plant chloroplast and availability of full genome sequence. Although cytosolic proteome has been explored a lot membrane proteins are still understudied as they are notoriously difficult to display using 2-D technology. Identification and characterization of these proteins is therefore required to elucidate and understand cellular mechanisms. The purpose of this study was to develop a protocol suitable for membrane protein extraction from Anabaena. Additionally, by homology comparison or domain assignment a possible function could be ascribed to novel uncharacterized proteins which will serve as a useful reference for further detailed studies of membrane system in filamentous cyanobacteria. Resolution of membrane proteins ranging from least (single transmembrane helix) to highly hydrophobic (several transmembrane helices) one on 2D gels recommends the gel based approach for identification of membrane proteomics from filamentous cyanobacteria. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Sonia Sen
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Chhavi Agrawal
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Yogesh Mishra
- Department of Botany, Punjab University, Sector 14, Chandigarh 160014, India
| | - Shweta Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Antra Chatterjee
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Shilpi Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - L C Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India.
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The Anabaena sp. PCC 7120 Exoproteome: Taking a Peek outside the Box. Life (Basel) 2015; 5:130-63. [PMID: 25782455 PMCID: PMC4390845 DOI: 10.3390/life5010130] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/31/2014] [Indexed: 01/13/2023] Open
Abstract
The interest in examining the subset of proteins present in the extracellular milieu, the exoproteome, has been growing due to novel insights highlighting their role on extracellular matrix organization and biofilm formation, but also on homeostasis and development. The cyanobacterial exoproteome is poorly studied, and the role of cyanobacterial exoproteins on cell wall biogenesis, morphology and even physiology is largely unknown. Here, we present a comprehensive examination of the Anabaena sp. PCC 7120 exoproteome under various growth conditions. Altogether, 139 proteins belonging to 16 different functional categories have been identified. A large fraction (48%) of the identified proteins is classified as "hypothetical", falls into the "other categories" set or presents no similarity to other proteins. The evidence presented here shows that Anabaena sp. PCC 7120 is capable of outer membrane vesicle formation and that these vesicles are likely to contribute to the exoproteome profile. Furthermore, the activity of selected exoproteins associated with oxidative stress has been assessed, suggesting their involvement in redox homeostasis mechanisms in the extracellular space. Finally, we discuss our results in light of other cyanobacterial exoproteome studies and focus on the potential of exploring cyanobacteria as cell factories to produce and secrete selected proteins.
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36
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Du G, Yang X, Hu M, Hao C, Gu Y, Zhi X, Jiang WG, He J, Cheng S. Designing a novel high-throughput AlphaLISA assay to quantify plasma NHERF1 as a non-small cell lung cancer biomarker. RSC Adv 2015. [DOI: 10.1039/c5ra16502d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel amplified luminescent proximity homogeneous immunoassay (AlphaLISA) has been developed and validated for the quantification of NHERF1 in human plasma.
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Affiliation(s)
- Guifang Du
- Department of Biochemistry and Molecular Biology
- Capital Medical University
- Beijing 100069
- China
- Beijing Key Laboratory of Cancer & Metastasis Research
| | - Xiaomei Yang
- Department of Biochemistry and Molecular Biology
- Capital Medical University
- Beijing 100069
- China
- Beijing Key Laboratory of Cancer & Metastasis Research
| | - Mu Hu
- Beijing Key Laboratory of Cancer & Metastasis Research
- Capital Medical University
- Beijing 100069
- China
- Department of Thoracic Surgery
| | - Chengcheng Hao
- Department of Biochemistry and Molecular Biology
- Capital Medical University
- Beijing 100069
- China
- Beijing Key Laboratory of Cancer & Metastasis Research
| | - Yanan Gu
- Department of Biochemistry and Molecular Biology
- Capital Medical University
- Beijing 100069
- China
- Beijing Key Laboratory of Cancer & Metastasis Research
| | - Xiuyi Zhi
- Beijing Key Laboratory of Cancer & Metastasis Research
- Capital Medical University
- Beijing 100069
- China
- Department of Thoracic Surgery
| | - Wen G. Jiang
- Department of Biochemistry and Molecular Biology
- Capital Medical University
- Beijing 100069
- China
- Beijing Key Laboratory of Cancer & Metastasis Research
| | - Junqi He
- Department of Biochemistry and Molecular Biology
- Capital Medical University
- Beijing 100069
- China
- Beijing Key Laboratory of Cancer & Metastasis Research
| | - Shan Cheng
- Department of Biochemistry and Molecular Biology
- Capital Medical University
- Beijing 100069
- China
- Beijing Key Laboratory of Cancer & Metastasis Research
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Salt acclimation of cyanobacteria and their application in biotechnology. Life (Basel) 2014; 5:25-49. [PMID: 25551682 PMCID: PMC4390839 DOI: 10.3390/life5010025] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/19/2014] [Indexed: 12/25/2022] Open
Abstract
The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the accumulation of compatible solutes. Cyanobacterial salt acclimation has been characterized in much detail using selected model cyanobacteria, but their salt sensing and regulatory mechanisms are less well understood. Here, we briefly review recent advances in the identification of salt acclimation processes and the essential genes/proteins involved in acclimation to high salt. This knowledge is of increasing importance because the necessary mass cultivation of cyanobacteria for future use in biotechnology will be performed in sea water. In addition, cyanobacterial salt resistance genes also can be applied to improve the salt tolerance of salt sensitive organisms, such as crop plants.
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Giner-Lamia J, López-Maury L, Florencio FJ. CopM is a novel copper-binding protein involved in copper resistance in Synechocystis sp. PCC 6803. Microbiologyopen 2014; 4:167-85. [PMID: 25545960 PMCID: PMC4335983 DOI: 10.1002/mbo3.231] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/13/2014] [Accepted: 11/20/2014] [Indexed: 01/15/2023] Open
Abstract
Copper resistance system in the cyanobacterium Synechocystis sp. PCC 6803 comprises two operons, copMRS and copBAC, which are expressed in response to copper in the media. copBAC codes for a heavy-metal efflux–resistance nodulation and division (HME-RND) system, while copMRS codes for a protein of unknown function, CopM, and a two-component system CopRS, which controls the expression of these two operons. Here, we report that CopM is a periplasmic protein able to bind Cu(I) with high affinity (KD ∼3 × 10−16). Mutants lacking copM showed a sensitive copper phenotype similar to mutants affected in copB, but lower than mutants of the two-component system CopRS, suggesting that CopBAC and CopM constitute two independent resistance mechanisms. Moreover, constitutive expression of copM is able to partially suppress the copper sensitivity of the copR mutant strain, pointing out that CopM per se is able to confer copper resistance. Furthermore, constitutive expression of copM was able to reduce total cellular copper content of the copR mutant to the levels determined in the wild-type (WT) strain. Finally, CopM was localized not only in the periplasm but also in the extracellular space, suggesting that CopM can also prevent copper accumulation probably by direct copper binding outside the cell.
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Affiliation(s)
- Joaquín Giner-Lamia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092, Sevilla, Spain
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Gao L, Ge H, Huang X, Liu K, Zhang Y, Xu W, Wang Y. Systematically ranking the tightness of membrane association for peripheral membrane proteins (PMPs). Mol Cell Proteomics 2014; 14:340-53. [PMID: 25505158 DOI: 10.1074/mcp.m114.044800] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic protein complexes as the landmarks, we found that proteins involved in two-component signal transduction systems and transporters are overall tightly associated with the membranes, whereas the associations of ribosomal proteins are much weaker. Moreover, we found that hypothetical proteins containing the same domains generally have similar tightness. This work provided a global view of the structural organization of the membrane proteome with respect to divergent functions, and built the foundation for future investigation of the dynamic membrane proteome reorganization in response to different environmental or internal stimuli.
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Affiliation(s)
- Liyan Gao
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Haitao Ge
- §State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Xiahe Huang
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Kehui Liu
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Yuanya Zhang
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Wu Xu
- ¶Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504
| | - Yingchun Wang
- From the ‡State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China;
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de Araujo C, Arefeen D, Tadesse Y, Long BM, Price GD, Rowlett RS, Kimber MS, Espie GS. Identification and characterization of a carboxysomal γ-carbonic anhydrase from the cyanobacterium Nostoc sp. PCC 7120. PHOTOSYNTHESIS RESEARCH 2014; 121:135-50. [PMID: 24907906 DOI: 10.1007/s11120-014-0018-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/19/2014] [Indexed: 05/26/2023]
Abstract
Carboxysomes are proteinaceous microcompartments that encapsulate carbonic anhydrase (CA) and ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco); carboxysomes, therefore, catalyze reversible HCO3 (-) dehydration and the subsequent fixation of CO2. The N- and C-terminal domains of the β-carboxysome scaffold protein CcmM participate in a network of protein-protein interactions that are essential for carboxysome biogenesis, organization, and function. The N-terminal domain of CcmM in the thermophile Thermosynechococcus elongatus BP-1 is also a catalytically active, redox regulated γ-CA. To experimentally determine if CcmM from a mesophilic cyanobacterium is active, we cloned, expressed and purified recombinant, full-length CcmM from Nostoc sp. PCC 7120 as well as the N-terminal 209 amino acid γ-CA-like domain. Both recombinant proteins displayed ethoxyzolamide-sensitive CA activity in mass spectrometric assays, as did the carboxysome-enriched TP fraction. NstCcmM209 was characterized as a moderately active and efficient γ-CA with a k cat of 2.0 × 10(4) s(-1) and k cat/K m of 4.1 × 10(6) M(-1) s(-1) at 25 °C and pH 8, a pH optimum between 8 and 9.5 and a temperature optimum spanning 25-35 °C. NstCcmM209 also catalyzed the hydrolysis of the CO2 analog carbonyl sulfide. Circular dichroism and intrinsic tryptophan fluorescence analysis demonstrated that NstCcmM209 was progressively and irreversibly denatured above 50 °C. NstCcmM209 activity was inhibited by the reducing agent tris(hydroxymethyl)phosphine, an effect that was fully reversed by a molar excess of diamide, a thiol oxidizing agent, consistent with oxidative activation being a universal regulatory mechanism of CcmM orthologs. Immunogold electron microscopy and Western blot analysis of TP pellets indicated that Rubisco and CcmM co-localize and are concentrated in Nostoc sp. PCC 7120 carboxysomes.
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Affiliation(s)
- Charlotte de Araujo
- Department of Cell & Systems Biology, University of Toronto, Mississauga, ON, Canada
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Matallana-Surget S, Derock J, Leroy B, Badri H, Deschoenmaeker F, Wattiez R. Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005. PLoS One 2014; 9:e99076. [PMID: 24914774 PMCID: PMC4051694 DOI: 10.1371/journal.pone.0099076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/09/2014] [Indexed: 11/19/2022] Open
Abstract
The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionation procedures were used and combined with LC-MS/MS analysis, enabling the overall identification of 1306 proteins, which represents 21% coverage of the theoretical proteome. A total of 30 proteins were found to be significantly differentially regulated under light/dark growth transition. Interestingly, most of the proteins showing differential abundance were related to photosynthesis, the Calvin cycle and translation processes. A novel aspect and major achievement of this work is the successful improvement of the cyanobacterial proteome coverage using a 3D LC-MS/MS approach, based on an immobilized metal affinity chromatography, a suitable tool that enabled us to eliminate the most abundant protein, the allophycocyanin. We also demonstrated that cell growth follows a light/dark cycle in A. platensis. This preliminary proteomic study has highlighted new characteristics of the Arthrospira platensis proteome in terms of diurnal regulation.
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Affiliation(s)
- Sabine Matallana-Surget
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
| | - Jérémy Derock
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
| | - Hanène Badri
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
- Unit of Microbiology, Expert Group Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Frédéric Deschoenmaeker
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
- * E-mail:
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Metabolomic analysis of the salt-sensitive mutants reveals changes in amino acid and fatty acid composition important to long-term salt stress in Synechocystis sp. PCC 6803. Funct Integr Genomics 2014; 14:431-40. [PMID: 24643737 DOI: 10.1007/s10142-014-0370-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 10/25/2022]
Abstract
Early studies in cyanobacteria have found that few genes induced by short-term salt shock (15-60 min) display a stable induction in the long-term (>1 day) salt-acclimated cells; meanwhile, most of the genes responsive to long-term salt stress were different from those by short-term salt shock, suggesting that different regulatory mechanisms may be involved for short-term and long-term salt stress responses. In our previous work using the model cyanobacterium Synechocystis sp. PCC 6803, sll1734 encoding CO2 uptake-related protein (CupA) and three genes encoding hypothetical proteins (i.e., ssr3402, slr1339, and ssr1853) were found induced significantly after a 3-day salt stress, and the corresponding gene knockout mutants were found salt sensitive. To further decipher the mechanisms that these genes may be involved, in this study, we performed a comparative metabolomic analysis of the wild-type Synechocystis and the four salt-sensitive mutants using a gas chromatography-mass spectrometry (GC-MS) approach. A metabolomic data set that consisted of 60 chemically classified metabolites was then subjected to a weighted correlation network analysis (WGCNA) to identify the metabolic modules and hub metabolites specifically related to each of the salt-stressed mutants. The results showed that two, one, zero, and two metabolic modules were identified specifically associated with the knockout events of sll1734, ssr3402, slr1339, and ssr1853, respectively. The mutant-associated modules included metabolites such as lysine and palmitic acid, suggesting that amino acid and fatty acid metabolisms are among the key protection mechanisms against long-term salt stresses in Synechocystis. The metabolomic results were further confirmed by quantitative reverse-transcription PCR analysis, which showed the upregulation of lysine and fatty acid synthesis-related genes. The study provided new insights on metabolic networks involved in long-term salt stress response in Synechocystis.
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Rai S, Agrawal C, Shrivastava AK, Singh PK, Rai LC. Comparative proteomics unveils cross species variations in Anabaena under salt stress. J Proteomics 2014; 98:254-70. [PMID: 24406298 DOI: 10.1016/j.jprot.2013.12.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 12/04/2013] [Accepted: 12/12/2013] [Indexed: 11/28/2022]
Abstract
UNLABELLED The present study compares protein diversity within three Anabaena species (Anabaena doliolum, Anabaena sp.PCC 7120 and Anabaena L31). 2-DE based analysis of 256 protein spots in control and 1, 3, 5, and 7days of salt treatment resulted into 96 proteins arching across fourteen functional categories were assigned to biochemical pathways using KOBAS 2.0. While 52.34% of the evaluated protein spots were common across three species, the remaining 47.66% fraction mainly comprised of the hypothetical and unknown proteins. PSORTb, CDD, Motifscan and Pfam revealed function and subcellular localization for 27 of the 31 hypothetical and unknown proteins. The differences in high salt tolerance (LC50) of A. doliolum over A. L31 was reflected by (i) many fold accumulation (as spot volumes) of Alr3090, Alr0803, peptidyl prolyl cis-trans isomerase and modulator of DNA gyrase proteins, and (ii) a better photosynthesis and energy homeostasis as indicated through photosystem activity, respiration, ATP and NADPH contents. Some common noteworthy salt effects include (i) photosystem damage, (ii) DNA damage repair, (iii) upregulated protein synthesis, (iv) enhanced sulphur metabolism, and (v) upregulated pentose phosphate pathway. 34 of the identified protein spots are novel entries to the Anabaena salt proteome. This study reveals the existence of separate strategies even within species to combat stress. BIOLOGICAL SIGNIFICANCE This study for the first time enumerates protein diversity in three Anabaena species employing their presence/absence and relative abundance. Proteomics integrated with physiology and bioinformatics deciphers differential salt tolerance among the studied species and is the first of its kind to predict the function of hypothetical and unknown proteins. Salt-induced proteomic alterations clearly demonstrate significant metabolic shifts and existence of separate molecular phenome among the species investigated. This may be responsible for niche specificity limiting their application as biofertilizer. Of the 96 identified proteins, a large chunk are new entries to the Anabaena salt proteome while some protein genes may be used as potential candidates for engineering salt tolerant cyanobacteria.
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Affiliation(s)
- Snigdha Rai
- Molecular Biology Section, Laboratory of Algal Biology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Chhavi Agrawal
- Molecular Biology Section, Laboratory of Algal Biology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Alok Kumar Shrivastava
- Molecular Biology Section, Laboratory of Algal Biology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Prashant Kumar Singh
- Molecular Biology Section, Laboratory of Algal Biology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - L C Rai
- Molecular Biology Section, Laboratory of Algal Biology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India.
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Qiao J, Huang S, Te R, Wang J, Chen L, Zhang W. Integrated proteomic and transcriptomic analysis reveals novel genes and regulatory mechanisms involved in salt stress responses in Synechocystis sp. PCC 6803. Appl Microbiol Biotechnol 2013; 97:8253-64. [PMID: 23925534 DOI: 10.1007/s00253-013-5139-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
Salt stress is a common stress that limits growth and productivity of photosynthetic microbes in natural environments. Although cellular responses of a model cyanobacterium Synechocystis sp. PCC6803 to high and changing salt concentration have been studied, it remains undefined of the gene components and their regulation in the long-term salt acclimation networks. In this study, we performed an integrated study coupling a quantitative iTRAQ-LC-MS/MS proteomics and a next-generation sequencing-based RNA-seq transcriptomics on Synechocystis under salt stress for an extended period of time. Comparative quantification of protein abundances led to the identification of 68 and 108 proteins differentially regulated by salt treatment at 24 and 48 h, respectively. RNA-seq transcriptomic analysis showed that genes involved in energy metabolism and protein synthesis, and genes encoding hypothetical proteins responded to salt stress in a phase-dependent pattern. Notably, a gene encoding CO2-uptake-related protein (CupA) and three genes encoding hypothetical proteins were induced significantly at either transcript or protein level after long-term salt stress. Gene knockout and comparative growth analysis demonstrated that these four genes were involved in salt tolerance in Synechocystis. In addition, a complementary proteome and transcriptome analysis showed that concordance between protein abundances and their corresponding mRNAs varied significantly between various gene-protein pairs, indicating divergent regulation of transcriptional and post-transcriptional processes during salt stress adaptation in Synechocystis. The study provided new insights on genes and regulatory mechanism involved in salt stress response in Synechocystis.
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Affiliation(s)
- Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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Wang H, Yang Y, Chen W, Ding L, Li P, Zhao X, Wang X, Li A, Bao Q. Identification of differentially expressed proteins of Arthrospira (Spirulina) plantensis-YZ under salt-stress conditions by proteomics and qRT-PCR analysis. Proteome Sci 2013; 11:6. [PMID: 23363438 PMCID: PMC3599948 DOI: 10.1186/1477-5956-11-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 12/23/2012] [Indexed: 11/10/2022] Open
Abstract
Arthrospira (Spirulina) platensis as a representative species of cyanobacteria has been recognized and used worldwide as a source of protein in the food, which possesses some unusual and valuable physiological characteristics, such as alkali and salt tolerance. Based on complete genome sequencing of Arthrospira (Spirulina) plantensis-YZ, we compared the protein expression profiles of this organism under different salt-stress conditions (i.e. 0.02 M, 0.5 M and 1.0 M NaCl, respectively), using 2-D electrophoresis and peptide mass fingerprinting, and retrieved 141 proteins showing significantly differential expression in response to salt-stress. Of the 141 proteins, 114 Arthrospira (Spirulina) plantensis-YZ proteins were found with significant homology to those found in Arthrospira (76 proteins in Arthrospira platensis str. Paraca and 38 in Arthrospira maxima CS-328). The remaining 27 proteins belong to other bacteria. Subsequently, we determined the transcriptional level of 29 genes in vivo in response to NaCl treatments and verified them by qRT-PCR. We found that 12 genes keep consistency at both transcription and protein levels, and transcription of all of them but one were up-regulated. We classified the 141 differentially expressed proteins into 18 types of function categories using COG database, and linked them to their respective KEGG metabolism pathways. These proteins are involved in 31 metabolism pathways, such as photosynthesis, glucose metabolism, cysteine and methionine metabolism, lysine synthesis, fatty acid metabolism, glutathione metabolism. Additionally, the SRPs, heat shock protein and ABC transporter proteins were identified, which probably render Arthrospira (Spirulina) plantensis's resistance against high salt stress.
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Affiliation(s)
- Huili Wang
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical College, Wenzhou, 325035, China.
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Zhang L, Selão TT, Pisareva T, Qian J, Sze SK, Carlberg I, Norling B. Deletion of Synechocystis sp. PCC 6803 leader peptidase LepB1 affects photosynthetic complexes and respiration. Mol Cell Proteomics 2013; 12:1192-203. [PMID: 23358502 DOI: 10.1074/mcp.m112.022145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The cyanobacterium Synechocystis sp. PCC 6803 possesses two leader peptidases, LepB1 (Sll0716) and LepB2 (Slr1377), responsible for the processing of signal peptide-containing proteins. Deletion of the gene for LepB1 results in an inability to grow photoautotrophically and an extreme light sensitivity. Here we show, using a combination of Blue Native/SDS-PAGE, Western blotting and iTRAQ analysis, that lack of LepB1 strongly affects the cell's ability to accumulate wild-type levels of both photosystem I (PSI) and cytochrome (Cyt) b6f complexes. The impaired assembly of PSI and Cyt b6f is considered to be caused by the no or slow processing of the integral subunits PsaF and Cyt f respectively. In particular, PsaF, one of the PSI subunits, was found incorporated into PSI in its unprocessed form, which could influence the assembly and/or stability of PSI. In contrast to these results, we found the amount of assembled photosystem II (PSII) unchanged, despite a slower processing of PsbO. Thus, imbalance in the ratios of PSI and Cyt b6f to photosystem II leads to an imbalanced photosynthetic electron flow up- and down-stream of the plastoquinone pool, resulting in the observed light sensitivity of the mutant. We conclude that LepB1 is the natural leader peptidase for PsaF, PsbO, and Cyt f. The maturation of PsbO and Cyt f can be partially performed by LepB2, whereas PsaF processing is completely dependent on LepB1. iTRAQ analysis also revealed a number of indirect effects accompanying the mutation, primarily a strong induction of the CydAB oxidase as well as a significant decrease in phycobiliproteins and chlorophyll/heme biosynthesis enzymes.
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Affiliation(s)
- Lifang Zhang
- Nanyang Technological University, School of Biological Sciences, 637551 Singapore
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Miranda H, Cheregi O, Netotea S, Hvidsten TR, Moritz T, Funk C. Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in Synechocystis sp. PCC 6803 exposed to temperature and high light stress. J Proteomics 2013; 78:294-311. [DOI: 10.1016/j.jprot.2012.09.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/14/2012] [Accepted: 09/30/2012] [Indexed: 11/26/2022]
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Yoshimura H, Ikeuchi M, Ohomori M. Cell surface-associated proteins in the filamentous cyanobacterium Anabaena sp. strain PCC 7120. Microbes Environ 2012; 27:538-43. [PMID: 23059722 PMCID: PMC4103569 DOI: 10.1264/jsme2.me12091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The cell surface senses environmental changes first and transfers signals into the cell. To understand the response to environmental changes, it is necessary to analyze cell surface components, particularly cell surface-associated proteins. We therefore investigated cell surface-associated proteins from the filamentous cyanobacterium Anabaena sp. strain PCC 7120. The cell surface-associated proteins extracted by an acidic buffer were resolved by SDS-PAGE. Eighteen proteins were identified from resolved bands by amino-terminal sequencing. Analysis of cell surface-associated proteins indicated that several proteins among them were involved in nucleic acid binding, protein synthesis, proteolytic activity and electron transfer, and other proteins were involved in the stress response.
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Affiliation(s)
- Hidehisa Yoshimura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3–8–1 Komaba, Meguro-ku, Tokyo 153–8902, Japan.
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Degradation of PsbO by the Deg protease HhoA Is thioredoxin dependent. PLoS One 2012; 7:e45713. [PMID: 23029195 PMCID: PMC3446894 DOI: 10.1371/journal.pone.0045713] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/24/2012] [Indexed: 02/02/2023] Open
Abstract
The widely distributed members of the Deg/HtrA protease family play an important role in the proteolysis of misfolded and damaged proteins. Here we show that the Deg protease rHhoA is able to degrade PsbO, the extrinsic protein of the Photosystem II (PSII) oxygen-evolving complex in Synechocystis sp. PCC 6803 and in spinach. PsbO is known to be stable in its oxidized form, but after reduction by thioredoxin it became a substrate for recombinant HhoA (rHhoA). rHhoA cleaved reduced eukaryotic (specifically, spinach) PsbO at defined sites and created distinct PsbO fragments that were not further degraded. As for the corresponding prokaryotic substrate (reduced PsbO of Synechocystis sp. PCC 6803), no PsbO fragments were observed. Assembly to PSII protected PsbO from degradation. For Synechocystis sp. PCC 6803, our results show that HhoA, HhoB, and HtrA are localized in the periplasma and/or at the thylakoid membrane. In agreement with the idea that PsbO could be a physiological substrate for Deg proteases, part of the cellular fraction of the three Deg proteases of Synechocystis sp. PCC 6803 (HhoA, HhoB, and HtrA) was detected in the PSII-enriched membrane fraction.
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Tonietto A, Petriz BA, Araújo WC, Mehta A, Magalhães BS, Franco OL. Comparative proteomics between natural Microcystis isolates with a focus on microcystin synthesis. Proteome Sci 2012; 10:38. [PMID: 22676507 PMCID: PMC3522533 DOI: 10.1186/1477-5956-10-38] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 05/09/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Microcystis aeruginosa is a species of cyanobacteria commonly found in a number of countries and frequently related to animal poisoning episodes due to its capacity to produce the cyanotoxin known as microcystin. Despite vast literature on microcystin structures and their deleterious effects, little is known about its synthesis by cyanobacteria. Therefore, this study used proteomic tools to compare two M. aeruginosa strains, contrasting them for microcystin production. RESULTS 2-DE gels were performed and 30 differential protein spots were chosen. Among them, 11 protein spots were unique in the toxin producing strain and 8 in the non-toxin producing strain, and 14 protein spots were shown on both 2-DE gels but expressed differently in intensity. Around 57% of the tandem mass spectrometry identified proteins were related to energy metabolism, with these proteins being up-regulated in the toxin producing strain. CONCLUSIONS These data suggest that the presence of higher quantities of metabolic enzymes could be related to microcystin metabolism in comparison to the non-toxin producing strain. Moreover, it was suggested that the production of microcystin could also be related to other proteins than those directly involved in its production, such as the enzymes involved in the Calvin cycle and glycolysis.
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Affiliation(s)
- Angela Tonietto
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Pós Graduação em Ciências Genômicas e Biotecnologia, SGAN 916 Norte Av, W5, Brasília, DF, Brazil.
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