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Li Z, Li Y, Xie E, Shen Y. Transcriptome analysis discloses antioxidant detoxification mechanism of Gracilaria bailinae under different cadmium concentrations and stress durations. FRONTIERS IN PLANT SCIENCE 2024; 15:1371818. [PMID: 39036355 PMCID: PMC11257999 DOI: 10.3389/fpls.2024.1371818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024]
Abstract
To remedy Cd pollution in the ocean, macroalgae are used as a bioremediation tool because of their ability to absorb and accumulate Cd. Gracilaria bailinae has high economic and ecological value and can survive in Cd contaminated waters; however, the underlying molecular mechanisms remain unclear. In this study, physiological and biochemical indexes were analyzed after 1, 3, 5, or 7 days of Cd2+ exposure; further, the transcriptome of G. bailinae was examined after a 7-day exposure to a Cd2+ culture environment with Cd levels of 0 mg L-1 (cd1, control), 1 mg L-1 (cd2, low concentration), and 2.5 mg L-1 (cd3, high concentration). The results showed that in the cd2 group, G. bailinae maintained a stable RGR that did not differ significantly (P > 0.05) from that of the cd1 group. However, the soluble protein and MDA contents, as well as the activities of SOD, CAT and POD, were significantly increased (P< 0.05) compared to the cd1 group. No significant differences (P > 0.05) were found among the different Cd2+ stress durations. In contrast, compared with the cd1 group, the RGR, soluble protein content, SOD, CAT, and POD activities were significantly decreased (P< 0.05), while the MDA content was significantly increased (P< 0.05) in the cd3 group. Furthermore, significant differences (P< 0.05) were observed among the various tested Cd2+ stress durations within the cd3 group. Compared to the cd1 group, a total of 30,072 DEGs and 21,680 were identified in the cd2 and cd3 treatments, respectively. More up-regulated genes were found in cd2 group than in cd3 group. GO enrichment analysis showed that these genes were related to peptidase activity, endopeptidase activity, ion transport, peptide biosynthetic and metabolism. In addition, DEGs related to histidine metabolism and the stilbene, diarylheptane, and gingerol pathways were significantly up-regulated in the cd2 group compared to the cd3 group, which resulted in enhanced activities of antioxidant enzymes and promoted cell wall regeneration. The results of this study reveal the response mechanism of G. bailinae to Cd2+ stress, providing valuable insights for assessing the bioremediation potential of G. bailinae for Cd-contaminated waters.
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Affiliation(s)
| | | | | | - Yuchun Shen
- Laboratory of Zhanjiang Key Marine Ecology and Aquaculture Environment, Fishery College, Guangdong Ocean University, Zhanjiang, China
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Enzymatic Mechanisms Involved in Evasion of Fungi to the Oxidative Stress: Focus on Scedosporium apiospermum. Mycopathologia 2017. [DOI: 10.1007/s11046-017-0160-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Zámocký M, Hofbauer S, Schaffner I, Gasselhuber B, Nicolussi A, Soudi M, Pirker KF, Furtmüller PG, Obinger C. Independent evolution of four heme peroxidase superfamilies. Arch Biochem Biophys 2015; 574:108-19. [PMID: 25575902 PMCID: PMC4420034 DOI: 10.1016/j.abb.2014.12.025] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 01/19/2023]
Abstract
Four heme peroxidase superfamilies (peroxidase-catalase, peroxidase-cyclooxygenase, peroxidase-chlorite dismutase and peroxidase-peroxygenase superfamily) arose independently during evolution, which differ in overall fold, active site architecture and enzymatic activities. The redox cofactor is heme b or posttranslationally modified heme that is ligated by either histidine or cysteine. Heme peroxidases are found in all kingdoms of life and typically catalyze the one- and two-electron oxidation of a myriad of organic and inorganic substrates. In addition to this peroxidatic activity distinct (sub)families show pronounced catalase, cyclooxygenase, chlorite dismutase or peroxygenase activities. Here we describe the phylogeny of these four superfamilies and present the most important sequence signatures and active site architectures. The classification of families is described as well as important turning points in evolution. We show that at least three heme peroxidase superfamilies have ancient prokaryotic roots with several alternative ways of divergent evolution. In later evolutionary steps, they almost always produced highly evolved and specialized clades of peroxidases in eukaryotic kingdoms with a significant portion of such genes involved in coding various fusion proteins with novel physiological functions.
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Affiliation(s)
- Marcel Zámocký
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria; Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia.
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria; Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Irene Schaffner
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Bernhard Gasselhuber
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Nicolussi
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Monika Soudi
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Katharina F Pirker
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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Zámocký M, Gasselhuber B, Furtmüller PG, Obinger C. Turning points in the evolution of peroxidase-catalase superfamily: molecular phylogeny of hybrid heme peroxidases. Cell Mol Life Sci 2014; 71:4681-96. [PMID: 24846396 PMCID: PMC4232752 DOI: 10.1007/s00018-014-1643-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/27/2022]
Abstract
Heme peroxidases and catalases are key enzymes of hydrogen peroxide metabolism and signaling. Here, the reconstruction of the molecular evolution of the peroxidase-catalase superfamily (annotated in pfam as PF00141) based on experimentally verified as well as numerous newly available genomic sequences is presented. The robust phylogenetic tree of this large enzyme superfamily was obtained from 490 full-length protein sequences. Besides already well-known families of heme b peroxidases arranged in three main structural classes, completely new (hybrid type) peroxidase families are described being located at the border of these classes as well as forming (so far missing) links between them. Hybrid-type A peroxidases represent a minor eukaryotic subfamily from Excavates, Stramenopiles and Rhizaria sharing enzymatic and structural features of ascorbate and cytochrome c peroxidases. Hybrid-type B peroxidases are shown to be spread exclusively among various fungi and evolved in parallel with peroxidases in land plants. In some ascomycetous hybrid-type B peroxidases, the peroxidase domain is fused to a carbohydrate binding (WSC) domain. Both here described hybrid-type peroxidase families represent important turning points in the complex evolution of the whole peroxidase-catalase superfamily. We present and discuss their phylogeny, sequence signatures and putative biological function.
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Affiliation(s)
- Marcel Zámocký
- Division of Biochemistry, Department of Chemistry, VIBT, Vienna Institute of BioTechnology, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria,
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Si J, Cui BK. A new fungal peroxidase with alkaline-tolerant, chloride-enhancing activity and dye decolorization capacity. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pricelius S, Ludwig R, Lant NJ, Haltrich D, Guebitz GM. In situ generation of hydrogen peroxide by carbohydrate oxidase and cellobiose dehydrogenase for bleaching purposes. Biotechnol J 2010; 6:224-30. [DOI: 10.1002/biot.201000246] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/20/2010] [Accepted: 10/11/2010] [Indexed: 11/10/2022]
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Evolution of structure and function of Class I peroxidases. Arch Biochem Biophys 2010; 500:45-57. [DOI: 10.1016/j.abb.2010.03.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/22/2010] [Accepted: 03/31/2010] [Indexed: 11/20/2022]
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Substrate specificity of Myriococcum thermophilum cellobiose dehydrogenase on mono-, oligo-, and polysaccharides related to in situ production of H2O2. Appl Microbiol Biotechnol 2009; 85:75-83. [DOI: 10.1007/s00253-009-2062-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 05/25/2009] [Accepted: 05/25/2009] [Indexed: 11/26/2022]
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Molecular cloning and characterization of a flower-specific class III peroxidase gene in G. hirsutum. Mol Biol Rep 2007; 36:461-9. [PMID: 18157701 DOI: 10.1007/s11033-007-9202-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 12/14/2007] [Indexed: 10/22/2022]
Abstract
A fundamental focus of plant biology is to understand the relationship between flowering and plant reproduction, but it is also of practical interest in agriculture. To investigate the genes involved in flowering, reproduction and male sterility, DDRT-PCR was performed in vegetative and reproductive tissues of the cotton genic male sterile line LangA. A 683 bp partial peroxidase cDNA was amplified from cotton (G. hirsutum) pollen, using degenerate oligonucleotide primers and arbitrary primers in DDRT-PCR. The full-length cDNA clone, designated Ghpod (cDNA GenBank accession number: EU196676), was isolated using 5'-RACE strategy and a partial 5'-UTR was isolated applying TAIL-PCR. Ghpod was characterized as a mature 330 amino acid protein, containing all evolutionarily conserved residues present in different members of the plant peroxidase family. The molecular mass of this unprocessed and unmodified deduced protein was estimated to be 35.54 kDa, and the pI value was 4.34. According to the Ghpod protein localization prediction by PSORT, Ghpod may be secreted extracellularly. Unlike other cotton class III peroxidases, Ghpod was expressed exclusively in reproductive organs, particularly pollen. A genomic DNA fragment encoding Ghpod was also cloned and fully sequenced, revealing a "three intron" structural organization in a category of genes belonging to a normal class III plant secretory peroxidase. In conclusion, the flower-specific expression of Ghpod, predominantly in pollen, suggested that the peroxidase is involved in the male reproductive processes of angiosperms.
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Wakita M, Masuda S, Motohashi K, Hisabori T, Ohta H, Takamiya KI. The significance of type II and PrxQ peroxiredoxins for antioxidative stress response in the purple bacterium Rhodobacter sphaeroides. J Biol Chem 2007; 282:27792-801. [PMID: 17644813 DOI: 10.1074/jbc.m702855200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two peroxiredoxins, classified as Type II and PrxQ, were characterized in the purple non-sulfur photosynthetic bacterium Rhodobacter sphaeroides. Both recombinant proteins showed remarkable thioredoxin-dependent peroxidase activity with broad substrate specificity in vitro. Nevertheless, PrxQ of R. sphaeroides, unlike typical PrxQs studied to date, does not contain one of the two conserved catalytic Cys residues. We found that R. sphaeroides PrxQ and other PrxQ-like proteins from several organisms conserve a different second Cys residue, indicating that these proteins should be categorized into a novel PrxQ subfamily. Disruption of either the Type II or PrxQ gene in R. sphaeroides had a dramatic effect on cell viability when the cells were grown under aerobic light or oxidative stress conditions created by exogenous addition of reactive oxygen species to the medium. Growth rates of the mutants were significantly decreased compared with that of wild type under aerobic but not anaerobic conditions. These results indicate that the peroxiredoxins are crucial for antioxidative stress response in this bacterium. The gene disruptants also demonstrated reduced levels of photopigment synthesis, suggesting that the peroxiredoxins are directly or indirectly involved in regulated synthesis of the photosynthetic apparatus.
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Affiliation(s)
- Masahiro Wakita
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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Passardi F, Bakalovic N, Teixeira FK, Margis-Pinheiro M, Penel C, Dunand C. Prokaryotic origins of the non-animal peroxidase superfamily and organelle-mediated transmission to eukaryotes. Genomics 2007; 89:567-79. [PMID: 17355904 DOI: 10.1016/j.ygeno.2007.01.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 01/12/2007] [Accepted: 01/18/2007] [Indexed: 11/15/2022]
Abstract
Members of the superfamily of plant, fungal, and bacterial peroxidases are known to be present in a wide variety of living organisms. Extensive searching within sequencing projects identified organisms containing sequences of this superfamily. Class I peroxidases, cytochrome c peroxidase (CcP), ascorbate peroxidase (APx), and catalase peroxidase (CP), are known to be present in bacteria, fungi, and plants, but have now been found in various protists. CcP sequences were detected in most mitochondria-possessing organisms except for green plants, which possess only ascorbate peroxidases. APx sequences had previously been observed only in green plants but were also found in chloroplastic protists, which acquired chloroplasts by secondary endosymbiosis. CP sequences that are known to be present in prokaryotes and in Ascomycetes were also detected in some Basidiomycetes and occasionally in some protists. Class II peroxidases are involved in lignin biodegradation and are found only in the Homobasidiomycetes. In fact class II peroxidases were identified in only three orders, although degenerate forms were found in different Pezizomycota orders. Class III peroxidases are specific for higher plants, and their evolution is thought to be related to the emergence of the land plants. We have found, however, that class III peroxidases are present in some green algae, which predate land colonization. The presence of peroxidases in all major phyla (except vertebrates) makes them powerful marker genes for understanding the early evolutionary events that led to the appearance of the ancestors of each eukaryotic group.
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Affiliation(s)
- Filippo Passardi
- Laboratory of Plant Physiology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
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