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A Proteomic Analysis for the Red Seaweed Asparagopsis taxiformis. BIOLOGY 2023; 12:biology12020167. [PMID: 36829446 PMCID: PMC9952816 DOI: 10.3390/biology12020167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
The red seaweed Asparagopsis taxiformis is a promising ruminant feed additive with anti-methanogenic properties that could contribute to global climate change solutions. Genomics has provided a strong foundation for in-depth molecular investigations, including proteomics. Here, we investigated the proteome of A. taxiformis (Lineage 6) in both sporophyte and gametophyte stages, using soluble and insoluble extraction methods. We identified 741 unique non-redundant proteins using a genome-derived database and 2007 using a transcriptome-derived database, which included numerous proteins predicted to be of fungal origin. We further investigated the genome-derived proteins to focus on seaweed-specific proteins. Ontology analysis indicated a relatively large proportion of ion-binding proteins (i.e., iron, zinc, manganese, potassium and copper), which may play a role in seaweed heavy metal tolerance. In addition, we identified 58 stress-related proteins (e.g., heat shock and vanadium-dependent haloperoxidases) and 44 photosynthesis-related proteins (e.g., phycobilisomes, photosystem I, photosystem II and ATPase), which were in general more abundantly identified from female gametophytes. Forty proteins were predicted to be secreted, including ten rhodophyte collagen-alpha-like proteins (RCAPs), which displayed overall high gene expression levels. These findings provide a comprehensive overview of expressed proteins in A. taxiformis, highlighting the potential for targeted protein extraction and functional characterisation for future biodiscovery.
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Samarathunga J, Wijesekara I, Jayasinghe M. Seaweed proteins as a novel protein alternative: Types, extractions, and functional food applications. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2021.2023564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Jayani Samarathunga
- Department of Food Science & Technology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Isuru Wijesekara
- Department of Food Science & Technology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Madhura Jayasinghe
- Department of Food Science & Technology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
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Wang D, You W, Chen N, Cao M, Tang X, Guan X, Qu W, Chen R, Mao Y, Poetsch A. Comparative Quantitative Proteomics Reveals the Desiccation Stress Responses of the Intertidal Seaweed NEOPORPHYRA haitanensis. JOURNAL OF PHYCOLOGY 2020; 56:1664-1675. [PMID: 33460107 DOI: 10.1111/jpy.13052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 07/06/2020] [Indexed: 06/12/2023]
Abstract
Neoporphyra haitanensis is an economically important red seaweed that inhabits upper intertidal zones. The thallus tolerates extreme fluctuating environmental stresses (e.g., surviving more than 80% water loss during low tides). To elucidate the global molecular responses relevant to this outstanding desiccation tolerance, a quantitative proteomics analysis of N. haitanensis under different desiccation treatments as well as rehydration was performed. According to the clustering of expression patterns and the functional interpretation of the 483 significantly differentially expressed proteins, a three-stage cellular response to desiccation stress and subsequent rehydration was proposed. Stage I: at the beginning of water loss, multiple signal transduction pathways were triggered including lipid signaling, protein phosphorylation cascades, and histone acetylation controlling acetate biosynthesis to further modulate downstream hormone signaling. Protein protection by peptidyl-prolyl isomerase and ROS scavenging systems were also immediately switched on. Stage II: with the aggravation of stress, increases in antioxidant systems, the accumulation of LEA proteins, and the temporary biosynthesis of branched starch were observed. Multiple enzymes involved in redox homeostasis, including peroxiredoxin, thioredoxin, ascorbate peroxidase, superoxide dismutase, glutathione peroxidase, and glutathione reductase, were hypothesized to function in specific cellular compartments. Stage III: when the desiccated thalli had rehydrated for 30 mins, photosynthesis and carbon fixation were recovered, and antioxidant activities and protein structure protection were maintained at a high level. This work increases the understanding of the molecular responses to environmental stresses via a proteomic approach in red seaweeds and paves the way for further functional studies and genetic engineering.
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Affiliation(s)
- Dongmei Wang
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Ministry of Education, Qingdao, 266003, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Wuxin You
- Plant Biochemistry, Ruhr University Bochum, Bochum, 44801, Germany
| | - Nianci Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Cao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xianghai Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiaowei Guan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Weihua Qu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Rui Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Ministry of Education, Qingdao, 266003, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Ministry of Education, Sanya, China
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, 44801, Germany
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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4
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Chi S, Wang G, Liu T, Wang X, Liu C, Jin Y, Yin H, Xu X, Yu J. Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:415-429. [PMID: 33248278 PMCID: PMC8242268 DOI: 10.1016/j.gpb.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/20/2018] [Accepted: 12/14/2018] [Indexed: 11/22/2022]
Abstract
As a carbon-storage compound and osmoprotectant in brown algae, mannitol is synthesized and then accumulated at high levels in Saccharina japonica (Sja); however, the underlying control mechanisms have not been studied. Our analysis of genomic and transcriptomic data from Sja shows that mannitol metabolism is a cyclic pathway composed of four distinct steps. A mannitol-1-phosphate dehydrogenase (M1PDH2) and two mannitol-1-phosphatases (M1Pase1 and MIPase2) work together or in combination to exhibit full enzymatic properties. Based on comprehensive transcriptomic data from different tissues, generations, and sexes as well as under different stress conditions, coupled with droplet digital PCR (ddPCR) and proteomic confirmation, we suggest that SjaM1Pase1 plays a major role in mannitol biosynthesis and that the basic mannitol anabolism and the carbohydrate pool dynamics are responsible for carbon storage and anti-stress mechanism. Our proteomic data indicate that mannitol metabolism remains constant during diurnal cycle in Sja. In addition, we discover that mannitol-metabolism-associated (MMA) genes show differential expression between the multicellular filamentous (gametophyte) and large parenchymal thallus (sporophyte) generations and respond differentially to environmental stresses, such as hyposaline and hyperthermia conditions. Our results indicate that the ecophysiological significance of such differentially expressed genes may be attributable to the evolution of heteromorphic generations (filamentous and thallus) and environmental adaptation of Laminariales.
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Affiliation(s)
- Shan Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Qingdao Haida BlueTek Biotechnology Co., Ltd., Qingdao 266003, China
| | - Guoliang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Tao Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, Yantai University, Yantai 264005, China.
| | - Cui Liu
- Qingdao Haida BlueTek Biotechnology Co., Ltd., Qingdao 266003, China
| | - Yuemei Jin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hongxin Yin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xin Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Cermeño M, Kleekayai T, Amigo‐Benavent M, Harnedy‐Rothwell P, FitzGerald RJ. Current knowledge on the extraction, purification, identification, and validation of bioactive peptides from seaweed. Electrophoresis 2020; 41:1694-1717. [DOI: 10.1002/elps.202000153] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Maria Cermeño
- Department of Biological Sciences University of Limerick Limerick Ireland
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6
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Morita K, Tokoro M, Hatanaka Y, Higuchi C, Ikegami H, Nagai K, Anzai M, Kato H, Mitani T, Taguchi Y, Yamagata K, Hosoi Y, Miyamoto K, Matsumoto K. Peroxiredoxin as a functional endogenous antioxidant enzyme in pronuclei of mouse zygotes. J Reprod Dev 2018; 64:161-171. [PMID: 29503398 PMCID: PMC5902904 DOI: 10.1262/jrd.2018-005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antioxidant mechanisms to adequately moderate levels of endogenous reactive oxygen species (ROS) are important for oocytes and embryos to obtain and maintain developmental competence,
respectively. Immediately after fertilization, ROS levels in zygotes are elevated but the antioxidant mechanisms during the maternal-to-zygotic transition (MZT) are not well understood.
First, we identified peroxiredoxin 1 (PRDX1) and PRDX2 by proteomics analysis as two of the most abundant endogenous antioxidant enzymes eliminating hydrogen peroxide
(H2O2). We here report the cellular localization of hyperoxidized PRDX and its involvement in the antioxidant mechanisms of freshly fertilized oocytes. Treatment of
zygotes at the pronuclear stage with H2O2 enhanced pronuclear localization of hyperoxidized PRDX in zygotes and concurrently impaired the generation of
5-hydroxymethylcytosine (5hmC) on the male genome, which is an epigenetic reprogramming event that occurs at the pronuclear stage. Thus, our results suggest that endogenous PRDX is involved
in antioxidant mechanisms and epigenetic reprogramming during MZT.
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Affiliation(s)
- Kohtaro Morita
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Mikiko Tokoro
- The Asada Institute for Reproductive Medicine, Asada Ladies Clinic, Kasugai, Aichi 486-0931, Japan
| | - Yuki Hatanaka
- RIKEN BioResource Center, Ibaraki 305-0074, Japan.,Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Chika Higuchi
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Haruka Ikegami
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Kouhei Nagai
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Masayuki Anzai
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan.,Institute of Advanced Technology, Kindai University, Wakayama 642-0017, Japan
| | - Hiromi Kato
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan.,Institute of Advanced Technology, Kindai University, Wakayama 642-0017, Japan
| | - Tasuku Mitani
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan.,Institute of Advanced Technology, Kindai University, Wakayama 642-0017, Japan
| | - Yoshitomo Taguchi
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Kazuo Yamagata
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Yoshihiko Hosoi
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Kei Miyamoto
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Kazuya Matsumoto
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
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7
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Peptidomic strategy for purification and identification of potential ACE-inhibitory and antioxidant peptides in Tetradesmus obliquus microalgae. Anal Bioanal Chem 2018; 410:3573-3586. [DOI: 10.1007/s00216-018-0925-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/15/2018] [Accepted: 01/29/2018] [Indexed: 01/10/2023]
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8
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Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S. Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:387-99. [DOI: 10.1089/omi.2016.0065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Debasish Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
| | - Santosh Noronha
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P. Wangikar
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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9
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Speciation of iodine-containing proteins in Nori seaweed by gel electrophoresis laser ablation ICP-MS. Talanta 2014; 127:175-80. [PMID: 24913873 DOI: 10.1016/j.talanta.2014.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/31/2014] [Accepted: 04/02/2014] [Indexed: 11/23/2022]
Abstract
An analytical approach providing an insight into speciation of iodine in water insoluble fraction of edible seaweed (Nori) was developed. The seaweed, harvested in the Galician coast (Northwestern Spain), contained 67.7±1.3 μg g(-1) iodine of which 25% was water soluble and could be identifies as iodide. Extraction conditions of water insoluble residue using urea, NaOH, SDS and Triton X-100 were investigated. The protein pellets obtained in optimized conditions (after precipitation of urea extracts with acetone), were digested with trypsin and protease XIV. Size exclusion chromatography-ICP-MS of both enzymatic digests demonstrated the occurrence of iodoaminoacids putatively present in proteins. Intact proteins could be separated by gel electrophoresis after an additional extraction of the protein extract with phenol. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) with laser ablation ICP-MS detection of (127)I indicated the presence of iodine in protein bands corresponding to molecular masses of 110 kDa, 40 kDa, 27 kDa, 20 kDa and 10 kDa. 2D IEF-SDS PAGE with laser ablation ICP-MS (127)I imaging allowed the detection of 5 iodine containing protein spots in the alkaline pI range.
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10
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Szuba A, Wojakowska A, Lorenc-Plucińska G. An optimized method to extract poplar leaf proteins for two-dimensional gel electrophoresis guided by analysis of polysaccharides and phenolic compounds. Electrophoresis 2013; 34:3234-43. [DOI: 10.1002/elps.201300223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Agnieszka Szuba
- Laboratory of Proteomics; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Anna Wojakowska
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
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11
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Nagai K, Morimoto K, Ikegami H, Kimura H, Yotsukura N. Investigation of proteomic profiles of lamina of Ecklonia kurome (Laminariales): homology-based cross-species protein identification and analysis of the post-translational processing of vanadium-dependent bromoperoxidases using MALDI-TOF/TOF. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:487-98. [PMID: 23547002 DOI: 10.1007/s10126-013-9498-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 03/13/2013] [Indexed: 06/02/2023]
Abstract
Proteomic profiles of the lamina of Ecklonia kurome Okamura, one of the Japanese dominant laminarialean kelps, were investigated by two-dimensional electrophoresis (2-DE) and MALDI-TOF/TOF. Due to the absence of E. kurome DNA or protein databases, homology-based cross-species protein identification was performed using a combination of three database-searching algorithms, Mascot peptide mass fingerprinting, Mascot MS/MS ion search, and mass spectrometry-based BLAST. Proteins were extracted from the lamina by an ethanol/phenol method and subjected to 2-DE (pI 4-7, 10 % polyacrylamide gel). More than 700 spots were detected in the 2-DE gel with CBB, and 93 spots (24 proteins) were successfully identified by MALDI-TOF/TOF and the cross-species database searching. The identified proteins mainly consisted of cytoplasmic carbohydrate metabolic enzymes, chloroplast proteins involved in photosynthesis, and haloperoxidases. Interestingly, vanadium-dependent bromoperoxidases (vBPO), which is thought to be involved in halogen uptake, synthesis of halogenated products, and detoxification of reactive oxygen species, were separated into at least 23 different spots. By comparing mass spectra, amino acid sequences predicted from tandem mass spectra and haloperoxidase activities of the vBPOs, we found that (1) at least two types of vBPOs were expressed in the lamina of E. kurome and (2) two pro-vBPOs might be activated by specific cleavage at N- and C-terminal regions.
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Affiliation(s)
- Kouhei Nagai
- Department of Genetic Engineering, Faculity of Biology-Oriented Science and Technology, Kinki University, Kinokawa, Wakayama 649-6493, Japan
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12
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Ndimba BK, Ndimba RJ, Johnson TS, Waditee-Sirisattha R, Baba M, Sirisattha S, Shiraiwa Y, Agrawal GK, Rakwal R. Biofuels as a sustainable energy source: an update of the applications of proteomics in bioenergy crops and algae. J Proteomics 2013; 93:234-44. [PMID: 23792822 DOI: 10.1016/j.jprot.2013.05.041] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/28/2013] [Accepted: 05/30/2013] [Indexed: 11/29/2022]
Abstract
Sustainable energy is the need of the 21st century, not because of the numerous environmental and political reasons but because it is necessary to human civilization's energy future. Sustainable energy is loosely grouped into renewable energy, energy conservation, and sustainable transport disciplines. In this review, we deal with the renewable energy aspect focusing on the biomass from bioenergy crops to microalgae to produce biofuels to the utilization of high-throughput omics technologies, in particular proteomics in advancing our understanding and increasing biofuel production. We look at biofuel production by plant- and algal-based sources, and the role proteomics has played therein. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Bongani Kaiser Ndimba
- Proteomics Research and Services Unit, Biotechnology Platform, Agricultural Research Council, Infruitec-Nietvoorbij Campus, Stellenbosch, South Africa; Proteomics Research Group, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
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Rodrigues PM, Silva TS, Dias J, Jessen F. PROTEOMICS in aquaculture: applications and trends. J Proteomics 2012; 75:4325-45. [PMID: 22498885 DOI: 10.1016/j.jprot.2012.03.042] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/18/2012] [Accepted: 03/24/2012] [Indexed: 01/15/2023]
Abstract
Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.
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Affiliation(s)
- Pedro M Rodrigues
- Centro de Ciências do Mar do Algarve (CCMar), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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14
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Tonon T, Eveillard D, Prigent S, Bourdon J, Potin P, Boyen C, Siegel A. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:883-92. [PMID: 22136637 DOI: 10.1089/omi.2011.0089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.
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Affiliation(s)
- Thierry Tonon
- UPMC Univ Paris 6 , UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France.
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15
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Jones BM, Edwards RJ, Skipp PJ, O'Connor CD, Iglesias-Rodriguez MD. Shotgun proteomic analysis of Emiliania huxleyi, a marine phytoplankton species of major biogeochemical importance. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:496-504. [PMID: 20924652 DOI: 10.1007/s10126-010-9320-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 09/07/2010] [Indexed: 05/30/2023]
Abstract
Emiliania huxleyi is a unicellular marine phytoplankton species known to play a significant role in global biogeochemistry. Through the dual roles of photosynthesis and production of calcium carbonate (calcification), carbon is transferred from the atmosphere to ocean sediments. Almost nothing is known about the molecular mechanisms that control calcification, a process that is tightly regulated within the cell. To initiate proteomic studies on this important and phylogenetically remote organism, we have devised efficient protein extraction protocols and developed a bioinformatics pipeline that allows the statistically robust assignment of proteins from MS/MS data using preexisting EST sequences. The bioinformatics tool, termed BUDAPEST (Bioinformatics Utility for Data Analysis of Proteomics using ESTs), is fully automated and was used to search against data generated from three strains. BUDAPEST increased the number of identifications over standard protein database searches from 37 to 99 proteins when data were amalgamated. Proteins involved in diverse cellular processes were uncovered. For example, experimental evidence was obtained for a novel type I polyketide synthase and for various photosystem components. The proteomic and bioinformatic approaches developed in this study are of wider applicability, particularly to the oceanographic community where genomic sequence data for species of interest are currently scarce.
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Affiliation(s)
- Bethan M Jones
- School of Ocean and Earth Science, National Oceanography Centre, Southampton, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, UK.
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Jiménez-Escrig A, Gómez-Ordóñez E, Rupérez P. Seaweed as a source of novel nutraceuticals: sulfated polysaccharides and peptides. ADVANCES IN FOOD AND NUTRITION RESEARCH 2011; 64:325-37. [PMID: 22054959 DOI: 10.1016/b978-0-12-387669-0.00026-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Seaweeds and seaweed-derived products are underexploited marine bioresources and a source of natural ingredients for functional foods. Nutritional studies on seaweeds indicate that brown and red seaweeds possess a good nutritional quality and could be used as an alternative source of dietary fiber, protein, and minerals. Moreover, bioactive sulfated polysaccharides are the main components of soluble fiber in seaweeds and also bioactive peptides can be prepared from seaweed protein. This chapter gives an overview of the main biological properties of sulfated polysaccharides and peptides from brown and red seaweeds. Recent studies have provided evidence that sulfated polysaccharides from seaweeds can play a vital role in human health and nutrition. Besides, peptides derived from algal protein are most promising as antihypertensive agents. Further research work, especially in vivo studies, are needed in order to gain a better knowledge of the relation structure-function by which bioactive compounds from seaweeds exert their bioactivity.
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Affiliation(s)
- A Jiménez-Escrig
- Metabolism and Nutrition Department, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), Consejo Superior de Investigaciones Científicas (CSIC), José Antonio Novais 10, Ciudad Universitaria, Madrid, Spain
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Pico de Coaña Y, Parody N, Fuertes MÁ, Carnés J, Roncarolo D, Ariano R, Sastre J, Mistrello G, Alonso C. Molecular cloning and characterization of Cup a 4, a new allergen from Cupressus arizonica. Biochem Biophys Res Commun 2010; 401:451-7. [DOI: 10.1016/j.bbrc.2010.09.079] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 09/21/2010] [Indexed: 11/16/2022]
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Bancel E, Rogniaux H, Debiton C, Chambon C, Branlard G. Extraction and Proteome Analysis of Starch Granule-Associated Proteins in Mature Wheat Kernel (Triticum aestivum L.). J Proteome Res 2010; 9:3299-310. [DOI: 10.1021/pr9010525] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuelle Bancel
- INRA UMR 1095 GDEC, 234 Avenue du Brézet, 63100 Clermont-Ferrand, France, INRA UR 1268 BIA, BISB Platform, Rue de la Géraudière, 44316 Nantes cedex 3, France, and INRA UR 370 PFEM-Plateau Protéomique, 63122 Saint-Genès-Champanelle, France
| | - Hélène Rogniaux
- INRA UMR 1095 GDEC, 234 Avenue du Brézet, 63100 Clermont-Ferrand, France, INRA UR 1268 BIA, BISB Platform, Rue de la Géraudière, 44316 Nantes cedex 3, France, and INRA UR 370 PFEM-Plateau Protéomique, 63122 Saint-Genès-Champanelle, France
| | - Clément Debiton
- INRA UMR 1095 GDEC, 234 Avenue du Brézet, 63100 Clermont-Ferrand, France, INRA UR 1268 BIA, BISB Platform, Rue de la Géraudière, 44316 Nantes cedex 3, France, and INRA UR 370 PFEM-Plateau Protéomique, 63122 Saint-Genès-Champanelle, France
| | - Christophe Chambon
- INRA UMR 1095 GDEC, 234 Avenue du Brézet, 63100 Clermont-Ferrand, France, INRA UR 1268 BIA, BISB Platform, Rue de la Géraudière, 44316 Nantes cedex 3, France, and INRA UR 370 PFEM-Plateau Protéomique, 63122 Saint-Genès-Champanelle, France
| | - Gérard Branlard
- INRA UMR 1095 GDEC, 234 Avenue du Brézet, 63100 Clermont-Ferrand, France, INRA UR 1268 BIA, BISB Platform, Rue de la Géraudière, 44316 Nantes cedex 3, France, and INRA UR 370 PFEM-Plateau Protéomique, 63122 Saint-Genès-Champanelle, France
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Kunii S, Morimoto K, Nagai K, Saito T, Sato K, Tonomura B. Actinidain-hydrolyzed type I collagen reveals a crucial amino acid sequence in fibril formation. J Biol Chem 2010; 285:17465-70. [PMID: 20392700 DOI: 10.1074/jbc.m110.110759] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We investigated the ability of type I collagen telopeptides to bind neighboring collagen molecules, which is thought to be the initial event in fibrillogenesis. Limited hydrolysis by actinidain protease produced monomeric collagen, which consisted almost entirely of alpha1 and alpha2 chains. As seen with ultrahigh resolution scanning electron microscopy, actinidain-hydrolyzed collagen exhibited unique self-assembly, as if at an intermediate stage, and formed a novel suprastructure characterized by poor fibrillogenesis. Then, the N- and C-terminal sequences of chicken type I collagen hydrolyzed by actinidain or pepsin were determined by Edman degradation and de novo sequence analysis with matrix-assisted laser desorption ionization-tandem time-of-flight mass spectrometry, respectively. In the C-telopeptide region of the alpha1 chain, pepsin cleaved between Asp(1035) and Phe(1036), and actinidain between Gly(1032) and Gly(1033). Thus, the actinidain-hydrolyzed alpha1 chain is shorter at the C terminus by three residues, Gly(1033), Phe(1034), and Asp(1035). In the alpha2 chain, both proteases cleaved between Glu(1030) and Val(1031). We demonstrated that a synthetic nonapeptide mimicking the alpha1 C-terminal sequence including GFD weakly inhibited the self-assembly of pepsin-hydrolyzed collagen, whereas it remarkably accelerated that of actinidain-hydrolyzed collagen. We conclude that the specific GFD sequence of the C-telopeptide of the alpha1 chain plays a crucial role in stipulating collagen suprastructure and in subsequent fibril formation.
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Affiliation(s)
- Saori Kunii
- Department of Biotechnological Science, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
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Wang C, Li X, Yao Y, Wang DA. Concurrent extraction of proteins and RNA from cell-laden hydrogel scaffold free of polysaccharide interference. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:3762-6. [PMID: 19782009 DOI: 10.1016/j.jchromb.2009.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 09/03/2009] [Accepted: 09/14/2009] [Indexed: 11/15/2022]
Abstract
Concurrent extractions of proteins and RNA from cell-laden scaffolds would be of great help to biomaterialists and tissue engineers. Here we describe a procedure to extract proteins from the discard solution generated during the RNA isolation from polysaccharide-rich hydrogel scaffolds. This approach allows to obtain proteins and RNA from same sample while eliminating the polysaccharide interference.
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Affiliation(s)
- Chunming Wang
- Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, N1.3-B2-13, Singapore 637457, Republic of Singapore
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Satoh M, Tokoro M, Ikegami H, Nagai K, Sono Y, Shin SW, Nishikawa S, Saeki K, Hosoi Y, Iritani A, Fukuda A, Morimoto Y, Matsumoto K. Proteomic analysis of the mouse ovary in response to two gonadotropins, follicle-stimulating hormone and luteinizing hormone. J Reprod Dev 2009; 55:316-26. [PMID: 19325216 DOI: 10.1262/jrd.20217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Functional and structural changes in the mammalian ovary are coordinately regulated by the pituitary glycoprotein hormones, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), leading to follicular development, ovulation and transformation of follicles into corpus lutea. To investigate protein profiles during these processes of the mouse ovarian cycle, we applied combined methods (two-dimensional gel electrophoresis [2-DE] for separation and visualization of proteins plus matrix laser desorption/ionization time-of-flight mass spectrometry [MALDI-TOF/MS] analysis for protein identification) for comparative proteomic analysis using immature mice at 3 weeks of age. Protein profiles were obtained from proteins extracted from intact ovaries that had been collected from pregnant mare serum gonadotropin (PMSG)/human chorionic gonadotropin (hCG)-primed immature mice at 0 (no PMSG), 24 and 48 h post PMSG, as well as at 10 and 20 h post hCG. The results showed that 1028 common protein spots were found in representative gels that had been separated in the 3 to 11 pH range and the 15-200 kDa range, 253 protein spots (24.6%) of which were differentially expressed (p<0.05) during the mouse ovarian cycle. Of these 253 protein spots, 99 were identified by MALDI-TOF/MS. This comparative proteomic approach to identifying proteins that were potentially involved in the complex process of the ovarian cycle could contribute to our understanding of the molecular basis of functional and structural changes in the ovary in response to gonadotropins. Furthermore, the interesting ovarian proteins identified in this study may eventually serve as diagnostic biomarker candidates of ovarian function.
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Affiliation(s)
- Manabu Satoh
- The Centre for Reproductive Medicine and Infertility, IVF Namba Clinic
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