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Uzlasir T, Isik O, Uslu LH, Selli S, Kelebek H. Impact of different salt concentrations on growth, biochemical composition and nutrition quality of Phaeodactylum tricornutum and Spirulina platensis. Food Chem 2023; 429:136843. [PMID: 37454614 DOI: 10.1016/j.foodchem.2023.136843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/20/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
The effects of different salt concentrations on the growth, aroma and quality parameters of P. tricornutum and S. platensis were investigated for the first time.Salt contents were 15, 25, 30 and 35‰ for the P. tricornutum and 20, 25, 30 and 35‰ for the S. platensis culture. Aroma compounds were analyzed by HS-SPME-GC/MS while the organic acid and sugar composition were studied by HPLC-PDA-RID.The main amino acids were glutamic acid (6.24-12.96 mg/100 g) and alanine (3.67-13.65 mg/100 g) while the prevailing sugars were sucrose (229-1099 mg/100 g) and glucose (192-2322 mg/100 g) in the P. tricornutum and S. platensis samples.The most prevailing aroma compound was acetic acid (113 µg/kg) in the P. tricornutum samples and heptadecane (36941 µg/kg) in the S. platensis samples.A significant reduction was found in the amount of aroma compounds, amino acids, sugars and organic acids with increasing salt concentration.The study results are valuable for producing high-quality and flavorful P. tricornutum and S. platensis products.
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Affiliation(s)
- Turkan Uzlasir
- Department of Food Engineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, 01250 Adana Turkey
| | - Oya Isik
- Department of Fishery Basic Sciences, Faculty of Fisheries, Cukurova University, 01330 Adana Turkey
| | - Leyla Hizarci Uslu
- Department of Fishery Basic Sciences, Faculty of Fisheries, Cukurova University, 01330 Adana Turkey
| | - Serkan Selli
- Department of Food Engineering, Faculty of Agriculture, Cukurova University, 01330 Adana Turkey
| | - Hasim Kelebek
- Department of Food Engineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, 01250 Adana Turkey.
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2
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Curcuraci E, Manuguerra S, Messina CM, Arena R, Renda G, Ioannou T, Amato V, Hellio C, Barba FJ, Santulli A. Culture Conditions Affect Antioxidant Production, Metabolism and Related Biomarkers of the Microalgae Phaeodactylum tricornutum. Antioxidants (Basel) 2022; 11:antiox11020411. [PMID: 35204292 PMCID: PMC8869413 DOI: 10.3390/antiox11020411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 12/10/2022] Open
Abstract
Phaeodactylum tricornutum (Bacillariophyta) is a worldwide-distributed diatom with the ability to adapt and survive in different environmental habitats and nutrient-limited conditions. In this research, we investigated the growth performance, the total lipids productivity, the major categories of fatty acids, and the antioxidant content in P. tricornutum subjected for 15 days to nitrogen deprivation (N-) compared to standard culture conditions (N+). Furthermore, genes and pathways related to lipid biosynthesis (i.e., glucose-6-phosphate dehydrogenase, acetyl-coenzyme A carboxylase, citrate synthase, and isocitrate dehydrogenase) and photosynthetic activity (i.e., ribulose-1,5-bisphospate carboxylase/oxygenase and fucoxanthin-chlorophyll a/c binding protein B) were investigated through molecular approaches. P. tricornutum grown under starvation condition (N-) increased lipids production (42.5 ± 0.19 g/100 g) and decreased secondary metabolites productivity (phenolic content: 3.071 ± 0.17 mg GAE g-1; carotenoids: 0.35 ± 0.01 mg g−1) when compared to standard culture conditions (N+). Moreover, N deprivation led to an increase in the expression of genes involved in fatty acid biosynthesis and a decrease in genes related to photosynthesis. These results could be used as indicators of nitrogen limitation for environmental or industrial monitoring of P. tricornutum.
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Affiliation(s)
- Eleonora Curcuraci
- Department of Earth and Marine Sciences DiSTeM, University of Palermo, Via Barlotta 4, 91100 Trapani, Italy; (E.C.); (S.M.); (R.A.); (G.R.); (A.S.)
| | - Simona Manuguerra
- Department of Earth and Marine Sciences DiSTeM, University of Palermo, Via Barlotta 4, 91100 Trapani, Italy; (E.C.); (S.M.); (R.A.); (G.R.); (A.S.)
| | - Concetta Maria Messina
- Department of Earth and Marine Sciences DiSTeM, University of Palermo, Via Barlotta 4, 91100 Trapani, Italy; (E.C.); (S.M.); (R.A.); (G.R.); (A.S.)
- Correspondence: (C.M.M.); (F.J.B.); Tel.: +39-923-560162 (C.M.M.); +34-963-544-972 (F.J.B.)
| | - Rosaria Arena
- Department of Earth and Marine Sciences DiSTeM, University of Palermo, Via Barlotta 4, 91100 Trapani, Italy; (E.C.); (S.M.); (R.A.); (G.R.); (A.S.)
| | - Giuseppe Renda
- Department of Earth and Marine Sciences DiSTeM, University of Palermo, Via Barlotta 4, 91100 Trapani, Italy; (E.C.); (S.M.); (R.A.); (G.R.); (A.S.)
| | - Theodora Ioannou
- Department of Chemistry, Faculty of Science, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Vito Amato
- L’Avannotteria Società Agricola a Responsabilità Limitata, Contrada Triglia Scaletta, 91020 Petrosino, Italy;
| | - Claire Hellio
- LEMAR, IRD, CNRS, Ifremer, Université de Brest, F-29280 Plouzane, France;
| | - Francisco J. Barba
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department, Faculty of Pharmacy, Universitat de València, Av. Vicent Andrés Estellés, s/n, 46100 Burjassot, València, Spain
- Correspondence: (C.M.M.); (F.J.B.); Tel.: +39-923-560162 (C.M.M.); +34-963-544-972 (F.J.B.)
| | - Andrea Santulli
- Department of Earth and Marine Sciences DiSTeM, University of Palermo, Via Barlotta 4, 91100 Trapani, Italy; (E.C.); (S.M.); (R.A.); (G.R.); (A.S.)
- Istituto di Biologia Marina, Consorzio Universitario della Provincia di Trapani, Via G. Barlotta 4, 91100 Trapani, Italy
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Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma TR. Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application. Front Bioeng Biotechnol 2020; 8:914. [PMID: 33014997 PMCID: PMC7494788 DOI: 10.3389/fbioe.2020.00914] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 01/14/2023] Open
Abstract
Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.
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Affiliation(s)
- Gulshan Kumar
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ajam Shekh
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru, India
| | - Sunaina Jakhu
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Yogesh Sharma
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ritu Kapoor
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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Launay H, Huang W, Maberly SC, Gontero B. Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates. FRONTIERS IN PLANT SCIENCE 2020; 11:1033. [PMID: 32765548 PMCID: PMC7378808 DOI: 10.3389/fpls.2020.01033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/23/2020] [Indexed: 05/08/2023]
Abstract
Diatoms belong to a major, diverse and species-rich eukaryotic clade, the Heterokonta, within the polyphyletic chromalveolates. They evolved as a result of secondary endosymbiosis with one or more Plantae ancestors, but their precise evolutionary history is enigmatic. Nevertheless, this has conferred them with unique structural and biochemical properties that have allowed them to flourish in a wide range of different environments and cope with highly variable conditions. We review the effect of pH, light and dark, and CO2 concentration on the regulation of carbon uptake and assimilation. We discuss the regulation of the Calvin-Benson-Bassham cycle, glycolysis, lipid synthesis, and carbohydrate synthesis at the level of gene transcripts (transcriptomics), proteins (proteomics) and enzyme activity. In contrast to Viridiplantae where redox regulation of metabolic enzymes is important, it appears to be less common in diatoms, based on the current evidence, but regulation at the transcriptional level seems to be widespread. The role of post-translational modifications such as phosphorylation, glutathionylation, etc., and of protein-protein interactions, has been overlooked and should be investigated further. Diatoms and other chromalveolates are understudied compared to the Viridiplantae, especially given their ecological importance, but we believe that the ever-growing number of sequenced genomes combined with proteomics, metabolomics, enzyme measurements, and the application of novel techniques will provide a better understanding of how this important group of algae maintain their productivity under changing conditions.
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Affiliation(s)
- Hélène Launay
- BIP, Aix Marseille Univ CNRS, BIP UMR 7281, Marseille, France
| | - Wenmin Huang
- BIP, Aix Marseille Univ CNRS, BIP UMR 7281, Marseille, France
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Stephen C. Maberly
- UK Centre for Ecology & Hydrology, Lake Ecosystems Group, Lancaster Environment Centre, Lancaster, United Kingdom
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5
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The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom. BIOLOGY 2020; 9:biology9070155. [PMID: 32640597 PMCID: PMC7408324 DOI: 10.3390/biology9070155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 01/23/2023]
Abstract
Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.
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Liu Z, Lv J, Liu Y, Wang J, Zhang Z, Chen W, Song J, Yang B, Tan F, Zou X, Ou L. Comprehensive Phosphoproteomic Analysis of Pepper Fruit Development Provides Insight into Plant Signaling Transduction. Int J Mol Sci 2020; 21:ijms21061962. [PMID: 32183026 PMCID: PMC7139842 DOI: 10.3390/ijms21061962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/29/2022] Open
Abstract
Limited knowledge is available for phosphorylation modifications in pepper (Capsicum annuum L.), especially in pepper fruit development. In this study, we conducted the first comprehensive phosphoproteomic analysis of pepper fruit at four development stage by Tandem Mass Tag proteomic approaches. A total of 2639 unique phosphopeptides spanning 1566 proteins with 4150 nonredundant sites of phosphorylation were identified, among which 2327 peptides in 1413 proteins were accurately quantified at four different stages. Mature Green (MG) to breaker stage showed the largest number of differentially expressed phosphoproteins and the number of downregulated phosphoproteins was significantly higher than that of upregulated after MG stage. Twenty seven phosphorylation motifs, including 22 pSer motifs and five pThr motifs and 85 kinase including 28 serine/threonine kinases, 14 receptor protein kinases, six mitogen-activated protein kinases, seven calcium-dependent protein kinases, two casein kinases, and some other kinases were quantified. Then the dynamic changes of phosphorylated proteins in ethylene and abscisic acid signaling transduction pathways during fruit development were analyzed. Our results provide a cascade of phosphoproteins and a regulatory network of phosphorylation signals, which help to further understand the mechanism of phosphorylation in pepper fruit development.
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Affiliation(s)
- Zhoubin Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
| | - Junheng Lv
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Yuhua Liu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Jing Wang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Wenchao Chen
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Jingshuang Song
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Bozhi Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
| | - Fangjun Tan
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Xuexiao Zou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
- Correspondence: (X.Z.); (L.O.); Tel.: +86-0731-84692619 (L.O.)
| | - Lijun Ou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
- Correspondence: (X.Z.); (L.O.); Tel.: +86-0731-84692619 (L.O.)
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7
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Ait-Mohamed O, Novák Vanclová AMG, Joli N, Liang Y, Zhao X, Genovesio A, Tirichine L, Bowler C, Dorrell RG. PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:590949. [PMID: 33178253 PMCID: PMC7596299 DOI: 10.3389/fpls.2020.590949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 05/04/2023]
Abstract
Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.
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Affiliation(s)
- Ouardia Ait-Mohamed
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anna M. G. Novák Vanclová
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Nathalie Joli
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Yue Liang
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Xue Zhao
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
| | - Auguste Genovesio
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
- *Correspondence: Leila Tirichine,
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Chris Bowler,
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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Yang M, Lin X, Liu X, Zhang J, Ge F. Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline. MOLECULAR PLANT 2018; 11:1292-1307. [PMID: 30176371 DOI: 10.1016/j.molp.2018.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the development of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry (MS)-based proteomics data. Our proteogenomic analysis unambiguously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricornutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https://sourceforge.net/projects/gapeproteogenomic.
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Affiliation(s)
- Mingkun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xin Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jia Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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9
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Matiiv AB, Chekunova EM. Aureochromes - Blue Light Receptors. BIOCHEMISTRY (MOSCOW) 2018; 83:662-673. [PMID: 30195323 DOI: 10.1134/s0006297918060044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A variety of living organisms including bacteria, fungi, animals, and plants use blue light (BL) to adapt to changing ambient light. Photosynthetic forms (plants and algae) require energy of light for photosynthesis, movements, development, and regulation of activity. Several complex light-sensitive systems evolved in eukaryotic cells to use the information of light efficiently with photoreceptors selectively absorbing various segments of the solar spectrum, being the first components in the light signal transduction chain. They are most diverse in algae. Photosynthetic stramenopiles, which received chloroplasts from red algae during secondary symbiosis, play an important role in ecosystems and aquaculture, being primary producers. These taxa acquired the ability to use BL for regulation of such processes as phototropism, chloroplast photo-relocation movement, and photomorphogenesis. A new type of BL receptor - aureochrome (AUREO) - was identified in Vaucheria frigida in 2007. AUREO consists of two domains: bZIP (basic-region leucine zipper) domain and LOV (light-oxygen-voltage-sensing) domain, and thus this photoreceptor is a BL-sensitive transcription factor. This review presents current data on the structure, mechanisms of action, and biochemical features of aureochromes.
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Affiliation(s)
- A B Matiiv
- St. Petersburg State University, Faculty of Biology, St. Petersburg, 199034, Russia
| | - E M Chekunova
- St. Petersburg State University, Faculty of Biology, St. Petersburg, 199034, Russia.
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10
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Essen LO, Franz S, Banerjee A. Structural and evolutionary aspects of algal blue light receptors of the cryptochrome and aureochrome type. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:27-37. [PMID: 28756992 DOI: 10.1016/j.jplph.2017.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Blue-light reception plays a pivotal role for algae to adapt to changing environmental conditions. In this review we summarize the current structural and mechanistic knowledge about flavin-dependent algal photoreceptors. We especially focus on the cryptochrome and aureochrome type photoreceptors in the context of their evolutionary divergence. Despite similar photochemical characteristics to orthologous photoreceptors from higher plants and animals the algal blue-light photoreceptors have developed a set of unique structural and mechanistic features that are summarized below.
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Affiliation(s)
- Lars-Oliver Essen
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology, Philipps-University, 35043 Marburg, Germany.
| | - Sophie Franz
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
| | - Ankan Banerjee
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
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11
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Ma Y, Yang M, Lin X, Liu X, Huang H, Ge F. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria. J Proteome Res 2017; 16:2030-2043. [DOI: 10.1021/acs.jproteome.7b00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yanyan Ma
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Huang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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12
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Longworth J, Wu D, Huete-Ortega M, Wright PC, Vaidyanathan S. Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion. ALGAL RES 2016; 18:213-224. [PMID: 27812494 PMCID: PMC5070409 DOI: 10.1016/j.algal.2016.06.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 05/08/2016] [Accepted: 06/14/2016] [Indexed: 11/26/2022]
Abstract
Nitrogen stress is a common strategy employed to stimulate lipid accumulation in microalgae, a biofuel feedstock of topical interest. Although widely investigated, the underlying mechanism of this strategy is still poorly understood. We examined the proteome response of lipid accumulation in the model diatom, Phaeodactylum tricornutum (CCAP 1055/1), at an earlier stage of exposure to selective nitrogen exclusion than previously investigated, and at a time point when changes would reflect lipid accumulation more than carbohydrate accumulation. In total 1043 proteins were confidently identified (≥ 2 unique peptides) with 645 significant (p < 0.05) changes observed, in the LC-MS/MS based iTRAQ investigation. Analysis of significant changes in KEGG pathways and individual proteins showed that under nitrogen starvation P. tricornutum reorganizes its proteome in favour of nitrogen scavenging and reduced lipid degradation whilst rearranging the central energy metabolism that deprioritizes photosynthetic pathways. By doing this, this species appears to increase nitrogen availability inside the cell and limit its use to the pathways where it is needed most. Compared to previously published proteomic analysis of nitrogen starvation in Chlamydomonas reinhardtii, central energy metabolism and photosynthesis appear to be affected more in the diatom, whilst the green algae appears to invest its energy in reorganizing respiration and the cellular organization pathways.
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Machado M, Bromke M, Domingues Júnior AP, Marçal Vieira Vaz MG, Rosa RM, Vinson CC, Sabir JS, Rocha DI, Martins MA, Araújo WL, Willmitzer L, Szymanski J, Nunes-Nesi A. Comprehensive metabolic reprograming in freshwater Nitzschia palea strains undergoing nitrogen starvation is likely associated with its ecological origin. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Fu W, Wichuk K, Brynjólfsson S. Developing diatoms for value-added products: challenges and opportunities. N Biotechnol 2015; 32:547-51. [DOI: 10.1016/j.nbt.2015.03.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 03/17/2015] [Accepted: 03/28/2015] [Indexed: 11/29/2022]
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Muhseen ZT, Xiong Q, Chen Z, Ge F. Proteomics studies on stress responses in diatoms. Proteomics 2015; 15:3943-53. [PMID: 26364674 DOI: 10.1002/pmic.201500165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/09/2015] [Accepted: 09/09/2015] [Indexed: 01/09/2023]
Abstract
Diatoms are a highly diverse group of eukaryotic phytoplankton that are distributed throughout marine and freshwater environments and are believed to be responsible for approximately 40% of the total marine primary productivity. The ecological success of diatoms suggests that they have developed a range of strategies to cope with various biotic and abiotic stress factors. It is of great interest to understand the adaptive responses of diatoms to different stresses in the marine environment. Proteomic technologies have been applied to the adaptive responses of marine diatoms under different growth conditions in recent years such as nitrogen starvation, iron limitation and phosphorus deficiency. These studies have provided clues to elucidate the sophisticated sensing mechanisms that control their adaptive responses. Although only a very limited number of proteomic studies were conducted in diatoms, the obtained data have led to a better understanding of the biochemical processes that contribute to their ecological success. This review presents the current status of proteomic studies of diatom stress responses and discusses the novel developments and applications for the analysis of protein post-translational modification in diatoms. The potential future application of proteomics could contribute to a better understanding of the physiological mechanisms underlying diatom acclimation to a given stress and the acquisition of an enhanced diatom stress tolerance. Future challenges and research opportunities in the proteomics studies of diatoms are also discussed.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
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Ca(2+)-regulated cyclic electron flow supplies ATP for nitrogen starvation-induced lipid biosynthesis in green alga. Sci Rep 2015; 5:15117. [PMID: 26450399 PMCID: PMC4598854 DOI: 10.1038/srep15117] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/16/2015] [Indexed: 02/07/2023] Open
Abstract
We previously showed that both the linear photosynthetic electron transportation rate and the respiration rate dropped significantly during N starvation-induced neutral lipid accumulation in an oil-producing microalga, Chlorella sorokiniana, and proposed a possible role for cyclic electron flow (CEF) in ATP supply. In this study, we further exploited this hypothesis in both Chlorella sorokiniana C3 and the model green alga Chlamydomonas. We found that both the rate of CEF around photosystem I and the activity of thylakoid membrane-located ATP synthetase increased significantly during N starvation to drive ATP production. Furthermore, we demonstrated that the Chlamydomonas mutant pgrl1, which is deficient in PGRL1-mediated CEF, accumulated less neutral lipids and had reduced rates of CEF under N starvation. Further analysis revealed that Ca(2+) signaling regulates N starvation-induced neutral lipid biosynthesis in Chlamydomonas by increasing calmodulin activity and boosting the expression of the calcium sensor protein that regulates Pgrl1-mediated CEF. Thus, Ca(2+)-regulated CEF supplies ATP for N starvation-induced lipid biosynthesis in green alga. The increased CEF may re-equilibrate the ATP/NADPH balance and recycle excess light energy in photosystems to prevent photooxidative damage, suggesting Ca(2+)-regulated CEF also played a key role in protecting and sustaining photosystems.
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Chen Z, Zhan J, Chen Y, Yang M, He C, Ge F, Wang Q. Effects of Phosphorylation of β Subunits of Phycocyanins on State Transition in the Model Cyanobacterium Synechocystis sp. PCC 6803. PLANT & CELL PHYSIOLOGY 2015; 56:1997-2013. [PMID: 26315596 DOI: 10.1093/pcp/pcv118] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/09/2015] [Indexed: 05/22/2023]
Abstract
Synechocystis sp. PCC 6803 (hereafter Synechocystis) is a model cyanobacterium and has been used extensively for studies concerned with photosynthesis and environmental adaptation. Although dozens of protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues have been predicted, only a few substrate proteins are known in Synechocystis. In this study, we report 194 in vivo phosphorylation sites from 149 proteins in Synechocystis, which were identified using a combination of peptide pre-fractionation, TiO(2) enrichment and liquid chromatograpy-tandem mass spectrometry (LC-MS/MS) analysis. These phosphorylated proteins are implicated in diverse biological processes, such as photosynthesis. Among all identified phosphoproteins involved in photosynthesis, the β subunits of phycocyanins (CpcBs) were found to be phosphorylated on Ser22, Ser49, Thr94 and Ser154. Four non-phosphorylated mutants were constructed by using site-directed mutagenesis. The in vivo characterization of the cpcB mutants showed a slower growth under high light irradiance and displayed fluorescence quenching to a lower level and less efficient energy transfer inside the phycobilisome (PBS). Notably, the non-phosphorylated mutants exhibited a slower state transition than the wild type. The current results demonstrated that the phosphorylation status of CpcBs affects the energy transfer and state transition of photosynthesis in Synechocystis. This study provides novel insights into the molecular mechanisms of protein phosphorylation in the regulation of photosynthesis in cyanobacteria and may facilitate the elucidation of the entire regulatory network by linking kinases to their physiological substrates.
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Affiliation(s)
- Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China These authors contributed equally to this work.
| | - Jiao Zhan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China University of Chinese Academy of Sciences, Beijing 100094, China These authors contributed equally to this work.
| | - Ying Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Mingkun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Chenliu He
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Qiang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
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Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase. PLoS One 2015; 10:e0139143. [PMID: 26401955 PMCID: PMC4581636 DOI: 10.1371/journal.pone.0139143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/08/2015] [Indexed: 11/19/2022] Open
Abstract
Sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. In this study, TiO2 enrichment and LC-MS/MS were used to uncover the site-specific Ser/Thr/Tyr phosphoproteome of S. meliloti in minimum medium at stationary phase. There are a total of 96 unique phosphorylated sites, with a Ser/Thr/Tyr distribution of 63:28:5, in 77 proteins. Phosphoproteins identified in S. meliloti showed a wide distribution pattern regarding to functional categories, such as replication, transcription, translation, posttranslational modification, transport and metabolism of amino acids, carbohydrate, inorganic ion, succinoglycan etc. Ser/Thr/Tyr phosphosites identified within the conserved motif in proteins of key cellular function indicate a crucial role of phosphorylation in modulating cellular physiology. Moreover, phosphorylation in proteins involved in processes related to rhizobial adaptation was also discussed, such as those identified in SMa0114 and PhaP2 (polyhydroxybutyrate synthesis), ActR (pH stress and microaerobic adaption), SupA (potassium stress), chaperonin GroEL2 (viability and potentially symbiosis), and ExoP (succinoglycan synthesis and secretion). These Ser/Thr/Tyr phosphosites identified herein would be helpful for our further investigation and understanding of the role of phosphorylation in rhizobial physiology.
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